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Mercury in PDB 3zzf: Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate

Enzymatic activity of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate

All present enzymatic activity of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate:
2.7.2.8;

Protein crystallography data

The structure of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate, PDB code: 3zzf was solved by S.De Cima, F.Gil-Ortiz, M.Crabeel, I.Fita, V.Rubio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.701, 99.299, 190.644, 90.00, 90.00, 90.00
R / Rfree (%) 17.87 / 21.812

Other elements in 3zzf:

The structure of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Mercury atom in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate (pdb code 3zzf). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 11 binding sites of Mercury where determined in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate, PDB code: 3zzf:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 11 in 3zzf

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Mercury binding site 1 out of 11 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1358

b:33.0
occ:0.70
SG A:CYS119 1.7 14.3 0.5
O A:CYS119 3.3 16.4 0.5
CL A:CL1362 3.3 61.5 1.0
O A:CYS119 3.5 15.7 0.5
CB A:CYS119 3.5 16.2 0.5
CB A:GLN335 3.9 31.7 1.0
CA A:GLN335 3.9 29.8 1.0
CG A:LEU123 3.9 16.0 1.0
CB A:CYS119 4.0 17.8 0.5
CA A:CYS119 4.0 16.2 0.5
C A:CYS119 4.0 16.5 0.5
N A:GLN335 4.0 28.5 1.0
CD2 A:LEU123 4.0 15.6 1.0
C A:CYS119 4.1 15.8 0.5
CA A:CYS119 4.1 17.7 0.5
CG A:LEU334 4.1 25.0 1.0
CD2 A:LEU334 4.1 25.4 1.0
CG A:GLN335 4.2 33.3 1.0
CD2 A:PHE122 4.2 17.9 1.0
CD1 A:LEU338 4.3 24.7 1.0
CD1 A:LEU123 4.5 16.2 1.0
NE2 A:GLN335 4.5 36.6 1.0
SG A:CYS119 4.5 22.3 0.5
CB A:LEU334 4.6 25.6 1.0
CB A:PHE122 4.6 16.6 1.0
O A:HOH2019 4.6 26.6 1.0
CE2 A:PHE339 4.7 31.3 1.0
C A:LEU334 4.7 27.1 1.0
CG A:PHE122 4.8 17.0 1.0
CD A:GLN335 4.9 35.8 1.0

Mercury binding site 2 out of 11 in 3zzf

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Mercury binding site 2 out of 11 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg1359

b:41.2
occ:0.40
CL A:CL1361 1.9 31.6 1.0
SG A:CYS171 2.4 31.3 1.0
O A:VAL167 3.2 21.0 1.0
N A:CYS171 3.4 25.6 1.0
CB A:CYS171 3.6 26.6 1.0
CG1 A:VAL167 3.7 19.0 1.0
CA A:CYS171 3.7 25.4 1.0
CG A:ARG143 3.7 30.2 1.0
OE2 A:GLU174 3.8 39.4 1.0
CB A:LYS170 3.9 29.1 1.0
CG A:LYS170 4.0 31.6 1.0
CB A:ARG143 4.0 28.1 1.0
C A:LYS170 4.1 25.5 1.0
C A:VAL167 4.1 20.4 1.0
CA A:VAL167 4.2 20.5 1.0
CA A:LYS170 4.5 26.4 1.0
CB A:VAL167 4.5 20.0 1.0
CD A:LYS170 4.5 36.2 1.0
CD A:ARG143 4.6 34.5 1.0
NE A:ARG143 4.7 38.1 1.0
O A:LYS170 4.8 24.7 1.0
CD A:GLU174 5.0 36.6 1.0

Mercury binding site 3 out of 11 in 3zzf

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Mercury binding site 3 out of 11 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg1359

b:44.9
occ:0.40
SG B:CYS119 2.6 20.5 0.5
CG B:GLN335 2.6 26.5 1.0
O B:CYS119 3.4 15.7 0.5
O B:CYS119 3.4 16.2 0.5
CD B:GLN335 3.6 31.6 1.0
NE2 B:GLN335 3.6 32.4 1.0
CB B:CYS119 3.7 16.5 0.5
N B:GLN335 3.7 21.6 1.0
CA B:GLN335 3.7 23.4 1.0
CB B:CYS119 3.7 15.4 0.5
CB B:GLN335 3.8 25.1 1.0
CG B:LEU123 3.9 13.8 1.0
C B:CYS119 3.9 15.5 0.5
C B:CYS119 3.9 16.0 0.5
CA B:CYS119 4.0 16.5 0.5
CA B:CYS119 4.0 15.6 0.5
CD2 B:LEU123 4.1 13.7 1.0
CG B:LEU334 4.1 18.5 1.0
CD2 B:LEU334 4.2 18.9 1.0
CD1 B:LEU123 4.3 13.5 1.0
CB B:LEU334 4.3 18.6 1.0
CD2 B:PHE122 4.3 15.2 1.0
C B:LEU334 4.3 20.1 1.0
O B:HOH2047 4.4 18.5 1.0
SG B:CYS119 4.4 16.2 0.5
CD1 B:LEU338 4.7 16.5 1.0
OE1 B:GLN335 4.7 34.4 1.0
O B:LEU334 4.8 20.2 1.0
CA B:LEU334 4.9 18.8 1.0
N B:LEU120 5.0 15.3 1.0

Mercury binding site 4 out of 11 in 3zzf

Go back to Mercury Binding Sites List in 3zzf
Mercury binding site 4 out of 11 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg1359

b:39.5
occ:0.35
SG B:CYS119 2.0 16.2 0.5
CL B:CL1364 2.2 40.3 1.0
O B:HOH2044 2.6 13.3 1.0
O B:HOH2009 2.8 16.0 1.0
O B:GLU115 3.2 15.6 1.0
CB B:CYS119 3.4 16.5 0.5
CB B:CYS119 3.4 15.4 0.5
N B:CYS119 3.4 15.6 0.5
N B:CYS119 3.4 16.1 0.5
CA B:CYS119 3.6 15.6 0.5
SG B:CYS119 3.6 20.5 0.5
CG B:GLU115 3.6 20.6 1.0
CA B:CYS119 3.6 16.5 0.5
CB B:SER118 4.0 16.8 1.0
C B:SER118 4.1 16.0 1.0
C B:GLU115 4.2 16.4 1.0
NE2 B:GLN335 4.3 32.4 1.0
CA B:GLU115 4.4 17.4 1.0
OE2 B:GLU115 4.5 26.4 1.0
CD B:GLU115 4.6 24.2 1.0
CB B:GLU115 4.6 18.0 1.0
CA B:SER118 4.6 16.2 1.0
O B:SER118 4.8 16.2 1.0
O B:HOH2047 4.9 18.5 1.0

Mercury binding site 5 out of 11 in 3zzf

Go back to Mercury Binding Sites List in 3zzf
Mercury binding site 5 out of 11 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg1360

b:39.5
occ:0.50
CL B:CL1363 2.3 10.6 1.0
SG B:CYS171 2.5 22.7 1.0
CL B:CL1362 2.7 30.1 1.0
O B:VAL167 3.2 14.8 1.0
N B:CYS171 3.3 18.4 1.0
CB B:CYS171 3.5 18.1 1.0
CG B:ARG143 3.6 24.5 1.0
CD B:ARG143 3.6 28.3 1.0
CA B:CYS171 3.6 18.8 1.0
NE B:ARG143 3.6 30.2 1.0
CG1 B:VAL167 3.7 13.2 1.0
O B:HOH2072 4.0 23.4 1.0
C B:LYS170 4.0 19.8 1.0
CB B:LYS170 4.0 20.4 1.0
C B:VAL167 4.1 14.7 1.0
CZ B:ARG143 4.1 31.8 1.0
CA B:VAL167 4.3 14.7 1.0
CB B:ARG143 4.3 21.6 1.0
CA B:LYS170 4.5 20.2 1.0
NH1 B:ARG143 4.5 33.2 1.0
CB B:VAL167 4.6 14.5 1.0
O B:LYS170 4.7 20.1 1.0
O B:HOH2055 4.8 17.6 1.0
NH2 B:ARG143 4.8 31.8 1.0

Mercury binding site 6 out of 11 in 3zzf

Go back to Mercury Binding Sites List in 3zzf
Mercury binding site 6 out of 11 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg1356

b:36.3
occ:0.75
SG C:CYS119 1.7 17.2 1.0
O C:CYS119 3.4 20.1 1.0
CB C:CYS119 3.6 21.4 1.0
CA C:GLN335 3.8 33.1 1.0
CB C:GLN335 3.8 33.5 1.0
CG C:LEU123 3.8 19.9 1.0
N C:GLN335 3.9 31.7 1.0
CD2 C:LEU123 4.0 20.4 1.0
C C:CYS119 4.1 20.0 1.0
CG C:GLN335 4.1 34.8 1.0
CD2 C:PHE122 4.1 23.1 1.0
CA C:CYS119 4.2 20.6 1.0
CD1 C:LEU123 4.2 19.4 1.0
CD1 C:LEU338 4.3 29.7 1.0
CG C:LEU334 4.3 27.3 1.0
CD2 C:LEU334 4.5 25.6 1.0
CE2 C:PHE339 4.5 32.6 1.0
CB C:PHE122 4.6 21.6 1.0
C C:LEU334 4.6 31.2 1.0
O C:HOH2076 4.6 24.3 1.0
NE2 C:GLN335 4.7 35.1 1.0
CB C:LEU334 4.7 28.1 1.0
CG C:PHE122 4.8 22.9 1.0
CD C:GLN335 4.9 35.5 1.0
CE2 C:PHE122 4.9 24.3 1.0

Mercury binding site 7 out of 11 in 3zzf

Go back to Mercury Binding Sites List in 3zzf
Mercury binding site 7 out of 11 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg1357

b:52.9
occ:0.60
SG C:CYS171 2.4 20.0 1.0
O C:HOH2024 3.0 14.2 1.0
CL C:CL1359 3.3 70.3 1.0
CG C:ARG143 3.5 33.5 1.0
O C:VAL167 3.6 22.7 1.0
CB C:LYS170 3.7 29.1 1.0
CG1 C:VAL167 3.7 24.4 1.0
CB C:CYS171 3.9 20.0 1.0
N C:CYS171 3.9 24.1 1.0
CD C:LYS170 3.9 36.9 1.0
CG C:LYS170 4.0 32.7 1.0
CA C:VAL167 4.1 24.6 1.0
CA C:CYS171 4.2 23.2 1.0
C C:VAL167 4.3 23.2 1.0
CD C:ARG143 4.3 37.1 1.0
CB C:ARG143 4.4 31.0 1.0
CB C:VAL167 4.5 25.3 1.0
C C:LYS170 4.5 25.1 1.0
NE C:ARG143 4.6 39.8 1.0
CA C:LYS170 4.7 26.6 1.0
NZ C:LYS170 4.9 41.0 1.0

Mercury binding site 8 out of 11 in 3zzf

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Mercury binding site 8 out of 11 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg1355

b:42.5
occ:0.40
SG D:CYS119 2.2 16.8 0.5
CL D:CL1358 2.2 39.2 1.0
O D:HOH2040 2.5 10.5 1.0
O D:HOH2007 3.1 20.2 1.0
CB D:CYS119 3.2 15.0 0.5
O D:GLU115 3.2 14.6 1.0
CB D:CYS119 3.2 14.6 0.5
N D:CYS119 3.3 14.8 0.5
N D:CYS119 3.3 14.9 0.5
CA D:CYS119 3.4 14.7 0.5
CA D:CYS119 3.5 15.1 0.5
CG D:GLU115 3.7 20.6 1.0
SG D:CYS119 4.0 18.0 0.5
CB D:SER118 4.1 16.7 1.0
C D:SER118 4.1 15.3 1.0
C D:GLU115 4.1 16.0 1.0
NE2 D:GLN335 4.3 30.1 1.0
CA D:GLU115 4.4 17.5 1.0
OE2 D:GLU115 4.5 27.1 1.0
O D:HOH2042 4.6 16.3 1.0
CD D:GLU115 4.7 24.0 1.0
CB D:GLU115 4.7 18.4 1.0
CA D:SER118 4.7 15.9 1.0
O D:SER118 4.7 15.3 1.0
C D:CYS119 5.0 14.2 0.5
C D:CYS119 5.0 14.4 0.5

Mercury binding site 9 out of 11 in 3zzf

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Mercury binding site 9 out of 11 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg1355

b:45.8
occ:0.30
SG D:CYS119 2.3 18.0 0.5
CG D:GLN335 2.6 24.6 1.0
O D:CYS119 3.3 14.4 0.5
O D:CYS119 3.3 14.6 0.5
NE2 D:GLN335 3.4 30.1 1.0
CD D:GLN335 3.4 28.4 1.0
CB D:GLN335 3.7 22.6 1.0
N D:GLN335 3.8 19.5 1.0
CA D:GLN335 3.8 21.0 1.0
CB D:CYS119 3.8 15.0 0.5
CB D:CYS119 3.8 14.6 0.5
CG D:LEU123 3.8 12.7 1.0
C D:CYS119 3.9 14.2 0.5
C D:CYS119 3.9 14.4 0.5
CD2 D:LEU123 4.0 12.6 1.0
CG D:LEU334 4.0 16.9 1.0
CA D:CYS119 4.0 14.7 0.5
CA D:CYS119 4.0 15.1 0.5
CD2 D:LEU334 4.0 17.2 1.0
SG D:CYS119 4.1 16.8 0.5
CD1 D:LEU123 4.2 12.5 1.0
CB D:LEU334 4.3 17.4 1.0
O D:HOH2042 4.3 16.3 1.0
CD2 D:PHE122 4.3 15.0 1.0
C D:LEU334 4.3 18.2 1.0
OE1 D:GLN335 4.6 30.2 1.0
CD1 D:LEU338 4.7 15.5 1.0
O D:LEU334 4.8 17.7 1.0
CA D:LEU334 4.9 17.4 1.0
N D:LEU120 5.0 14.0 1.0

Mercury binding site 10 out of 11 in 3zzf

Go back to Mercury Binding Sites List in 3zzf
Mercury binding site 10 out of 11 in the Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Crystal Structure of the Amino Acid Kinase Domain From Saccharomyces Cerevisiae Acetylglutamate Kinase Complexed with Its Substrate N-Acetylglutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg1356

b:52.1
occ:0.50
HG D:HG1356 0.0 52.1 0.5
SG D:CYS171 2.3 20.5 0.5
O D:HOH2071 2.7 25.4 1.0
O D:VAL167 3.5 18.9 1.0
CB D:LYS170 3.6 24.8 1.0
O D:HOH2056 3.6 13.7 1.0
CG D:ARG143 3.6 27.9 1.0
CG D:LYS170 3.7 28.7 1.0
SG D:CYS171 3.9 19.0 0.5
CG1 D:VAL167 3.9 18.7 1.0
N D:CYS171 4.0 20.8 0.5
NE D:ARG143 4.0 38.5 1.0
N D:CYS171 4.0 21.0 0.5
CB D:CYS171 4.1 19.5 0.5
CA D:VAL167 4.1 19.8 1.0
CD D:LYS170 4.1 32.5 1.0
CD D:ARG143 4.2 33.1 1.0
C D:VAL167 4.2 19.0 1.0
C D:LYS170 4.4 22.7 1.0
CA D:CYS171 4.5 20.4 0.5
CA D:CYS171 4.5 20.1 0.5
CB D:VAL167 4.5 19.9 1.0
CB D:CYS171 4.5 18.7 0.5
CB D:ARG143 4.5 23.6 1.0
CA D:LYS170 4.6 23.9 1.0
NZ D:LYS170 4.7 36.8 1.0
CG2 D:VAL167 4.9 20.2 1.0
HG D:HG1356 4.9 51.7 0.5

Reference:

S.De Cima, F.Gil-Ortiz, M.Crabeel, I.Fita, V.Rubio. Insight on An Arginine Synthesis Metabolon From the Tetrameric Structure of Yeast Acetylglutamate Kinase Plos One V. 7 34734 2012.
ISSN: ISSN 1932-6203
PubMed: 22529931
DOI: 10.1371/JOURNAL.PONE.0034734
Page generated: Wed Oct 28 18:43:13 2020

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