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Mercury in PDB 6iqv: Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum

Enzymatic activity of Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum

All present enzymatic activity of Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum:
1.2.1.12;

Protein crystallography data

The structure of Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum, PDB code: 6iqv was solved by K.Yoneda, H.Kinoshita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 101.86 / 2.13
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 126.043, 172.949, 149.235, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.9

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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum (pdb code 6iqv). 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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum, PDB code: 6iqv:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 11 in 6iqv

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Mercury binding site 1 out of 11 in the Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum


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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg402

b:0.1
occ:1.00
 SG A:CYS160 2.3 38.5 1.0
CB A:THR248 3.0 26.9 1.0
OG1 A:THR248 3.1 28.0 1.0
C A:CYS160 3.1 32.0 1.0
N A:LEU161 3.2 30.6 1.0
O A:CYS160 3.3 31.3 1.0
CB A:CYS160 3.3 30.6 1.0
O A:HOH501 3.3 37.8 1.0
CA A:LEU161 3.5 33.1 1.0
CB A:ALA318 3.7 27.6 1.0
CG2 A:THR248 3.7 30.1 1.0
CA A:CYS160 3.8 30.6 1.0
O A:ALA318 4.1 27.6 1.0
CB A:LEU161 4.2 29.2 1.0
CA A:THR248 4.3 31.0 1.0
OG A:SER296 4.4 33.8 1.0
O A:THR248 4.5 29.6 1.0
N A:THR248 4.5 30.9 1.0
CD2 A:LEU164 4.5 37.1 1.0
CA A:ALA318 4.6 29.5 1.0
C A:ALA318 4.7 31.1 1.0
C A:LEU161 4.7 34.8 1.0
C A:THR248 4.7 31.4 1.0
N A:ALA318 4.8 29.4 1.0
CB A:LEU164 4.8 33.5 1.0

Mercury binding site 2 out of 11 in 6iqv

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Mercury binding site 2 out of 11 in the Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum


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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg403

b:66.1
occ:1.00
 SG A:CYS328 3.1 36.9 1.0
CE2 A:TYR324 3.3 48.0 1.0
CD2 A:TYR324 3.3 38.9 1.0
CZ A:TYR324 3.4 46.8 1.0
CG A:TYR324 3.5 38.7 1.0
O A:TYR324 3.5 31.7 1.0
CE1 A:TYR324 3.5 37.9 1.0
CD1 A:TYR324 3.6 43.9 1.0
CB A:ARG20 3.7 35.7 1.0
CB A:THR327 3.8 31.5 1.0
CG2 A:THR327 3.8 28.5 1.0
O A:LEU16 3.9 23.9 1.0
CA A:TYR324 4.0 34.9 1.0
OH A:TYR324 4.1 55.3 1.0
CG A:ARG20 4.2 36.6 1.0
N A:CYS328 4.2 29.6 1.0
C A:TYR324 4.2 32.9 1.0
CB A:LEU16 4.3 30.6 1.0
CB A:TYR324 4.3 36.6 1.0
C A:LEU16 4.4 25.7 1.0
CB A:CYS328 4.5 27.7 1.0
C A:THR327 4.5 30.2 1.0
CD A:ARG20 4.5 40.1 1.0
CA A:CYS328 4.7 28.2 1.0
CA A:THR327 4.7 30.8 1.0
OG1 A:THR327 4.7 38.2 1.0
CA A:ARG20 4.8 34.7 1.0
CA A:LEU16 4.8 29.8 1.0

Mercury binding site 3 out of 11 in 6iqv

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Mercury binding site 3 out of 11 in the Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum


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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg404

b:0.5
occ:1.00
 SG A:CYS101 1.7 47.6 1.0
OG A:SER125 3.1 32.1 1.0
O A:HOH637 3.2 35.3 1.0
CG1 A:ILE13 3.3 36.5 1.0
CB A:CYS101 3.5 39.9 1.0
CB A:ILE13 3.5 29.9 1.0
O A:HOH628 3.6 56.1 1.0
O A:CYS101 3.9 35.3 1.0
CB A:SER125 3.9 35.2 1.0
CG2 A:ILE13 4.0 32.1 1.0
O A:SER125 4.2 37.0 1.0
CA A:CYS101 4.2 34.5 1.0
C A:CYS101 4.5 37.1 1.0
CD1 A:ILE13 4.7 39.9 1.0
CA A:ILE13 4.9 30.7 1.0
C A:SER125 5.0 38.2 1.0

Mercury binding site 4 out of 11 in 6iqv

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Mercury binding site 4 out of 11 in the Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum


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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg403

b:0.2
occ:1.00
 SG B:CYS160 2.3 38.0 1.0
CB B:THR248 2.8 33.2 1.0
OG1 B:THR248 2.9 41.8 1.0
C B:CYS160 3.2 29.8 1.0
O B:CYS160 3.2 30.3 1.0
N B:LEU161 3.2 30.0 1.0
CG2 B:THR248 3.3 30.2 1.0
CA B:LEU161 3.4 33.3 1.0
CB B:CYS160 3.4 33.6 1.0
CA B:CYS160 3.9 31.1 1.0
CB B:ALA318 3.9 30.6 1.0
CB B:LEU161 4.1 32.1 1.0
CA B:THR248 4.1 33.3 1.0
O B:ALA318 4.3 28.0 1.0
CD2 B:LEU164 4.3 41.2 1.0
O B:THR248 4.5 31.0 1.0
OG B:SER296 4.5 39.1 1.0
N B:THR248 4.5 32.0 1.0
C B:LEU161 4.5 36.1 1.0
C B:THR248 4.6 33.5 1.0
CD1 B:LEU161 4.7 31.9 1.0
CA B:ALA318 4.7 31.4 1.0
N B:ALA318 4.7 28.4 1.0
CB B:LEU164 4.8 34.6 1.0
O B:LEU161 4.8 34.9 1.0
C B:ALA318 4.8 29.7 1.0

Mercury binding site 5 out of 11 in 6iqv

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Mercury binding site 5 out of 11 in the Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum


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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg404

b:74.5
occ:1.00
 CE1 B:TYR324 3.4 54.4 1.0
SG B:CYS328 3.4 44.6 1.0
CD1 B:TYR324 3.4 42.0 1.0
CZ B:TYR324 3.4 57.2 1.0
CG B:TYR324 3.5 34.5 1.0
CE2 B:TYR324 3.5 43.9 1.0
O B:TYR324 3.5 35.3 1.0
CD2 B:TYR324 3.5 39.3 1.0
CG2 B:THR327 3.6 35.3 1.0
CB B:ARG20 3.6 32.1 1.0
CG B:ARG20 3.8 33.9 1.0
CB B:THR327 3.8 36.4 1.0
O B:LEU16 3.9 27.1 1.0
CA B:TYR324 4.1 33.5 1.0
OH B:TYR324 4.1 70.6 1.0
N B:CYS328 4.1 29.6 1.0
C B:TYR324 4.2 35.7 1.0
CB B:TYR324 4.3 34.1 1.0
CD B:ARG20 4.4 33.6 1.0
CB B:LEU16 4.4 34.9 1.0
C B:LEU16 4.5 33.0 1.0
C B:THR327 4.5 33.7 1.0
CB B:CYS328 4.6 26.8 1.0
CA B:CYS328 4.6 30.5 1.0
CA B:ARG20 4.7 37.6 1.0
CA B:THR327 4.8 35.7 1.0
OG1 B:THR327 4.8 34.8 1.0
CA B:LEU16 5.0 33.2 1.0
N B:ARG20 5.0 32.8 1.0

Mercury binding site 6 out of 11 in 6iqv

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Mercury binding site 6 out of 11 in the Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum


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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg405

b:0.2
occ:1.00
 SG B:CYS101 2.9 45.5 1.0
N B:GLY11 3.1 36.7 1.0
C B:GLY9 3.4 43.1 1.0
CA B:GLY11 3.5 33.4 1.0
CA B:GLY9 3.5 38.7 1.0
O B:GLY9 3.6 42.9 1.0
O B:HOH503 3.7 57.6 1.0
N B:PHE10 3.8 40.4 1.0
O B:CYS101 3.8 44.0 1.0
C B:PHE10 4.1 39.4 1.0
CA B:THR102 4.3 48.0 1.0
C B:CYS101 4.3 41.3 1.0
CA B:PHE10 4.5 42.6 1.0
CB B:CYS101 4.6 37.6 1.0
N B:THR102 4.6 44.2 1.0
O B:HOH638 4.7 42.1 1.0
C B:GLY11 4.7 34.8 1.0
O B:HOH618 4.8 38.6 1.0
OD2 B:ASP38 4.8 45.4 1.0
N B:GLY9 4.8 39.4 1.0
CG2 B:THR102 4.8 50.2 1.0
CB B:THR102 5.0 53.6 1.0

Mercury binding site 7 out of 11 in 6iqv

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Mercury binding site 7 out of 11 in the Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum


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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg402

b:74.2
occ:1.00
 SG C:CYS328 3.0 44.1 1.0
CZ C:TYR324 3.4 48.5 1.0
CE2 C:TYR324 3.4 49.2 1.0
CE1 C:TYR324 3.5 44.7 1.0
CD2 C:TYR324 3.5 43.7 1.0
O C:TYR324 3.5 32.3 1.0
CD1 C:TYR324 3.5 36.0 1.0
CG C:TYR324 3.6 37.4 1.0
CB C:ARG20 3.6 39.7 1.0
CB C:THR327 3.7 38.6 1.0
CG2 C:THR327 3.7 41.1 1.0
O C:LEU16 3.8 32.7 1.0
OH C:TYR324 4.0 55.2 1.0
N C:CYS328 4.1 37.7 1.0
CA C:TYR324 4.1 35.2 1.0
CG C:ARG20 4.2 40.5 1.0
C C:TYR324 4.2 37.6 1.0
CB C:LEU16 4.3 37.3 1.0
C C:LEU16 4.3 31.0 1.0
CB C:CYS328 4.4 38.0 1.0
C C:THR327 4.4 42.2 1.0
CB C:TYR324 4.5 38.2 1.0
CD C:ARG20 4.5 41.5 1.0
CA C:CYS328 4.6 35.5 1.0
CA C:THR327 4.7 38.8 1.0
OG1 C:THR327 4.7 37.6 1.0
CA C:ARG20 4.8 43.3 1.0
CA C:LEU16 4.8 34.8 1.0
N C:ARG20 5.0 48.4 1.0

Mercury binding site 8 out of 11 in 6iqv

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Mercury binding site 8 out of 11 in the Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum


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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg403

b:0.4
occ:1.00
 SG C:CYS160 2.2 43.0 1.0
CB C:THR248 3.1 31.9 1.0
OG1 C:THR248 3.1 34.1 1.0
O C:HOH505 3.2 30.3 1.0
C C:CYS160 3.2 35.9 1.0
O C:CYS160 3.3 35.2 1.0
N C:LEU161 3.3 34.5 1.0
CA C:LEU161 3.4 38.2 1.0
CB C:CYS160 3.5 35.5 1.0
CG2 C:THR248 3.6 35.4 1.0
CA C:CYS160 4.0 34.1 1.0
CB C:ALA318 4.0 38.9 1.0
CB C:LEU161 4.1 37.2 1.0
O C:ALA318 4.4 30.0 1.0
CA C:THR248 4.4 36.4 1.0
CD2 C:LEU164 4.6 39.4 1.0
C C:LEU161 4.6 39.5 1.0
O C:THR248 4.6 37.4 1.0
OG C:SER296 4.7 42.0 1.0
N C:THR248 4.7 38.9 1.0
CD1 C:LEU161 4.8 33.8 1.0
CA C:ALA318 4.8 35.0 1.0
C C:ALA318 4.9 36.4 1.0
CB C:LEU164 4.9 33.9 1.0
C C:THR248 4.9 34.8 1.0
N C:ALA318 4.9 32.0 1.0
O C:LEU161 4.9 39.0 1.0

Mercury binding site 9 out of 11 in 6iqv

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Mercury binding site 9 out of 11 in the Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum


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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg402

b:0.1
occ:1.00
 CD1 D:LEU99 2.8 34.8 1.0
CE D:MET330 3.1 30.1 1.0
O D:GLU100 3.1 42.8 1.0
SG D:CYS101 3.2 56.5 1.0
C D:GLU100 3.5 38.2 1.0
SD D:MET330 3.5 51.3 1.0
CG D:LEU99 3.7 43.7 1.0
CB D:CYS101 3.9 48.8 1.0
N D:GLU100 3.9 39.0 1.0
N D:CYS101 4.0 39.2 1.0
CA D:CYS101 4.0 41.8 1.0
O D:LEU123 4.2 40.8 1.0
CA D:GLU100 4.3 40.7 1.0
C D:LEU99 4.5 40.3 1.0
CD2 D:LEU99 4.6 45.0 1.0
CB D:SER125 4.7 48.0 1.0
C D:ILE124 4.8 41.2 1.0
CB D:LEU99 4.9 44.2 1.0
CA D:ILE124 4.9 42.2 1.0
CG D:MET330 4.9 45.9 1.0
C D:LEU123 4.9 38.9 1.0
CA D:LEU99 4.9 41.3 1.0
N D:SER125 4.9 46.4 1.0

Mercury binding site 10 out of 11 in 6iqv

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Mercury binding site 10 out of 11 in the Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum


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 Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase Complexed with HG2+ From Lactobacillus Plantarum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg403

b:0.7
occ:1.00
 SG D:CYS160 2.4 48.3 1.0
OG1 D:THR248 2.8 47.8 1.0
CB D:THR248 2.9 39.1 1.0
C D:CYS160 3.3 31.9 1.0
N D:LEU161 3.3 31.7 1.0
CB D:CYS160 3.4 33.8 1.0
O D:CYS160 3.4 31.5 1.0
CA D:LEU161 3.5 36.2 1.0
CG2 D:THR248 3.7 37.2 1.0
CA D:CYS160 3.9 34.7 1.0
CB D:ALA318 4.0 30.4 1.0
CB D:LEU161 4.2 38.9 1.0
CA D:THR248 4.2 34.6 1.0
N D:THR248 4.4 31.2 1.0
O D:ALA318 4.5 33.9 1.0
OG D:SER296 4.6 30.4 1.0
O D:THR248 4.6 34.3 1.0
CE1 D:TYR320 4.8 25.7 1.0
C D:THR248 4.8 32.1 1.0
CA D:ALA318 4.8 29.5 1.0
C D:LEU161 4.8 40.5 1.0
CD1 D:TYR320 4.9 26.9 1.0
C D:ALA318 4.9 32.8 1.0
CD2 D:LEU164 4.9 39.4 1.0
N D:ALA318 5.0 30.0 1.0
CD1 D:LEU161 5.0 38.6 1.0
CB D:LEU164 5.0 34.5 1.0

Reference:

K.Yoneda, M.Ogata, K.Nishiyama, K.Fukuda, S.Yasuda, K.Igoshi, H.Kinoshita. Crystal Structure of Cell Surface Glyceraldehyde-3-Phosphate Dehydrogenase From Lactobacillus Plantarum: Insight Into the Mercury Binding Mechanism Milk Sci V. 68 3 2019.
ISSN: ISSN 1343-0289
DOI: 10.11465/MILK.68.3
Page generated: Sun Aug 11 07:25:03 2024

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