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Mercury in PDB 7zd1: Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions

Enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions

All present enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions, PDB code: 7zd1 was solved by P.H.Malecki, M.Gawel, K.Brzezinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.47 / 1.56
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.418, 134.199, 108.729, 90, 105.95, 90
R / Rfree (%) 12.3 / 17.9

Other elements in 7zd1:

The structure of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Potassium (K) 4 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Mercury atom in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions (pdb code 7zd1). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 20 binding sites of Mercury where determined in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions, PDB code: 7zd1:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 20 in 7zd1

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Mercury binding site 1 out of 20 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg507

b:27.9
occ:0.25
 NE2 A:HIS323 1.9 28.1 1.0
SG A:CYS85 2.3 26.8 1.0
O A:ASP139 2.6 26.7 1.0
CD2 A:HIS323 2.9 25.2 1.0
CE1 A:HIS323 3.0 31.9 1.0
CB A:CYS85 3.1 23.6 1.0
OD1 A:ASP139 3.1 29.1 1.0
O5' A:ADN502 3.3 28.4 1.0
O A:HOH626 3.5 34.0 1.0
C A:ASP139 3.5 22.5 1.0
O A:CYS85 3.6 30.1 1.0
CG A:ASP139 3.6 29.9 1.0
NE2 A:HIS61 3.6 22.9 1.0
O A:HOH805 3.7 35.4 1.0
CE1 A:HIS61 3.7 23.1 1.0
CG A:HIS323 4.0 31.0 1.0
ND1 A:HIS323 4.1 38.2 1.0
CB A:ASP139 4.1 25.8 1.0
C A:CYS85 4.2 25.8 1.0
HG A:HG508 4.2 36.7 0.3
CA A:CYS85 4.2 25.6 1.0
OD2 A:ASP139 4.3 28.9 1.0
N A:GLY140 4.3 22.9 1.0
CA A:GLY140 4.3 22.9 1.0
O A:HOH806 4.3 45.6 1.0
CA A:ASP139 4.4 24.1 1.0
ND1 A:HIS61 4.6 22.2 1.0
CD2 A:HIS61 4.6 22.0 1.0
C5' A:ADN502 4.7 43.0 1.0

Mercury binding site 2 out of 20 in 7zd1

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Mercury binding site 2 out of 20 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg508

b:36.7
occ:0.26
 CB A:CYS85 1.9 23.6 1.0
O A:CYS59 2.2 27.5 1.0
C A:CYS59 2.7 26.5 1.0
SG A:CYS59 2.7 31.4 1.0
CA A:CYS85 3.0 25.6 1.0
SG A:CYS85 3.0 26.8 1.0
O A:ASP139 3.0 26.7 1.0
CB A:CYS59 3.1 28.3 1.0
N A:ILE60 3.3 24.3 1.0
O A:HOH806 3.4 45.6 1.0
CA A:CYS59 3.5 24.9 1.0
N A:CYS85 3.5 24.8 1.0
CA A:ILE60 3.6 26.2 1.0
OD1 A:ASP138 3.8 28.4 1.0
N A:ASP139 3.8 25.2 1.0
C A:ASP139 3.9 22.5 1.0
CB A:ASP139 4.1 25.8 1.0
CA A:ASP139 4.1 24.1 1.0
HG A:HG507 4.2 27.9 0.2
C A:SER84 4.3 27.4 1.0
C A:CYS85 4.3 25.8 1.0
O A:CYS85 4.6 30.1 1.0
O A:SER84 4.6 28.8 1.0
C A:ILE60 4.6 23.4 1.0
CB A:ILE60 4.6 27.4 1.0
N A:CYS59 4.7 24.1 1.0
O A:HOH626 4.7 34.0 1.0
OH A:TYR116 4.8 32.8 1.0
C A:ASP138 4.9 22.2 1.0
N A:HIS61 4.9 22.9 1.0
CG A:ASP139 5.0 29.9 1.0

Mercury binding site 3 out of 20 in 7zd1

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Mercury binding site 3 out of 20 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg509

b:51.3
occ:0.25
 SG A:CYS119 1.9 30.3 1.0
OE2 A:GLU111 2.8 30.2 1.0
CD A:GLU111 2.8 26.6 1.0
CH2 A:TRP108 3.0 31.2 1.0
CZ3 A:TRP108 3.1 32.9 1.0
CG A:GLU111 3.2 30.0 1.0
O A:GLU115 3.2 29.5 1.0
CZ2 A:TRP108 3.3 32.2 1.0
CB A:CYS119 3.3 26.9 1.0
OE1 A:GLU111 3.5 32.1 1.0
CE3 A:TRP108 3.5 26.7 1.0
CE2 A:TRP108 3.7 31.2 1.0
C A:GLU115 3.7 27.2 1.0
CD2 A:TRP108 3.8 27.0 1.0
O A:HOH674 3.9 27.9 1.0
CB A:GLU115 4.2 34.1 1.0
CB A:GLU111 4.2 27.9 1.0
N A:TYR116 4.2 29.4 1.0
CA A:CYS119 4.4 26.5 1.0
O A:PHE106 4.4 24.4 1.0
CA A:TYR116 4.4 26.6 1.0
CA A:GLU115 4.5 30.7 1.0
CA A:ALA107 4.5 26.6 1.0
N A:CYS119 4.5 27.4 1.0
N A:ALA107 4.6 25.6 1.0
NE1 A:TRP108 4.6 32.2 1.0
N A:TRP108 4.6 24.6 1.0
C A:PHE106 4.6 26.5 1.0
CG A:TRP108 4.8 26.4 1.0
CE3 A:TRP118 4.9 26.6 1.0
O A:HOH824 4.9 28.8 1.0
C A:ALA107 5.0 26.2 1.0

Mercury binding site 4 out of 20 in 7zd1

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Mercury binding site 4 out of 20 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg510

b:52.2
occ:0.25
 O A:HOH993 2.2 63.8 1.0
NE2 A:HIS170 2.2 42.5 1.0
O D:HOH894 2.3 62.9 1.0
O D:TYR453 3.0 32.3 1.0
CE1 A:HIS170 3.1 49.9 1.0
CD2 A:HIS170 3.2 48.5 1.0
C D:TYR453 4.0 25.9 1.0
ND1 A:HIS170 4.2 45.0 1.0
O D:GLU452 4.3 29.4 1.0
CG A:HIS170 4.3 35.6 1.0
OD1 A:ASP174 4.3 47.9 1.0
O A:HOH1034 4.3 47.3 1.0
CG A:ASP174 4.4 52.1 1.0
N D:GLY455 4.4 26.6 1.0
C D:ILE454 4.5 29.1 1.0
CB A:ASP174 4.6 39.4 1.0
CA D:ILE454 4.6 26.7 1.0
O D:HOH695 4.6 50.7 1.0
O A:HOH906 4.6 49.6 1.0
N D:ILE454 4.7 27.4 1.0
CA D:GLY455 4.8 30.7 1.0
O D:ILE454 4.9 30.9 1.0
CA D:TYR453 4.9 26.2 1.0
OD2 A:ASP174 5.0 61.6 1.0

Mercury binding site 5 out of 20 in 7zd1

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Mercury binding site 5 out of 20 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg511

b:69.8
occ:0.15
 O A:HOH938 1.9 21.0 0.8
O C:HOH793 2.1 21.3 0.8
SG A:CYS261 2.3 24.7 1.0
CB A:CYS261 3.4 22.9 1.0
N A:VAL267 3.5 21.1 1.0
CB D:PHE439 3.5 25.7 1.0
O A:PHE265 3.6 21.1 1.0
CB A:VAL267 3.8 21.0 1.0
CG2 A:VAL267 3.9 24.7 1.0
CA A:CYS261 3.9 20.7 1.0
CA D:GLY441 4.1 22.0 1.0
CA A:VAL267 4.2 20.1 1.0
CG D:PHE439 4.2 22.4 1.0
CA A:GLU266 4.2 22.6 1.0
O D:HOH818 4.2 45.2 1.0
C A:GLU266 4.3 21.2 1.0
N D:GLY441 4.3 22.6 1.0
O D:PHE439 4.5 28.2 1.0
C A:PHE265 4.6 18.6 1.0
O C:GLY221 4.6 23.5 1.0
N A:CYS261 4.6 21.8 1.0
CD2 D:PHE439 4.7 22.6 1.0
CA D:PHE439 4.7 24.6 1.0
C D:PHE439 4.8 26.0 1.0
O C:HOH675 4.8 34.6 1.0
O A:VAL267 4.8 22.9 1.0
O D:VAL436 4.9 22.1 1.0
N A:GLU266 4.9 20.2 1.0
CD1 D:PHE439 4.9 25.4 1.0

Mercury binding site 6 out of 20 in 7zd1

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Mercury binding site 6 out of 20 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg506

b:42.8
occ:0.30
 CB B:CYS85 1.9 38.9 1.0
O B:CYS59 2.2 40.1 1.0
C B:CYS59 2.8 35.8 1.0
SG B:CYS59 2.8 42.8 1.0
SG B:CYS85 2.9 33.5 1.0
CA B:CYS85 3.0 34.2 1.0
O B:ASP139 3.0 33.9 1.0
CB B:CYS59 3.2 39.4 1.0
O B:HOH771 3.3 55.4 1.0
N B:ILE60 3.4 33.3 1.0
N B:CYS85 3.5 36.3 1.0
CA B:CYS59 3.6 29.8 1.0
CA B:ILE60 3.6 33.2 1.0
OD1 B:ASP138 3.8 39.9 1.0
N B:ASP139 3.9 29.5 1.0
C B:ASP139 3.9 27.8 1.0
CB B:ASP139 4.0 30.0 1.0
HG B:HG507 4.1 42.2 0.3
CA B:ASP139 4.1 28.9 1.0
C B:CYS85 4.2 35.2 1.0
C B:SER84 4.4 36.6 1.0
O B:HOH611 4.4 44.5 1.0
O B:CYS85 4.5 37.5 1.0
C B:ILE60 4.6 30.0 1.0
CB B:ILE60 4.7 35.9 1.0
O B:SER84 4.7 39.7 1.0
OH B:TYR116 4.7 43.5 1.0
N B:CYS59 4.9 32.8 1.0
N B:HIS61 4.9 28.0 1.0
CG B:ASP139 5.0 37.1 1.0
C B:ASP138 5.0 29.7 1.0

Mercury binding site 7 out of 20 in 7zd1

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Mercury binding site 7 out of 20 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg507

b:42.2
occ:0.28
 NE2 B:HIS323 1.9 36.9 1.0
SG B:CYS85 2.4 33.5 1.0
O B:ASP139 2.7 33.9 1.0
CD2 B:HIS323 2.8 33.3 1.0
CE1 B:HIS323 3.0 43.1 1.0
CB B:CYS85 3.1 38.9 1.0
OD1 B:ASP139 3.2 33.5 1.0
O5' B:ADN502 3.2 35.0 1.0
O B:HOH611 3.3 44.5 1.0
NE2 B:HIS61 3.5 27.8 1.0
C B:ASP139 3.5 27.8 1.0
O B:HOH739 3.6 39.4 1.0
CG B:ASP139 3.6 37.1 1.0
CE1 B:HIS61 3.7 28.2 1.0
O B:CYS85 3.7 37.5 1.0
CG B:HIS323 4.0 38.5 1.0
CB B:ASP139 4.0 30.0 1.0
ND1 B:HIS323 4.0 40.0 1.0
HG B:HG506 4.1 42.8 0.3
C B:CYS85 4.2 35.2 1.0
CA B:GLY140 4.2 30.2 1.0
OD2 B:ASP139 4.3 38.0 1.0
N B:GLY140 4.3 27.2 1.0
CA B:CYS85 4.3 34.2 1.0
CA B:ASP139 4.4 28.9 1.0
O B:HOH771 4.5 55.4 1.0
CD2 B:HIS61 4.5 27.7 1.0
ND1 B:HIS61 4.6 26.9 1.0
C5' B:ADN502 4.7 45.1 1.0

Mercury binding site 8 out of 20 in 7zd1

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Mercury binding site 8 out of 20 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg508

b:53.0
occ:0.30
 SG B:CYS119 2.1 38.9 1.0
OE2 B:GLU111 2.8 39.0 1.0
CD B:GLU111 2.8 32.0 1.0
CG B:GLU111 3.0 39.1 1.0
CH2 B:TRP108 3.0 37.1 1.0
CZ3 B:TRP108 3.1 39.0 1.0
O B:GLU115 3.2 39.4 1.0
CZ2 B:TRP108 3.2 39.1 1.0
CB B:CYS119 3.4 41.2 1.0
OE1 B:GLU111 3.5 39.4 1.0
CE3 B:TRP108 3.5 31.9 1.0
CE2 B:TRP108 3.6 35.0 1.0
C B:GLU115 3.7 33.5 1.0
CD2 B:TRP108 3.7 32.8 1.0
O B:HOH700 4.0 37.4 1.0
CB B:GLU115 4.0 39.0 1.0
CB B:GLU111 4.1 33.2 1.0
N B:TYR116 4.2 39.7 1.0
CA B:GLU115 4.4 35.8 1.0
CA B:TYR116 4.5 35.2 1.0
O B:PHE106 4.5 34.0 1.0
CA B:ALA107 4.5 30.6 1.0
NE1 B:TRP108 4.5 40.7 1.0
CA B:CYS119 4.5 32.6 1.0
N B:TRP108 4.6 29.3 1.0
N B:CYS119 4.7 36.8 1.0
N B:ALA107 4.7 33.1 1.0
CG B:TRP108 4.7 31.7 1.0
C B:PHE106 4.7 33.6 1.0
C B:ALA107 4.9 28.7 1.0
CE3 B:TRP118 5.0 43.7 1.0

Mercury binding site 9 out of 20 in 7zd1

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Mercury binding site 9 out of 20 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg509

b:39.6
occ:0.10
 O B:HOH887 1.9 20.1 0.9
O D:HOH767 2.0 20.4 0.9
SG B:CYS261 2.2 23.0 1.0
CB B:CYS261 3.3 21.7 1.0
CB C:PHE439 3.3 23.9 1.0
N B:VAL267 3.7 20.6 1.0
O B:PHE265 3.7 23.1 1.0
CA B:CYS261 3.8 19.3 1.0
CB B:VAL267 3.9 23.1 1.0
CG2 B:VAL267 3.9 24.5 1.0
CG C:PHE439 4.0 22.0 1.0
CA C:GLY441 4.2 23.6 1.0
O C:HOH889 4.2 52.5 1.0
N C:GLY441 4.3 22.3 1.0
O C:PHE439 4.4 30.1 1.0
CD2 C:PHE439 4.4 22.2 1.0
CA B:VAL267 4.4 19.3 1.0
CA B:GLU266 4.5 22.3 1.0
O D:GLY221 4.5 21.0 1.0
C B:GLU266 4.6 22.4 1.0
CA C:PHE439 4.6 23.5 1.0
N B:CYS261 4.6 20.5 1.0
C C:PHE439 4.6 29.1 1.0
O C:VAL436 4.7 22.3 1.0
O D:HOH686 4.8 32.8 1.0
C B:PHE265 4.8 21.8 1.0
CD1 C:PHE439 4.8 26.3 1.0

Mercury binding site 10 out of 20 in 7zd1

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Mercury binding site 10 out of 20 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions


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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg510

b:69.2
occ:0.22
 OD2 B:ASP174 2.3 95.8 1.0
NE2 B:HIS170 2.4 52.9 1.0
O C:TYR453 3.0 41.7 1.0
CE1 B:HIS170 3.1 52.4 1.0
CD2 B:HIS170 3.4 55.6 1.0
CG B:ASP174 3.5 70.6 1.0
C C:TYR453 4.0 38.0 1.0
O C:GLU452 4.2 36.8 1.0
OD1 B:ASP174 4.2 75.1 1.0
ND1 B:HIS170 4.2 47.3 1.0
N C:GLY455 4.4 37.0 1.0
C C:ILE454 4.4 37.6 1.0
CG B:HIS170 4.4 45.6 1.0
CA C:GLY455 4.6 35.9 1.0
CA C:ILE454 4.6 33.2 1.0
N C:ILE454 4.7 35.5 1.0
O C:ILE454 4.7 35.7 1.0
CB B:ASP174 4.8 42.7 1.0
CA C:TYR453 5.0 37.0 1.0

Reference:

P.H.Malecki, M.Gawel, K.Brzezinski. Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Inhibited By HG2+ Ions To Be Published.
Page generated: Sun Aug 11 08:54:51 2024

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