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Silver in PDB 7cgd: Silver-Bound E.Coli Malate Dehydrogenase

Enzymatic activity of Silver-Bound E.Coli Malate Dehydrogenase

All present enzymatic activity of Silver-Bound E.Coli Malate Dehydrogenase:
1.1.1.37;

Protein crystallography data

The structure of Silver-Bound E.Coli Malate Dehydrogenase, PDB code: 7cgd was solved by H.Wang, M.Wang, H.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.18 / 2.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.641, 124.681, 85.148, 90.00, 106.99, 90.00
R / Rfree (%) 21.3 / 24.7

Silver Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Silver atom in the Silver-Bound E.Coli Malate Dehydrogenase (pdb code 7cgd). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 27 binding sites of Silver where determined in the Silver-Bound E.Coli Malate Dehydrogenase, PDB code: 7cgd:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 27 in 7cgd

Go back to Silver Binding Sites List in 7cgd
Silver binding site 1 out of 27 in the Silver-Bound E.Coli Malate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Silver-Bound E.Coli Malate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag401

b:65.9
occ:0.56
 SG A:CYS109 2.5 60.9 1.0
O A:HOH512 2.9 29.3 1.0
AG A:AG402 3.0 73.4 0.7
CA A:GLY69 3.1 41.9 1.0
C A:GLY69 3.2 41.3 1.0
O A:ALA70 3.4 26.6 1.0
N A:GLY69 3.4 41.6 1.0
N A:ALA70 3.5 26.1 1.0
O A:GLY69 3.7 41.7 1.0
CB A:CYS109 3.9 58.0 1.0
C A:ALA70 4.1 26.1 1.0
CA A:ALA70 4.4 25.4 1.0
O A:HOH511 4.5 29.3 1.0
C A:GLU68 4.6 55.1 1.0
CA A:CYS109 4.7 58.3 1.0
O A:LEU67 4.8 35.0 1.0

Silver binding site 2 out of 27 in 7cgd

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Silver binding site 2 out of 27 in the Silver-Bound E.Coli Malate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Silver-Bound E.Coli Malate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag402

b:73.4
occ:0.67
 O A:HOH511 2.3 29.3 1.0
SG A:CYS109 2.4 60.9 1.0
O A:THR108 2.9 46.7 1.0
AG A:AG401 3.0 65.9 0.6
CA A:CYS109 3.4 58.3 1.0
C A:THR108 3.4 45.4 1.0
CB A:CYS109 3.5 58.0 1.0
N A:CYS109 3.7 58.3 1.0
N A:GLY69 3.9 41.6 1.0
CG2 A:THR108 4.1 43.9 1.0
OE1 A:GLU68 4.2 58.5 1.0
O A:LEU67 4.3 35.0 1.0
CA A:GLU68 4.5 54.9 1.0
CA A:THR108 4.6 46.1 1.0
CA A:GLY69 4.6 41.9 1.0
C A:GLU68 4.7 55.1 1.0
C A:CYS109 4.8 57.1 1.0
CB A:THR108 4.8 44.2 1.0
CD A:PRO110 5.0 62.8 1.0

Silver binding site 3 out of 27 in 7cgd

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Silver binding site 3 out of 27 in the Silver-Bound E.Coli Malate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Silver-Bound E.Coli Malate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag403

b:44.2
occ:0.91
 NZ A:LYS111 2.6 81.6 1.0
AG A:AG404 2.8 34.0 0.7
SG A:CYS113 2.9 33.8 1.0
O A:ASP71 3.1 28.0 1.0
N A:CYS113 3.3 33.3 1.0
CE A:LYS111 3.4 80.4 1.0
CD1 A:LEU242 3.4 22.4 1.0
CD A:LYS111 3.7 78.5 1.0
CD2 A:LEU242 3.8 21.9 1.0
CB A:CYS113 3.8 31.5 1.0
CA A:CYS113 4.1 31.1 1.0
C A:ALA112 4.1 33.1 1.0
C A:ASP71 4.2 27.6 1.0
CA A:ALA112 4.2 35.4 1.0
CG A:LEU242 4.2 22.2 1.0
NZ A:LYS142 4.4 30.0 1.0
CG A:LYS111 4.5 79.2 1.0
O A:LYS111 4.7 73.9 1.0
CA A:ASP71 4.7 28.1 1.0
CB A:ASP71 4.8 28.4 1.0
N A:ALA112 4.9 36.9 1.0
C A:LYS111 5.0 75.2 1.0

Silver binding site 4 out of 27 in 7cgd

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Silver binding site 4 out of 27 in the Silver-Bound E.Coli Malate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of Silver-Bound E.Coli Malate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag404

b:34.0
occ:0.69
 SG A:CYS113 2.5 33.8 1.0
NZ A:LYS142 2.5 30.0 1.0
AG A:AG403 2.8 44.2 0.9
CG A:LYS142 3.1 28.6 1.0
CD A:LYS142 3.1 29.4 1.0
CE A:LYS142 3.3 30.0 1.0
N A:CYS113 3.4 33.3 1.0
O A:LYS111 3.6 73.9 1.0
O A:ASN273 3.6 38.2 1.0
CB A:LYS142 3.6 28.0 1.0
CA A:CYS113 3.6 31.1 1.0
CB A:CYS113 3.6 31.5 1.0
CD A:LYS111 3.8 78.5 1.0
C A:ASN273 3.8 38.7 1.0
C A:ALA112 4.0 33.1 1.0
CE A:LYS111 4.1 80.4 1.0
N A:GLY274 4.1 30.5 1.0
CA A:LYS142 4.3 27.2 1.0
NZ A:LYS111 4.3 81.6 1.0
CA A:GLY274 4.4 29.4 1.0
O A:ALA112 4.4 31.6 1.0
C A:LYS111 4.5 75.2 1.0
CA A:ASN273 4.5 40.0 1.0
CA A:ALA112 4.7 35.4 1.0

Silver binding site 5 out of 27 in 7cgd

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Silver binding site 5 out of 27 in the Silver-Bound E.Coli Malate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of Silver-Bound E.Coli Malate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag405

b:23.6
occ:0.79
 N A:VAL173 2.2 25.9 1.0
SG A:CYS251 2.3 27.1 1.0
O A:VAL173 2.5 25.0 1.0
C A:VAL173 3.0 25.4 1.0
CA A:VAL173 3.1 25.8 1.0
C A:PRO172 3.1 22.4 1.0
CB A:CYS251 3.2 26.4 1.0
CA A:PRO172 3.2 22.4 1.0
AG A:AG406 3.3 48.9 1.0
CB A:VAL173 3.8 25.6 1.0
CB A:PRO172 3.9 22.7 1.0
CD1 A:ILE151 4.0 18.0 1.0
N A:ILE174 4.2 22.4 1.0
CG1 A:ILE151 4.2 18.0 1.0
O A:PRO172 4.3 23.0 1.0
O A:VAL171 4.3 22.7 1.0
CG2 A:VAL173 4.5 26.1 1.0
N A:PRO172 4.5 22.9 1.0
CG2 A:ILE174 4.6 22.7 1.0
CA A:CYS251 4.6 26.8 1.0
CA A:ILE174 4.9 22.2 1.0
C A:VAL171 4.9 23.2 1.0

Silver binding site 6 out of 27 in 7cgd

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Silver binding site 6 out of 27 in the Silver-Bound E.Coli Malate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 6 of Silver-Bound E.Coli Malate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag406

b:48.9
occ:1.00
 SG A:CYS251 2.4 27.1 1.0
O A:HOH513 2.9 29.3 1.0
CB A:CYS251 3.2 26.4 1.0
AG A:AG405 3.3 23.6 0.8
N A:CYS251 3.4 27.1 1.0
CA A:CYS251 3.8 26.8 1.0
C A:GLU250 4.1 31.8 1.0
CD1 A:ILE151 4.1 18.0 1.0
CA A:PRO267 4.5 27.2 1.0
CB A:PRO267 4.5 27.6 1.0
CG A:PRO267 4.5 27.4 1.0
CA A:GLU250 4.5 32.1 1.0
CA A:PRO172 4.7 22.4 1.0
O A:GLU250 4.8 32.2 1.0
N A:PRO267 5.0 27.1 1.0

Silver binding site 7 out of 27 in 7cgd

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Silver binding site 7 out of 27 in the Silver-Bound E.Coli Malate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 7 of Silver-Bound E.Coli Malate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag407

b:38.5
occ:0.43
 NE2 A:HIS177 2.5 25.0 1.0
SD A:MET227 2.7 29.1 1.0
O A:HOH509 2.7 29.3 1.0
O A:HOH503 3.3 29.0 1.0
CE1 A:HIS177 3.4 25.0 1.0
CD2 A:HIS177 3.5 25.0 1.0
CE A:MET227 3.6 28.5 1.0
ND2 A:ASN119 3.7 38.5 1.0
CD2 A:LEU149 4.0 20.9 1.0
CG A:MET227 4.2 29.3 1.0
CB A:LEU149 4.3 19.7 1.0
O A:VAL146 4.5 22.3 1.0
CG A:ASN119 4.5 36.9 1.0
ND1 A:HIS177 4.5 24.9 1.0
O A:ILE117 4.6 28.4 1.0
OD1 A:ASN119 4.6 35.4 1.0
CG A:HIS177 4.6 24.9 1.0
CG A:LEU149 4.8 20.5 1.0

Silver binding site 8 out of 27 in 7cgd

Go back to Silver Binding Sites List in 7cgd
Silver binding site 8 out of 27 in the Silver-Bound E.Coli Malate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 8 of Silver-Bound E.Coli Malate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ag401

b:57.8
occ:0.70
 SG B:CYS109 2.4 33.4 1.0
O B:ALA70 2.6 20.3 1.0
CB B:CYS109 2.7 33.2 1.0
O B:HOH513 2.7 29.8 1.0
N B:ALA70 3.1 19.7 1.0
C B:GLY69 3.4 24.0 1.0
AG B:AG402 3.4 65.0 0.7
C B:ALA70 3.5 19.5 1.0
CA B:GLY69 3.6 25.4 1.0
N B:GLY69 3.7 25.5 1.0
CA B:ALA70 3.8 19.3 1.0
CA B:CYS109 3.9 33.8 1.0
O B:LEU67 4.0 21.7 1.0
O B:GLY69 4.1 24.0 1.0
CB B:ALA70 4.5 19.8 1.0
N B:ASP71 4.7 23.1 1.0
C B:GLU68 4.8 38.8 1.0
C B:CYS109 4.8 33.9 1.0
O B:CYS109 4.9 33.0 1.0
CB B:ALA112 5.0 21.4 1.0
N B:CYS109 5.0 33.0 1.0

Silver binding site 9 out of 27 in 7cgd

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Silver binding site 9 out of 27 in the Silver-Bound E.Coli Malate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 9 of Silver-Bound E.Coli Malate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ag402

b:65.0
occ:0.67
 O B:HOH513 2.4 29.8 1.0
SG B:CYS109 2.4 33.4 1.0
O B:THR108 2.9 34.8 1.0
CB B:CYS109 3.4 33.2 1.0
CA B:CYS109 3.4 33.8 1.0
AG B:AG401 3.4 57.8 0.7
C B:THR108 3.7 34.0 1.0
N B:CYS109 3.9 33.0 1.0
CG2 B:THR108 4.5 33.3 1.0
N B:GLY69 4.5 25.5 1.0
C B:CYS109 4.8 33.9 1.0
CA B:THR108 4.9 33.0 1.0
CD B:PRO110 5.0 35.5 1.0

Silver binding site 10 out of 27 in 7cgd

Go back to Silver Binding Sites List in 7cgd
Silver binding site 10 out of 27 in the Silver-Bound E.Coli Malate Dehydrogenase


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 10 of Silver-Bound E.Coli Malate Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ag403

b:44.1
occ:0.97
 O B:HOH512 2.8 29.3 1.0
AG B:AG404 2.9 35.7 0.6
O B:ASP71 3.0 24.8 1.0
SG B:CYS113 3.1 26.6 1.0
N B:CYS113 3.4 27.4 1.0
CD1 B:LEU242 3.4 23.9 1.0
AG B:AG405 3.7 32.2 0.5
CB B:CYS113 3.7 25.2 1.0
CD2 B:LEU242 4.0 22.8 1.0
O B:LYS111 4.0 29.3 1.0
C B:ASP71 4.0 24.1 1.0
C B:ALA112 4.1 20.4 1.0
CA B:CYS113 4.1 25.7 1.0
CA B:ALA112 4.3 22.0 1.0
CG B:LEU242 4.3 23.4 1.0
NZ B:LYS142 4.4 20.1 1.0
CA B:ASP71 4.5 23.6 1.0
CB B:ASP71 4.6 23.6 1.0
O B:LYS272 4.9 32.8 1.0
C B:LYS111 5.0 30.0 1.0

Reference:

H.Wang, X.Yang, M.Wang, M.Hu, X.Xu, A.Yan, Q.Hao, H.Li, H.Sun. Atomic Differentiation of Silver Binding Preference in Protein Targets: Escherichia Coli Malate Dehydrogenase As A Paradigm Chem Sci 2020.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC04151C
Page generated: Wed Jul 10 08:42:56 2024

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