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Silver in PDB 5ffe: Copm in the Ag-Bound Form (By Soaking)

Protein crystallography data

The structure of Copm in the Ag-Bound Form (By Soaking), PDB code: 5ffe was solved by S.Zhao, X.Wang, L.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.74 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.984, 67.035, 85.614, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.7

Silver Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Silver atom in the Copm in the Ag-Bound Form (By Soaking) (pdb code 5ffe). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 12 binding sites of Silver where determined in the Copm in the Ag-Bound Form (By Soaking), PDB code: 5ffe:
Jump to Silver binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Silver binding site 1 out of 12 in 5ffe

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Silver binding site 1 out of 12 in the Copm in the Ag-Bound Form (By Soaking)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 1 of Copm in the Ag-Bound Form (By Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag201

b:15.2
occ:1.00
 ND1 A:HIS57 2.1 13.1 1.0
ND1 A:HIS56 2.1 13.8 1.0
CE1 A:HIS57 2.9 13.0 1.0
N A:HIS57 3.0 13.9 1.0
SD A:MET53 3.0 16.1 1.0
CE1 A:HIS56 3.1 14.2 1.0
CG A:HIS56 3.1 15.2 1.0
O A:HOH352 3.1 14.8 1.0
CG A:HIS57 3.2 14.3 1.0
CA A:HIS57 3.3 14.0 1.0
C A:HIS56 3.4 15.4 1.0
CB A:HIS56 3.5 15.2 1.0
O A:MET53 3.6 16.5 1.0
CB A:HIS57 3.7 13.7 1.0
O A:HIS56 3.8 16.0 1.0
CE A:MET53 3.9 16.3 1.0
CG A:MET53 3.9 14.1 1.0
CB A:ALA152 4.0 11.7 1.0
CA A:HIS56 4.0 15.2 1.0
NE2 A:HIS57 4.1 13.7 1.0
OE1 A:GLN87 4.2 14.0 1.0
NE2 A:HIS56 4.2 14.3 1.0
CD2 A:HIS56 4.2 14.1 1.0
CD2 A:HIS57 4.3 12.4 1.0
CE1 A:HIS148 4.4 15.1 1.0
C A:MET53 4.6 15.8 1.0
C A:HIS57 4.7 15.1 1.0
CA A:MET53 4.8 15.6 1.0
CA A:ALA152 4.9 14.7 1.0
NE2 A:GLN179 4.9 14.8 1.0
CB A:MET53 5.0 16.8 1.0
N A:HIS56 5.0 15.1 1.0

Silver binding site 2 out of 12 in 5ffe

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Silver binding site 2 out of 12 in the Copm in the Ag-Bound Form (By Soaking)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 2 of Copm in the Ag-Bound Form (By Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag202

b:14.5
occ:1.00
 ND1 A:HIS148 2.1 14.2 1.0
ND1 A:HIS149 2.1 12.7 1.0
CE1 A:HIS149 2.8 14.2 1.0
CG A:HIS148 3.0 15.2 1.0
N A:HIS149 3.1 13.2 1.0
CE1 A:HIS148 3.1 15.1 1.0
O A:HOH352 3.1 14.8 1.0
SD A:MET145 3.2 13.8 1.0
CB A:HIS148 3.3 14.0 1.0
CG A:HIS149 3.3 13.5 1.0
C A:HIS148 3.3 12.6 1.0
CA A:HIS149 3.4 13.7 1.0
O A:HIS148 3.7 12.8 1.0
O A:MET145 3.8 15.5 1.0
CB A:HIS149 3.8 13.4 1.0
CB A:ALA60 3.9 14.0 1.0
CA A:HIS148 3.9 14.2 1.0
OE1 A:GLN179 4.0 14.2 1.0
NE2 A:HIS149 4.1 13.5 1.0
CD2 A:HIS148 4.2 13.4 1.0
CG A:MET145 4.2 14.7 1.0
NE2 A:HIS148 4.2 14.2 1.0
CD2 A:HIS149 4.3 12.5 1.0
CE1 A:HIS56 4.6 14.2 1.0
NE2 A:GLN87 4.7 13.0 1.0
C A:MET145 4.7 15.4 1.0
C A:HIS149 4.8 15.4 1.0
CA A:MET145 4.8 16.4 1.0
CE A:MET145 4.9 17.4 1.0
N A:HIS148 4.9 15.0 1.0
CA A:ALA60 4.9 15.9 1.0

Silver binding site 3 out of 12 in 5ffe

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Silver binding site 3 out of 12 in the Copm in the Ag-Bound Form (By Soaking)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 3 of Copm in the Ag-Bound Form (By Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag203

b:22.4
occ:1.00
 NE2 A:HIS73 2.1 14.1 1.0
CE1 A:HIS73 2.8 18.5 1.0
O A:HOH410 3.0 18.6 1.0
CD1 A:TRP193 3.1 17.8 1.0
CD2 A:HIS73 3.3 15.5 1.0
CG A:TRP193 3.3 17.1 1.0
O A:HOH411 3.5 28.3 1.0
NE1 A:TRP193 3.6 16.1 1.0
CB A:TRP193 3.8 18.6 1.0
CD2 A:TRP193 3.9 16.2 1.0
CE2 A:TRP193 4.0 16.2 1.0
ND1 A:HIS73 4.0 18.1 1.0
CG A:HIS73 4.3 18.8 1.0
CA A:TRP193 4.3 19.1 1.0
O A:HOH426 4.4 31.3 1.0
O A:HOH342 4.7 16.2 1.0
CE3 A:TRP193 4.8 16.4 1.0
CZ2 A:TRP193 5.0 16.7 1.0

Silver binding site 4 out of 12 in 5ffe

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Silver binding site 4 out of 12 in the Copm in the Ag-Bound Form (By Soaking)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 4 of Copm in the Ag-Bound Form (By Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag204

b:41.6
occ:1.00
 O A:HOH434 2.6 31.5 1.0
SD A:MET155 3.0 27.8 1.0
SD A:MET151 3.1 30.4 1.0
CG A:MET155 3.5 18.7 1.0
CG A:MET151 3.5 20.1 1.0
CE A:MET155 4.0 19.6 1.0
CE A:MET151 4.1 25.9 1.0
CZ2 A:TRP44 4.2 29.0 1.0
CH2 A:TRP44 4.6 27.7 1.0
O A:HOH417 4.9 25.2 1.0
O A:MET151 4.9 17.6 1.0
CB A:MET155 5.0 17.4 1.0

Silver binding site 5 out of 12 in 5ffe

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Silver binding site 5 out of 12 in the Copm in the Ag-Bound Form (By Soaking)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 5 of Copm in the Ag-Bound Form (By Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag205

b:53.1
occ:0.99
 SD A:MET63 3.0 28.3 0.8
CE A:MET63 3.3 18.7 1.0
OE1 A:GLN144 3.5 27.4 0.7
CG A:MET63 3.6 21.9 1.0
CB A:ASP59 4.6 20.2 1.0
CD A:GLN144 4.7 26.7 1.0
O A:ASP59 4.7 18.4 1.0
CG A:ASP59 5.0 21.1 1.0

Silver binding site 6 out of 12 in 5ffe

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Silver binding site 6 out of 12 in the Copm in the Ag-Bound Form (By Soaking)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 6 of Copm in the Ag-Bound Form (By Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ag206

b:48.1
occ:0.58
 SD A:MET66 3.0 36.1 1.0
NZ A:LYS70 3.0 42.2 1.0
CG A:MET66 3.4 24.4 1.0
O A:LEU131 3.5 43.1 1.0
CB A:MET66 3.5 20.9 1.0
CD A:LYS70 3.5 32.7 1.0
CE A:LYS70 3.7 40.1 1.0
CA A:ALA132 3.7 46.6 1.0
C A:LEU131 4.1 43.0 1.0
N A:ALA132 4.2 46.2 1.0
O A:ALA132 4.3 46.1 1.0
CE1 A:PHE137 4.4 24.1 1.0
CB A:ALA132 4.5 49.1 1.0
C A:ALA132 4.5 46.6 1.0
CE A:MET66 4.6 27.3 1.0
CA A:MET66 4.8 21.2 1.0
CG A:LYS70 4.8 26.7 1.0
CD1 A:PHE137 4.9 24.0 1.0
CG A:LEU131 5.0 34.5 1.0

Silver binding site 7 out of 12 in 5ffe

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Silver binding site 7 out of 12 in the Copm in the Ag-Bound Form (By Soaking)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 7 of Copm in the Ag-Bound Form (By Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ag201

b:14.3
occ:1.00
 ND1 B:HIS57 2.0 13.1 1.0
ND1 B:HIS56 2.1 14.7 1.0
CE1 B:HIS57 2.8 12.7 1.0
N B:HIS57 3.0 14.2 1.0
CG B:HIS56 3.1 14.7 1.0
SD B:MET53 3.1 17.1 1.0
CE1 B:HIS56 3.1 16.0 1.0
O B:HOH343 3.2 13.7 1.0
CG B:HIS57 3.2 13.8 1.0
C B:HIS56 3.3 15.7 1.0
CA B:HIS57 3.3 14.1 1.0
CB B:HIS56 3.4 15.9 1.0
O B:MET53 3.7 15.3 1.0
CB B:HIS57 3.8 12.3 1.0
O B:HIS56 3.8 16.2 1.0
CA B:HIS56 4.0 16.0 1.0
CG B:MET53 4.0 15.0 1.0
NE2 B:HIS57 4.0 14.9 1.0
CB B:ALA152 4.0 13.2 1.0
OE1 B:GLN87 4.2 15.0 1.0
CE B:MET53 4.2 16.6 1.0
NE2 B:HIS56 4.2 15.6 1.0
CD2 B:HIS56 4.2 14.9 1.0
CD2 B:HIS57 4.2 12.5 1.0
CE1 B:HIS148 4.4 15.1 1.0
C B:MET53 4.6 15.6 1.0
C B:HIS57 4.8 16.8 1.0
CA B:MET53 4.8 14.9 1.0
NE2 B:GLN179 4.9 15.9 1.0
N B:HIS56 4.9 14.6 1.0

Silver binding site 8 out of 12 in 5ffe

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Silver binding site 8 out of 12 in the Copm in the Ag-Bound Form (By Soaking)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 8 of Copm in the Ag-Bound Form (By Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ag202

b:16.0
occ:1.00
 ND1 B:HIS148 2.1 14.3 1.0
ND1 B:HIS149 2.1 12.6 1.0
CE1 B:HIS149 2.8 12.6 1.0
CG B:HIS148 3.0 15.6 1.0
O B:HOH343 3.1 13.7 1.0
N B:HIS149 3.1 14.6 1.0
CE1 B:HIS148 3.1 15.1 1.0
SD B:MET145 3.2 17.4 1.0
CB B:HIS148 3.3 16.3 1.0
CG B:HIS149 3.3 13.1 1.0
C B:HIS148 3.4 15.2 1.0
CA B:HIS149 3.4 13.4 1.0
O B:MET145 3.8 16.4 1.0
CB B:HIS149 3.8 13.0 1.0
O B:HIS148 3.8 13.7 1.0
CB B:ALA60 3.9 14.1 1.0
CA B:HIS148 3.9 16.3 1.0
NE2 B:HIS149 4.0 12.6 1.0
OE1 B:GLN179 4.1 12.6 1.0
CD2 B:HIS148 4.2 15.6 1.0
NE2 B:HIS148 4.2 15.9 1.0
CG B:MET145 4.2 16.9 1.0
CD2 B:HIS149 4.3 12.3 1.0
CE1 B:HIS56 4.6 16.0 1.0
C B:MET145 4.8 16.7 1.0
CE B:MET145 4.8 20.3 1.0
C B:HIS149 4.8 14.8 1.0
NE2 B:GLN87 4.8 14.0 1.0
CA B:MET145 4.9 18.9 1.0
N B:HIS148 4.9 17.4 1.0
CA B:ALA60 4.9 17.6 1.0

Silver binding site 9 out of 12 in 5ffe

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Silver binding site 9 out of 12 in the Copm in the Ag-Bound Form (By Soaking)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 9 of Copm in the Ag-Bound Form (By Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ag203

b:26.0
occ:0.61
 NE2 B:HIS73 2.7 21.2 1.0
CD1 B:TRP193 3.2 21.1 1.0
O B:HOH374 3.2 26.8 1.0
CD2 B:HIS73 3.3 20.3 1.0
NE1 B:TRP193 3.5 20.5 1.0
CG B:TRP193 3.7 20.0 1.0
CE1 B:HIS73 3.8 23.4 1.0
CE2 B:TRP193 4.2 19.4 1.0
CB B:TRP193 4.3 21.8 1.0
CD2 B:TRP193 4.3 19.1 1.0
CA B:TRP193 4.5 22.7 1.0
CG B:HIS73 4.6 21.8 1.0
O B:HOH319 4.6 18.8 1.0
ND1 B:HIS73 4.8 23.1 1.0

Silver binding site 10 out of 12 in 5ffe

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Silver binding site 10 out of 12 in the Copm in the Ag-Bound Form (By Soaking)


Mono view


Stereo pair view

A full contact list of Silver with other atoms in the Ag binding site number 10 of Copm in the Ag-Bound Form (By Soaking) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ag204

b:42.8
occ:1.00
 O B:HOH410 2.9 31.2 1.0
SD B:MET151 3.0 30.5 1.0
SD B:MET155 3.0 23.8 0.7
CG B:MET151 3.4 20.3 1.0
CG B:MET155 3.5 18.2 1.0
CE B:MET155 3.8 21.2 1.0
CE B:MET151 4.1 25.7 1.0
CZ2 B:TRP44 4.3 26.5 1.0
O B:HOH397 4.6 27.6 1.0
CH2 B:TRP44 4.8 25.1 1.0
CB B:MET151 4.9 16.7 1.0
CB B:MET155 4.9 17.0 1.0

Reference:

S.Zhao, X.Wang, G.Niu, W.Dong, J.Wang, Y.Fang, Y.Lin, L.Liu. Structural Basis For Copper/Silver Binding By the Synechocystis Metallochaperone Copm Acta Crystallogr.,Sect.D V. 72 997 2016.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798316011943
Page generated: Wed Jul 10 08:24:52 2024

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