Silver in PDB 5ffd: Copm in the Ag-Bound Form (By Co-Crystallization)

The structure of Copm in the Ag-Bound Form (By Co-Crystallization), PDB code: 5ffd 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)	33.60 / 1.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.872, 85.959, 31.729, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 19.3

The binding sites of Silver atom in the Copm in the Ag-Bound Form (By Co-Crystallization) (pdb code 5ffd). This binding sites where shown within 5.0 Angstroms radius around Silver atom.
In total 3 binding sites of Silver where determined in the Copm in the Ag-Bound Form (By Co-Crystallization), PDB code: 5ffd:
Jump to Silver binding site number: 1; 2; 3;

Silver binding site 1 out of 3 in the Copm in the Ag-Bound Form (By Co-Crystallization)


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 Co-Crystallization) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag201 b:13.8 occ:1.00 ND1 A:HIS57 2.2 11.3 1.0 ND1 A:HIS56 2.2 11.6 1.0 CE1 A:HIS57 3.0 11.7 1.0 O A:HOH370 3.0 12.6 1.0 SD A:MET53 3.0 14.6 1.0 N A:HIS57 3.0 7.9 1.0 CE1 A:HIS56 3.2 12.1 1.0 CG A:HIS56 3.2 11.1 1.0 CG A:HIS57 3.3 10.7 1.0 CA A:HIS57 3.3 8.5 1.0 C A:HIS56 3.4 9.0 1.0 CB A:HIS56 3.5 10.7 1.0 CB A:HIS57 3.8 9.8 1.0 O A:HIS56 3.8 9.4 1.0 O A:MET53 3.8 10.4 1.0 OE1 A:GLN87 4.0 17.1 1.0 CA A:HIS56 4.0 9.4 1.0 CG A:MET53 4.1 11.4 1.0 NE2 A:HIS57 4.2 11.5 1.0 CB A:ALA152 4.2 10.3 1.0 NE2 A:HIS56 4.3 12.3 1.0 CE1 A:HIS148 4.3 11.6 1.0 CD2 A:HIS56 4.3 12.1 1.0 CD2 A:HIS57 4.3 10.6 1.0 CE A:MET53 4.6 16.8 1.0 NE2 A:GLN179 4.6 14.6 1.0 C A:HIS57 4.7 8.6 1.0 C A:MET53 4.7 9.7 1.0 CA A:MET53 4.9 9.8 1.0 CD A:GLN87 5.0 15.1 1.0 N A:HIS56 5.0 9.4 1.0

Silver binding site 2 out of 3 in the Copm in the Ag-Bound Form (By Co-Crystallization)


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 Co-Crystallization) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag202 b:11.7 occ:1.00 ND1 A:HIS149 2.2 10.3 1.0 ND1 A:HIS148 2.2 10.7 1.0 CE1 A:HIS149 2.9 10.8 1.0 O A:HOH370 3.0 12.6 1.0 N A:HIS149 3.1 7.7 1.0 CG A:HIS148 3.1 10.8 1.0 CE1 A:HIS148 3.2 11.6 1.0 SD A:MET145 3.2 10.7 1.0 CG A:HIS149 3.3 9.5 1.0 C A:HIS148 3.3 8.6 1.0 CA A:HIS149 3.4 9.2 1.0 CB A:HIS148 3.4 9.7 1.0 O A:MET145 3.8 9.3 1.0 CB A:HIS149 3.8 9.7 1.0 O A:HIS148 3.8 8.6 1.0 OE1 A:GLN179 3.9 16.8 1.0 CA A:HIS148 4.0 10.1 1.0 CB A:ALA60 4.0 8.9 1.0 CG A:MET145 4.1 10.1 1.0 NE2 A:HIS149 4.1 11.1 1.0 NE2 A:HIS148 4.3 11.8 1.0 CD2 A:HIS148 4.3 11.4 1.0 CD2 A:HIS149 4.3 10.4 1.0 CE1 A:HIS56 4.4 12.1 1.0 C A:MET145 4.7 8.1 1.0 C A:HIS149 4.8 10.3 1.0 NE2 A:GLN87 4.8 15.7 1.0 CA A:MET145 4.9 7.9 1.0 CE A:MET145 4.9 12.5 1.0 N A:HIS148 4.9 9.6 1.0 CD A:GLN179 5.0 15.1 1.0

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


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 Co-Crystallization) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ag203 b:30.8 occ:0.52 O A:HOH488 3.0 37.7 1.0 SD A:MET155 3.0 21.2 0.8 O A:HOH514 3.1 39.8 1.0 SD A:MET151 3.2 27.2 1.0 CG A:MET151 3.4 21.4 1.0 CG A:MET155 3.6 18.4 1.0 CZ2 A:TRP44 3.7 23.0 1.0 CE A:MET155 4.0 21.4 1.0 CH2 A:TRP44 4.2 23.2 1.0 CE A:MET151 4.4 27.3 1.0 CE2 A:TRP44 4.8 22.0 1.0 CB A:MET151 5.0 16.5 1.0

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