Copper in PDB 5nqo: Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus

The structure of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus, PDB code: 5nqo was solved by A.Basle, S.Platsaki, C.Dennison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.62 / 1.15
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	44.901, 105.691, 45.625, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 14.5

The structure of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus also contains other interesting chemical elements:

Sodium

(Na)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Copper atom in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus (pdb code 5nqo). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 22 binding sites of Copper where determined in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus, PDB code: 5nqo:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 22 in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu203 b:13.5 occ:0.80 SG A:CYS90 2.1 9.7 1.0 SG A:CYS125 2.2 11.9 1.0 CU A:CU1204 2.6 10.0 0.9 CU A:CU1206 2.9 10.2 0.9 SG A:CYS28 3.0 11.1 1.0 CB A:CYS90 3.0 9.2 1.0 CU A:CU1205 3.2 8.6 0.6 CU A:CU1205 3.3 12.3 0.2 CB A:CYS125 3.4 10.3 1.0 SG A:CYS121 3.8 9.2 1.0 CA A:CYS90 4.2 8.6 1.0 C A:CYS90 4.2 8.3 1.0 SG A:CYS65 4.2 9.2 1.0 CB A:ALA68 4.3 8.8 1.0 O A:CYS121 4.4 9.0 1.0 O A:CYS90 4.4 8.8 1.0 SG A:CYS94 4.4 11.6 1.0 CB A:CYS28 4.5 8.2 1.0 N A:ALA91 4.6 8.8 1.0 CA A:CYS125 4.7 9.6 1.0 CD2 A:LEU87 4.8 15.5 1.0 CA A:CYS28 4.9 7.9 1.0

Copper binding site 2 out of 22 in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu204 b:10.0 occ:0.90 SG A:CYS121 2.1 9.2 1.0 SG A:CYS125 2.1 11.9 1.0 O A:CYS121 2.2 9.0 1.0 CU A:CU1203 2.6 13.5 0.8 CU A:CU1205 2.8 12.3 0.2 C A:CYS121 2.9 8.3 1.0 CU A:CU1205 3.2 8.6 0.6 CB A:CYS121 3.2 8.6 1.0 CB A:CYS125 3.3 10.3 1.0 CA A:CYS121 3.3 8.4 1.0 N A:CYS125 3.7 9.2 1.0 SG A:CYS28 3.9 11.1 1.0 N A:GLU122 4.0 8.8 1.0 CA A:CYS125 4.0 9.6 1.0 CU A:CU1206 4.0 10.2 0.9 SG A:CYS94 4.4 11.6 1.0 SG A:CYS90 4.5 9.7 1.0 CA A:GLU122 4.5 8.7 1.0 CB A:MET27 4.5 10.1 1.0 CB A:ALA124 4.5 9.9 1.0 N A:CYS28 4.6 7.4 1.0 C A:ALA124 4.7 9.4 1.0 O A:CYS24 4.7 8.7 1.0 N A:CYS121 4.7 8.6 1.0 CA A:CYS28 4.8 7.9 1.0 C A:MET27 4.9 7.6 1.0 C A:GLU122 5.0 9.2 1.0 CB A:CYS28 5.0 8.2 1.0

Copper binding site 3 out of 22 in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu205 b:8.6 occ:0.60 CU A:CU1205 0.0 8.6 0.6 CU A:CU1205 1.5 12.3 0.2 SG A:CYS121 2.1 9.2 1.0 SG A:CYS65 2.2 9.2 1.0 CU A:CU1207 2.6 12.6 0.2 CU A:CU1207 2.8 8.6 0.6 CU A:CU1206 3.0 10.2 0.9 SG A:CYS94 3.1 11.6 1.0 CU A:CU1204 3.2 10.0 0.9 CU A:CU1203 3.2 13.5 0.8 CB A:CYS121 3.3 8.6 1.0 CB A:CYS65 3.5 7.2 1.0 CB A:CYS31 3.5 8.7 1.0 SG A:CYS90 3.7 9.7 1.0 CU A:CU1208 3.7 9.6 0.9 CA A:CYS28 3.8 7.9 1.0 SG A:CYS31 3.8 9.2 1.0 SG A:CYS28 4.0 11.1 1.0 CB A:CYS28 4.3 8.2 1.0 CA A:CYS65 4.3 6.4 1.0 O A:MET27 4.4 8.9 1.0 O A:CYS28 4.4 7.2 1.0 N A:CYS28 4.5 7.4 1.0 CA A:CYS121 4.6 8.4 1.0 SG A:CYS125 4.6 11.9 1.0 C A:CYS28 4.6 6.7 1.0 C A:MET27 4.7 7.6 1.0 C A:CYS121 4.7 8.3 1.0 CB A:CYS94 4.8 8.5 1.0 O A:CYS121 4.8 9.0 1.0 CA A:CYS31 4.9 7.4 1.0

Copper binding site 4 out of 22 in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu205 b:12.3 occ:0.25 CU A:CU1205 0.0 12.3 0.2 CU A:CU1205 1.5 8.6 0.6 SG A:CYS94 1.9 11.6 1.0 SG A:CYS121 2.2 9.2 1.0 CU A:CU1207 2.4 8.6 0.6 CU A:CU1206 2.4 10.2 0.9 CB A:CYS121 2.7 8.6 1.0 CU A:CU1204 2.8 10.0 0.9 CU A:CU1207 3.0 12.6 0.2 SG A:CYS65 3.1 9.2 1.0 CU A:CU1203 3.3 13.5 0.8 CB A:CYS94 3.4 8.5 1.0 C A:CYS121 3.6 8.3 1.0 CA A:CYS121 3.7 8.4 1.0 O A:CYS121 3.8 9.0 1.0 SG A:CYS31 3.9 9.2 1.0 SG A:CYS90 3.9 9.7 1.0 N A:GLU122 4.0 8.8 1.0 CU A:CU1208 4.0 9.6 0.9 CB A:CYS31 4.1 8.7 1.0 O A:CYS90 4.5 8.8 1.0 SG A:CYS125 4.5 11.9 1.0 CA A:CYS94 4.6 8.1 1.0 CB A:CYS65 4.7 7.2 1.0 O A:CYS118 4.7 8.9 1.0 CA A:GLU122 4.7 8.7 1.0 N A:CYS121 4.9 8.6 1.0

Copper binding site 5 out of 22 in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu206 b:10.2 occ:0.90 SG A:CYS94 2.1 11.6 1.0 SG A:CYS90 2.2 9.7 1.0 O A:CYS90 2.3 8.8 1.0 CU A:CU1205 2.4 12.3 0.2 CU A:CU1203 2.9 13.5 0.8 C A:CYS90 2.9 8.3 1.0 CU A:CU1205 3.0 8.6 0.6 SG A:CYS65 3.2 9.2 1.0 CB A:CYS90 3.2 9.2 1.0 CA A:CYS90 3.3 8.6 1.0 CB A:CYS94 3.4 8.5 1.0 CU A:CU1207 3.7 8.6 0.6 N A:CYS94 3.8 7.7 1.0 N A:ALA91 3.8 8.8 1.0 CU A:CU1208 3.9 9.6 0.9 CU A:CU1204 4.0 10.0 0.9 CA A:CYS94 4.1 8.1 1.0 CU A:CU1207 4.2 12.6 0.2 CA A:ALA91 4.3 9.3 1.0 SG A:CYS121 4.4 9.2 1.0 SG A:CYS125 4.6 11.9 1.0 CB A:MET93 4.7 7.8 1.0 N A:CYS90 4.8 8.8 1.0 SG A:CYS61 4.8 8.1 1.0 CG2 A:ILE64 4.8 9.7 1.0 CB A:CYS65 4.8 7.2 1.0 C A:MET93 4.9 7.4 1.0 C A:ALA91 4.9 10.0 1.0

Copper binding site 6 out of 22 in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu207 b:8.6 occ:0.60 CU A:CU1207 0.0 8.6 0.6 CU A:CU1207 1.5 12.6 0.2 SG A:CYS94 2.1 11.6 1.0 SG A:CYS31 2.2 9.2 1.0 CU A:CU1205 2.4 12.3 0.2 CU A:CU1205 2.8 8.6 0.6 CU A:CU1208 2.8 9.6 0.9 CU A:CU1209 2.9 8.3 0.7 SG A:CYS65 3.1 9.2 1.0 CU A:CU1209 3.1 10.3 0.1 CB A:CYS31 3.3 8.7 1.0 CU A:CU1210 3.3 8.6 0.9 SG A:CYS61 3.4 8.1 1.0 CB A:CYS94 3.4 8.5 1.0 CB A:CYS121 3.6 8.6 1.0 CU A:CU1206 3.7 10.2 0.9 SG A:CYS121 3.8 9.2 1.0 CA A:CYS118 4.1 7.8 1.0 CA A:CYS94 4.1 8.1 1.0 SG A:CYS118 4.2 11.6 1.0 CB A:CYS118 4.4 7.5 1.0 O A:CYS118 4.5 8.9 1.0 CA A:CYS31 4.6 7.4 1.0 CB A:CYS65 4.7 7.2 1.0 C A:CYS118 4.8 8.4 1.0 C A:CYS31 4.8 6.7 1.0 N A:CYS94 4.8 7.7 1.0 SG A:CYS35 4.9 8.5 1.0 N A:CYS118 4.9 7.7 1.0 CA A:CYS121 4.9 8.4 1.0 O A:CYS31 4.9 8.0 1.0 CB A:CYS61 5.0 7.7 1.0

Copper binding site 7 out of 22 in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu207 b:12.6 occ:0.25 CU A:CU1207 0.0 12.6 0.2 CU A:CU1207 1.5 8.6 0.6 SG A:CYS31 2.1 9.2 1.0 SG A:CYS65 2.2 9.2 1.0 CU A:CU1208 2.3 9.6 0.9 CU A:CU1205 2.6 8.6 0.6 CB A:CYS31 2.6 8.7 1.0 CU A:CU1210 2.8 8.6 0.9 CU A:CU1205 3.0 12.3 0.2 CU A:CU1209 3.0 10.3 0.1 SG A:CYS94 3.3 11.6 1.0 CU A:CU1209 3.4 8.3 0.7 CB A:CYS65 3.5 7.2 1.0 SG A:CYS61 3.6 8.1 1.0 C A:CYS31 3.6 6.7 1.0 CA A:CYS31 3.6 7.4 1.0 O A:CYS31 3.8 8.0 1.0 SG A:CYS121 3.9 9.2 1.0 N A:ALA32 4.0 6.6 1.0 O A:CYS61 4.2 8.7 1.0 CU A:CU1206 4.2 10.2 0.9 CB A:CYS121 4.2 8.6 1.0 SG A:CYS35 4.5 8.5 1.0 O A:CYS28 4.7 7.2 1.0 N A:CYS31 4.7 7.2 1.0 CB A:CYS94 4.8 8.5 1.0 CA A:ALA32 4.8 6.8 1.0 CA A:CYS65 4.8 6.4 1.0 CB A:CYS61 4.9 7.7 1.0 C A:CYS61 4.9 6.9 1.0 SG A:CYS118 4.9 11.6 1.0

Copper binding site 8 out of 22 in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu208 b:9.6 occ:0.90 SG A:CYS65 2.1 9.2 1.0 SG A:CYS61 2.2 8.1 1.0 CU A:CU1207 2.3 12.6 0.2 O A:CYS61 2.4 8.7 1.0 CU A:CU1209 2.7 10.3 0.1 CU A:CU1207 2.8 8.6 0.6 C A:CYS61 3.0 6.9 1.0 CB A:CYS61 3.2 7.7 1.0 CB A:CYS65 3.2 7.2 1.0 CA A:CYS61 3.3 7.1 1.0 CU A:CU1209 3.4 8.3 0.7 SG A:CYS94 3.6 11.6 1.0 CU A:CU1205 3.7 8.6 0.6 CU A:CU1206 3.9 10.2 0.9 CU A:CU1210 3.9 8.6 0.9 N A:CYS65 4.0 6.1 1.0 CU A:CU1205 4.0 12.3 0.2 SG A:CYS31 4.1 9.2 1.0 N A:ALA62 4.1 6.4 1.0 CA A:CYS65 4.1 6.4 1.0 CG A:MET93 4.6 8.7 1.0 CA A:ALA62 4.7 6.3 1.0 N A:CYS61 4.7 6.9 1.0 SG A:CYS35 4.7 8.5 1.0 CB A:CYS31 4.7 8.7 1.0 SG A:CYS90 4.8 9.7 1.0 CA A:CYS94 4.9 8.1 1.0 CB A:CYS94 4.9 8.5 1.0 O A:CYS31 4.9 8.0 1.0 C A:ILE64 5.0 6.5 1.0 N A:CYS94 5.0 7.7 1.0

Copper binding site 9 out of 22 in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu209 b:8.3 occ:0.70 CU A:CU1209 0.0 8.3 0.7 CU A:CU1209 1.4 10.3 0.1 SG A:CYS118 2.1 11.6 1.0 SG A:CYS61 2.2 8.1 1.0 CU A:CU1211 2.3 9.6 0.2 CU A:CU1211 2.7 7.8 0.7 CU A:CU1210 2.8 8.6 0.9 SG A:CYS35 2.8 8.5 1.0 CU A:CU1207 2.9 8.6 0.6 CB A:CYS61 3.3 7.7 1.0 SG A:CYS31 3.4 9.2 1.0 CU A:CU1207 3.4 12.6 0.2 CB A:CYS118 3.4 7.5 1.0 CU A:CU1208 3.4 9.6 0.9 CB A:CYS97 3.6 8.3 1.0 CU A:CU1212 3.6 8.7 1.0 SG A:CYS97 3.8 8.8 1.0 CA A:CYS118 4.1 7.8 1.0 CA A:CYS94 4.2 8.1 1.0 SG A:CYS94 4.2 11.6 1.0 CB A:CYS35 4.4 6.6 1.0 CB A:CYS94 4.5 8.5 1.0 CA A:CYS61 4.6 7.1 1.0 O A:CYS94 4.7 8.8 1.0 N A:CYS118 4.9 7.7 1.0 CA A:CYS97 4.9 8.5 1.0 O A:CYS31 5.0 8.0 1.0 C A:CYS94 5.0 8.4 1.0 CU A:CU1214 5.0 9.3 0.9

Copper binding site 10 out of 22 in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu209 b:10.3 occ:0.15 CU A:CU1209 0.0 10.3 0.1 CU A:CU1209 1.4 8.3 0.7 SG A:CYS61 2.0 8.1 1.0 CU A:CU1210 2.2 8.6 0.9 SG A:CYS35 2.2 8.5 1.0 CB A:CYS61 2.7 7.7 1.0 CU A:CU1208 2.7 9.6 0.9 CU A:CU1211 2.8 7.8 0.7 CU A:CU1207 3.0 12.6 0.2 CU A:CU1211 3.0 9.6 0.2 CU A:CU1207 3.1 8.6 0.6 SG A:CYS118 3.3 11.6 1.0 CB A:CYS35 3.4 6.6 1.0 SG A:CYS31 3.4 9.2 1.0 CA A:CYS61 3.8 7.1 1.0 C A:CYS61 3.9 6.9 1.0 O A:CYS31 4.0 8.0 1.0 O A:CYS61 4.0 8.7 1.0 SG A:CYS97 4.2 8.8 1.0 CU A:CU1212 4.2 8.7 1.0 CB A:CYS97 4.4 8.3 1.0 N A:ALA62 4.4 6.4 1.0 SG A:CYS65 4.4 9.2 1.0 SG A:CYS94 4.6 11.6 1.0 C A:CYS31 4.7 6.7 1.0 CB A:CYS118 4.7 7.5 1.0 CA A:CYS35 4.7 6.1 1.0 CB A:CYS31 4.7 8.7 1.0 N A:CYS61 5.0 6.9 1.0

A.Basle, S.Platsaki, C.Dennison. Visualizing Biological Copper Storage: the Importance of Thiolate-Coordinated Tetranuclear Clusters. Angew. Chem. Int. Ed. Engl. V. 56 8697 2017.
ISSN: ESSN 1521-3773
PubMed: 28504850
DOI: 10.1002/ANIE.201703107