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

The structure of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus, PDB code: 5nqm 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 / 1.59
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	44.650, 106.680, 45.620, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 20.7

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

Sodium

(Na)

1 atom

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

Copper binding site 1 out of 4 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:Cu211 b:18.8 occ:0.25 SG A:CYS118 2.0 18.0 1.0 SG A:CYS97 2.0 15.8 1.0 CU A:CU1212 2.6 15.8 0.3 CU A:CU1214 2.7 17.6 0.3 CB A:CYS97 2.7 14.0 1.0 CU A:CU1213 3.1 17.3 0.3 SG A:CYS35 3.1 14.8 1.0 OD1 A:ASN58 3.5 17.8 1.0 CB A:CYS118 3.6 13.3 1.0 CA A:CYS97 3.8 14.1 1.0 SG A:CYS114 3.8 16.5 1.0 C A:CYS97 3.8 12.7 1.0 SG A:CYS61 4.0 14.8 1.0 O A:CYS97 4.1 14.5 1.0 N A:GLU98 4.2 13.3 1.0 SG A:CYS101 4.2 20.2 1.0 CB A:CYS61 4.2 13.8 1.0 CG A:ASN58 4.5 16.1 1.0 CB A:CYS35 4.6 11.7 1.0 O A:CYS114 4.7 14.6 1.0 CA A:CYS118 4.8 11.9 1.0 CA A:GLU98 4.9 15.2 1.0 N A:CYS97 4.9 13.3 1.0 O A:CYS94 4.9 12.6 1.0

Copper binding site 2 out of 4 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:Cu212 b:15.8 occ:0.35 SG A:CYS114 2.0 16.5 1.0 SG A:CYS118 2.3 18.0 1.0 O A:CYS114 2.5 14.6 1.0 CU A:CU1211 2.6 18.8 0.2 CU A:CU1213 2.7 17.3 0.3 C A:CYS114 2.9 13.7 1.0 CB A:CYS114 3.1 14.9 1.0 CA A:CYS114 3.2 14.4 1.0 SG A:CYS35 3.4 14.8 1.0 CB A:CYS118 3.5 13.3 1.0 N A:ALA115 3.9 13.4 1.0 N A:CYS118 3.9 10.6 1.0 OD1 A:ASN58 4.1 17.8 1.0 CU A:CU1214 4.1 17.6 0.3 CA A:CYS118 4.2 11.9 1.0 SG A:CYS101 4.4 20.2 1.0 CA A:ALA115 4.4 12.7 1.0 SG A:CYS97 4.4 15.8 1.0 N A:CYS114 4.7 13.6 1.0 SG A:CYS31 4.7 16.6 1.0 CG2 A:THR34 4.7 13.6 1.0 CA A:CYS35 4.8 10.9 1.0 CB A:CYS35 4.8 11.7 1.0 CB A:VAL117 4.9 13.7 1.0 N A:CYS35 4.9 10.1 1.0 C A:VAL117 4.9 12.0 1.0

Copper binding site 3 out of 4 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:Cu213 b:17.3 occ:0.35 SG A:CYS114 2.0 16.5 1.0 SG A:CYS101 2.2 20.2 1.0 OD1 A:ASN58 2.4 17.8 1.0 CU A:CU1214 2.7 17.6 0.3 CU A:CU1212 2.7 15.8 0.3 CB A:CYS114 2.9 14.9 1.0 CU A:CU1211 3.1 18.8 0.2 CG A:ASN58 3.2 16.1 1.0 ND2 A:ASN58 3.3 20.9 1.0 CB A:CYS101 3.6 15.9 1.0 SG A:CYS97 3.7 15.8 1.0 SG A:CYS38 3.8 15.1 1.0 CA A:CYS114 4.0 14.4 1.0 CB A:CYS38 4.0 13.3 1.0 C A:CYS114 4.1 13.7 1.0 SG A:CYS118 4.3 18.0 1.0 SG A:CYS35 4.3 14.8 1.0 O A:CYS114 4.4 14.6 1.0 N A:ALA115 4.5 13.4 1.0 CB A:ASN58 4.7 11.4 1.0 O A:CYS97 4.7 14.5 1.0 CA A:CYS35 4.8 10.9 1.0 CA A:CYS101 4.9 14.1 1.0

Copper binding site 4 out of 4 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:Cu214 b:17.6 occ:0.35 SG A:CYS97 2.0 15.8 1.0 SG A:CYS101 2.2 20.2 1.0 O A:CYS97 2.4 14.5 1.0 CU A:CU1211 2.7 18.8 0.2 CU A:CU1213 2.7 17.3 0.3 C A:CYS97 2.9 12.7 1.0 CB A:CYS97 3.0 14.0 1.0 CA A:CYS97 3.1 14.1 1.0 OD1 A:ASN58 3.4 17.8 1.0 CB A:CYS101 3.4 15.9 1.0 CG A:ASN58 3.8 16.1 1.0 N A:GLU98 3.9 13.3 1.0 ND2 A:ASN58 3.9 20.9 1.0 N A:CYS101 3.9 12.4 1.0 CU A:CU1212 4.1 15.8 0.3 CA A:CYS101 4.2 14.1 1.0 SG A:CYS118 4.3 18.0 1.0 CA A:GLU98 4.5 15.2 1.0 SG A:CYS114 4.5 16.5 1.0 N A:CYS97 4.6 13.3 1.0 N A:ASN58 4.8 8.7 1.0 SG A:CYS54 4.9 17.8 1.0 CB A:LEU57 5.0 11.3 1.0 CA A:ASN58 5.0 9.8 1.0 O A:CYS54 5.0 13.3 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