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

Protein crystallography data

The structure of Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus, PDB code: 5nqn 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) 45.60 / 1.62
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 44.899, 106.126, 45.604, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 21.1

Other elements in 5nqn:

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

Sodium (Na) 1 atom

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Copper atom in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus (pdb code 5nqn). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 18 binding sites of Copper where determined in the Cu(I)-CSP3 (Copper Storage Protein 3) From Methylosinus, PDB code: 5nqn:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 18 in 5nqn

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Copper binding site 1 out of 18 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:29.1
occ:0.55
SG A:CYS90 2.0 23.5 1.0
SG A:CYS125 2.2 27.8 1.0
CU A:CU1204 2.6 22.0 0.6
CU A:CU1206 2.9 24.1 0.7
SG A:CYS28 2.9 25.3 1.0
CB A:CYS90 2.9 21.9 1.0
CU A:CU1205 3.2 23.8 0.5
CU A:CU1205 3.3 21.5 0.1
CB A:CYS125 3.5 20.3 1.0
SG A:CYS121 3.7 20.4 1.0
CA A:CYS90 4.1 18.3 1.0
C A:CYS90 4.2 17.0 1.0
CB A:ALA68 4.2 18.7 1.0
SG A:CYS65 4.3 21.7 1.0
CB A:CYS28 4.5 19.3 1.0
O A:CYS90 4.5 16.1 1.0
O A:CYS121 4.6 16.9 1.0
SG A:CYS94 4.6 21.5 1.0
N A:ALA91 4.6 18.3 1.0
CD2 A:LEU87 4.8 29.1 1.0
CA A:CYS125 4.8 18.1 1.0
CA A:CYS28 4.9 17.2 1.0

Copper binding site 2 out of 18 in 5nqn

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Copper binding site 2 out of 18 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:22.0
occ:0.60
SG A:CYS121 2.0 20.4 1.0
SG A:CYS125 2.2 27.8 1.0
O A:CYS121 2.3 16.9 1.0
CU A:CU1203 2.6 29.1 0.6
CU A:CU1205 2.7 21.5 0.1
C A:CYS121 2.8 16.4 1.0
CB A:CYS121 3.1 16.7 1.0
CA A:CYS121 3.2 15.8 1.0
CU A:CU1205 3.2 23.8 0.5
CB A:CYS125 3.3 20.3 1.0
N A:CYS125 3.8 18.4 1.0
SG A:CYS28 3.9 25.3 1.0
N A:GLU122 3.9 17.1 1.0
CU A:CU1206 4.0 24.1 0.7
CA A:CYS125 4.1 18.1 1.0
SG A:CYS90 4.3 23.5 1.0
SG A:CYS94 4.5 21.5 1.0
CB A:ALA124 4.5 17.2 1.0
CA A:GLU122 4.5 17.5 1.0
CB A:MET27 4.5 18.8 1.0
N A:CYS121 4.6 15.7 1.0
N A:CYS28 4.7 16.8 1.0
C A:ALA124 4.7 17.2 1.0
CA A:CYS28 4.8 17.2 1.0
O A:CYS24 4.8 16.9 1.0
C A:MET27 4.9 15.7 1.0
C A:GLU122 5.0 18.1 1.0

Copper binding site 3 out of 18 in 5nqn

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Copper binding site 3 out of 18 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:23.8
occ:0.50
CU A:CU1205 0.0 23.8 0.5
CU A:CU1205 1.7 21.5 0.1
SG A:CYS121 2.0 20.4 1.0
SG A:CYS65 2.3 21.7 1.0
CU A:CU1207 2.7 18.4 0.1
CU A:CU1207 2.7 25.4 0.5
CU A:CU1206 3.0 24.1 0.7
SG A:CYS94 3.1 21.5 1.0
CU A:CU1204 3.2 22.0 0.6
CU A:CU1203 3.2 29.1 0.6
CB A:CYS121 3.3 16.7 1.0
CB A:CYS31 3.5 19.1 1.0
CB A:CYS65 3.5 17.5 1.0
SG A:CYS90 3.5 23.5 1.0
CU A:CU1208 3.7 23.7 0.7
SG A:CYS31 3.7 21.1 1.0
CA A:CYS28 3.8 17.2 1.0
SG A:CYS28 4.0 25.3 1.0
O A:MET27 4.4 18.8 1.0
CA A:CYS65 4.4 15.4 1.0
CB A:CYS28 4.4 19.3 1.0
O A:CYS28 4.4 14.8 1.0
CA A:CYS121 4.5 15.8 1.0
N A:CYS28 4.5 16.8 1.0
C A:CYS28 4.6 15.2 1.0
SG A:CYS125 4.7 27.8 1.0
C A:MET27 4.7 15.7 1.0
C A:CYS121 4.8 16.4 1.0
CB A:CYS94 4.8 15.8 1.0
CA A:CYS31 4.9 16.4 1.0
O A:CYS121 5.0 16.9 1.0

Copper binding site 4 out of 18 in 5nqn

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Copper binding site 4 out of 18 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:21.5
occ:0.15
CU A:CU1205 0.0 21.5 0.1
CU A:CU1205 1.7 23.8 0.5
SG A:CYS94 1.9 21.5 1.0
SG A:CYS121 2.1 20.4 1.0
CU A:CU1206 2.4 24.1 0.7
CU A:CU1207 2.5 25.4 0.5
CB A:CYS121 2.6 16.7 1.0
CU A:CU1204 2.7 22.0 0.6
CU A:CU1203 3.3 29.1 0.6
CU A:CU1207 3.4 18.4 0.1
SG A:CYS65 3.4 21.7 1.0
CB A:CYS94 3.4 15.8 1.0
C A:CYS121 3.5 16.4 1.0
CA A:CYS121 3.6 15.8 1.0
SG A:CYS90 3.7 23.5 1.0
O A:CYS121 3.9 16.9 1.0
N A:GLU122 3.9 17.1 1.0
SG A:CYS31 4.0 21.1 1.0
CU A:CU1208 4.1 23.7 0.7
CB A:CYS31 4.3 19.1 1.0
O A:CYS90 4.3 16.1 1.0
SG A:CYS125 4.4 27.8 1.0
CA A:GLU122 4.6 17.5 1.0
CA A:CYS94 4.7 15.5 1.0
O A:CYS118 4.7 16.6 1.0
N A:CYS121 4.8 15.7 1.0
C A:CYS90 4.9 17.0 1.0
CB A:CYS65 5.0 17.5 1.0

Copper binding site 5 out of 18 in 5nqn

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Copper binding site 5 out of 18 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:24.1
occ:0.70
SG A:CYS90 2.1 23.5 1.0
SG A:CYS94 2.2 21.5 1.0
O A:CYS90 2.4 16.1 1.0
CU A:CU1205 2.4 21.5 0.1
C A:CYS90 2.9 17.0 1.0
CU A:CU1203 2.9 29.1 0.6
CU A:CU1205 3.0 23.8 0.5
CB A:CYS90 3.2 21.9 1.0
CA A:CYS90 3.3 18.3 1.0
SG A:CYS65 3.3 21.7 1.0
CB A:CYS94 3.5 15.8 1.0
CU A:CU1207 3.7 25.4 0.5
CU A:CU1208 3.8 23.7 0.7
N A:ALA91 3.8 18.3 1.0
N A:CYS94 4.0 14.0 1.0
CU A:CU1204 4.0 22.0 0.6
SG A:CYS121 4.2 20.4 1.0
CA A:CYS94 4.2 15.5 1.0
CU A:CU1207 4.3 18.4 0.1
CA A:ALA91 4.4 18.7 1.0
SG A:CYS125 4.5 27.8 1.0
CB A:MET93 4.7 15.5 1.0
N A:CYS90 4.7 16.3 1.0
SG A:CYS61 4.8 18.8 1.0
CB A:CYS65 4.9 17.5 1.0
CG2 A:ILE64 4.9 16.3 1.0
C A:MET93 5.0 14.8 1.0
CB A:CYS121 5.0 16.7 1.0

Copper binding site 6 out of 18 in 5nqn

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Copper binding site 6 out of 18 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:25.4
occ:0.45
CU A:CU1207 0.0 25.4 0.5
CU A:CU1207 1.6 18.4 0.1
SG A:CYS31 2.0 21.1 1.0
SG A:CYS94 2.2 21.5 1.0
CU A:CU1205 2.5 21.5 0.1
CU A:CU1205 2.7 23.8 0.5
CU A:CU1208 2.8 23.7 0.7
CU A:CU1209 3.0 24.9 0.6
SG A:CYS65 3.1 21.7 1.0
CB A:CYS31 3.2 19.1 1.0
CU A:CU1210 3.3 18.4 0.5
SG A:CYS61 3.4 18.8 1.0
CB A:CYS121 3.5 16.7 1.0
CB A:CYS94 3.5 15.8 1.0
SG A:CYS121 3.7 20.4 1.0
CU A:CU1206 3.7 24.1 0.7
CA A:CYS118 4.1 14.5 1.0
SG A:CYS118 4.1 23.5 1.0
CA A:CYS94 4.2 15.5 1.0
CB A:CYS118 4.4 18.2 1.0
CA A:CYS31 4.5 16.4 1.0
O A:CYS118 4.5 16.6 1.0
CB A:CYS65 4.7 17.5 1.0
C A:CYS31 4.8 15.8 1.0
SG A:CYS35 4.8 20.9 1.0
C A:CYS118 4.8 16.0 1.0
CA A:CYS121 4.9 15.8 1.0
N A:CYS118 4.9 13.6 1.0
O A:CYS31 5.0 16.9 1.0
N A:CYS94 5.0 14.0 1.0
O A:VAL117 5.0 17.2 1.0

Copper binding site 7 out of 18 in 5nqn

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Copper binding site 7 out of 18 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:18.4
occ:0.15
CU A:CU1207 0.0 18.4 0.1
CU A:CU1207 1.6 25.4 0.5
SG A:CYS31 2.0 21.1 1.0
CU A:CU1208 2.1 23.7 0.7
SG A:CYS65 2.2 21.7 1.0
CB A:CYS31 2.6 19.1 1.0
CU A:CU1210 2.7 18.4 0.5
CU A:CU1205 2.7 23.8 0.5
CU A:CU1205 3.4 21.5 0.1
CU A:CU1209 3.4 24.9 0.6
CB A:CYS65 3.4 17.5 1.0
SG A:CYS94 3.4 21.5 1.0
C A:CYS31 3.5 15.8 1.0
SG A:CYS61 3.5 18.8 1.0
CA A:CYS31 3.6 16.4 1.0
O A:CYS31 3.8 16.9 1.0
N A:ALA32 3.9 14.7 1.0
SG A:CYS121 4.1 20.4 1.0
O A:CYS61 4.2 15.7 1.0
SG A:CYS35 4.3 20.9 1.0
CU A:CU1206 4.3 24.1 0.7
CB A:CYS121 4.4 16.7 1.0
N A:CYS31 4.7 14.2 1.0
O A:CYS28 4.7 14.8 1.0
CA A:ALA32 4.7 15.8 1.0
C A:CYS61 4.7 14.7 1.0
CA A:CYS65 4.7 15.4 1.0
CB A:CYS61 4.8 16.6 1.0
SG A:CYS118 4.8 23.5 1.0
CB A:CYS94 5.0 15.8 1.0

Copper binding site 8 out of 18 in 5nqn

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Copper binding site 8 out of 18 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:23.7
occ:0.65
SG A:CYS65 2.0 21.7 1.0
CU A:CU1207 2.1 18.4 0.1
SG A:CYS61 2.2 18.8 1.0
O A:CYS61 2.6 15.7 1.0
CU A:CU1207 2.8 25.4 0.5
C A:CYS61 3.1 14.7 1.0
CB A:CYS65 3.2 17.5 1.0
CB A:CYS61 3.2 16.6 1.0
CA A:CYS61 3.4 14.5 1.0
CU A:CU1209 3.4 24.9 0.6
SG A:CYS94 3.5 21.5 1.0
CU A:CU1205 3.7 23.8 0.5
CU A:CU1206 3.8 24.1 0.7
CU A:CU1210 3.9 18.4 0.5
SG A:CYS31 3.9 21.1 1.0
N A:CYS65 4.0 13.4 1.0
CA A:CYS65 4.1 15.4 1.0
CU A:CU1205 4.1 21.5 0.1
N A:ALA62 4.2 14.2 1.0
SG A:CYS35 4.6 20.9 1.0
CB A:CYS31 4.7 19.1 1.0
SG A:CYS90 4.7 23.5 1.0
CG A:MET93 4.7 17.2 1.0
N A:CYS61 4.8 12.4 1.0
CA A:ALA62 4.8 14.9 1.0
CB A:CYS94 4.9 15.8 1.0
CA A:CYS94 4.9 15.5 1.0

Copper binding site 9 out of 18 in 5nqn

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Copper binding site 9 out of 18 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:24.9
occ:0.60
SG A:CYS118 2.2 23.5 1.0
SG A:CYS61 2.2 18.8 1.0
CU A:CU1211 2.5 23.9 0.2
CU A:CU1211 2.6 19.1 0.5
CU A:CU1210 2.8 18.4 0.5
SG A:CYS35 2.9 20.9 1.0
CU A:CU1207 3.0 25.4 0.5
CB A:CYS61 3.3 16.6 1.0
CU A:CU1207 3.4 18.4 0.1
SG A:CYS31 3.4 21.1 1.0
CU A:CU1208 3.4 23.7 0.7
CB A:CYS118 3.5 18.2 1.0
CB A:CYS97 3.6 17.4 1.0
CU A:CU1212 3.7 19.3 0.7
SG A:CYS97 3.7 19.1 1.0
SG A:CYS94 4.1 21.5 1.0
CA A:CYS94 4.2 15.5 1.0
CA A:CYS118 4.2 14.5 1.0
CB A:CYS94 4.5 15.8 1.0
CB A:CYS35 4.5 16.0 1.0
CA A:CYS61 4.6 14.5 1.0
O A:CYS94 4.7 16.6 1.0
CU A:CU1214 4.9 20.6 0.7
CA A:CYS97 5.0 17.2 1.0
C A:CYS94 5.0 16.4 1.0
SG A:CYS65 5.0 21.7 1.0
N A:CYS118 5.0 13.6 1.0

Copper binding site 10 out of 18 in 5nqn

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Copper binding site 10 out of 18 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:Cu210

b:18.4
occ:0.50
SG A:CYS31 2.1 21.1 1.0
SG A:CYS35 2.1 20.9 1.0
O A:CYS31 2.3 16.9 1.0
CU A:CU1207 2.7 18.4 0.1
CU A:CU1209 2.8 24.9 0.6
C A:CYS31 2.9 15.8 1.0
CB A:CYS31 3.1 19.1 1.0
CA A:CYS31 3.2 16.4 1.0
CU A:CU1207 3.3 25.4 0.5
CB A:CYS35 3.3 16.0 1.0
SG A:CYS118 3.5 23.5 1.0
CU A:CU1212 3.8 19.3 0.7
CU A:CU1211 3.8 19.1 0.5
N A:CYS35 3.9 13.7 1.0
CU A:CU1208 3.9 23.7 0.7
N A:ALA32 4.0 14.7 1.0
SG A:CYS61 4.1 18.8 1.0
CA A:CYS35 4.1 14.3 1.0
CU A:CU1211 4.2 23.9 0.2
CA A:ALA32 4.6 15.8 1.0
N A:CYS31 4.6 14.2 1.0
SG A:CYS65 4.7 21.7 1.0
SG A:CYS114 4.7 20.8 1.0
CB A:CYS61 4.7 16.6 1.0
CB A:THR34 4.8 13.7 1.0
C A:THR34 4.8 13.8 1.0
CG1 A:VAL117 4.9 20.1 1.0
CA A:CYS118 4.9 14.5 1.0
CB A:CYS118 4.9 18.2 1.0
N A:CYS118 5.0 13.6 1.0

Reference:

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
Page generated: Wed Jul 31 04:47:37 2024

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