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Copper in PDB 5fje: Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B

Protein crystallography data

The structure of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B, PDB code: 5fje was solved by N.Vita, S.Platsaki, A.Basle, S.J.Allen, N.G.Paterson, A.T.Crombie, J.C.Murrell, K.J.Waldron, C.Dennison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.06 / 1.90
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 44.410, 41.420, 53.130, 90.00, 92.96, 90.00
R / Rfree (%) 19.819 / 23.166

Other elements in 5fje:

The structure of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Copper atom in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B (pdb code 5fje). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 26 binding sites of Copper where determined in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B, PDB code: 5fje:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 26 in 5fje

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Copper binding site 1 out of 26 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1123

b:32.2
occ:1.00
SG A:CYS117 2.1 31.8 1.0
SG A:CYS113 2.3 29.6 1.0
O A:CYS113 2.3 33.6 1.0
CU A:CU11124 2.4 30.1 1.0
CU A:CU11125 2.9 31.3 1.0
C A:CYS113 3.0 30.1 1.0
CB A:CYS113 3.2 32.6 1.0
CB A:CYS117 3.2 38.0 1.0
CD1 A:LEU19 3.3 25.6 1.0
N A:CYS117 3.4 32.9 1.0
CA A:CYS113 3.4 33.7 1.0
CA A:CYS117 3.7 34.2 1.0
N A:ALA114 3.9 30.2 1.0
SG A:CYS87 4.0 31.0 1.0
OG A:SER23 4.2 31.2 1.0
CD2 A:LEU65 4.3 27.9 1.0
C A:GLU116 4.4 32.4 1.0
CA A:ALA114 4.5 30.0 1.0
CB A:GLU116 4.5 42.2 1.0
CU A:CU11126 4.6 31.2 1.0
SG A:CYS62 4.7 30.1 1.0
OG A:SER22 4.7 37.7 1.0
CG A:LEU19 4.8 26.1 1.0
C A:ALA114 4.9 30.6 1.0
CA A:GLU116 4.9 36.6 1.0
N A:CYS113 4.9 32.8 1.0
N A:GLU116 4.9 35.6 1.0
O A:ALA114 4.9 32.5 1.0

Copper binding site 2 out of 26 in 5fje

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Copper binding site 2 out of 26 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1124

b:30.1
occ:1.00
SG A:CYS117 2.1 31.8 1.0
SG A:CYS87 2.2 31.0 1.0
CU A:CU11123 2.4 32.2 1.0
CU A:CU11125 3.3 31.3 1.0
CB A:CYS87 3.4 30.4 1.0
CB A:CYS117 3.4 38.0 1.0
O A:VAL83 3.5 28.0 1.0
O A:CYS113 3.5 33.6 1.0
CG1 A:VAL83 3.6 29.5 1.0
C A:VAL83 3.7 29.1 1.0
C A:CYS113 3.7 30.1 1.0
CA A:ALA84 3.8 32.9 1.0
CU A:CU11126 3.8 31.2 1.0
N A:ALA84 3.8 30.1 1.0
SG A:CYS113 3.9 29.6 1.0
N A:ALA114 3.9 30.2 1.0
SG A:CYS62 3.9 30.1 1.0
CA A:ALA114 4.0 30.0 1.0
CB A:CYS113 4.1 32.6 1.0
CB A:VAL83 4.3 30.1 1.0
C A:ALA84 4.6 33.5 1.0
CA A:CYS87 4.6 30.1 1.0
CA A:CYS113 4.6 33.7 1.0
CA A:VAL83 4.6 29.0 1.0
CA A:CYS117 4.6 34.2 1.0
N A:CYS87 4.6 31.4 1.0
O A:ALA84 4.6 31.1 1.0
CD2 A:LEU65 4.8 27.9 1.0
N A:CYS117 4.9 32.9 1.0
C A:ALA114 4.9 30.6 1.0
CB A:ALA84 4.9 33.3 1.0
O A:ALA114 5.0 32.5 1.0

Copper binding site 3 out of 26 in 5fje

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Copper binding site 3 out of 26 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1125

b:31.3
occ:1.00
SG A:CYS113 2.1 29.6 1.0
SG A:CYS62 2.1 30.1 1.0
CU A:CU11126 2.5 31.2 1.0
CU A:CU11123 2.9 32.2 1.0
CB A:CYS113 3.1 32.6 1.0
OG A:SER23 3.2 31.2 1.0
CU A:CU11124 3.3 30.1 1.0
CB A:CYS62 3.3 30.2 1.0
SG A:CYS87 3.4 31.0 1.0
CA A:SER23 3.6 28.3 1.0
SG A:CYS26 3.7 28.4 1.0
CB A:SER23 3.8 29.5 1.0
SG A:CYS117 4.2 31.8 1.0
CB A:CYS26 4.2 25.5 1.0
N A:SER23 4.2 29.3 1.0
CA A:CYS62 4.3 28.0 1.0
O A:SER22 4.4 31.3 1.0
CA A:CYS113 4.4 33.7 1.0
CG1 A:VAL83 4.4 29.5 1.0
C A:SER22 4.5 29.1 1.0
CD2 A:LEU65 4.6 27.9 1.0
C A:CYS113 4.7 30.1 1.0
C A:SER23 4.7 29.9 1.0
O A:CYS113 4.7 33.6 1.0
O A:SER23 4.7 27.4 1.0
CD1 A:LEU19 4.9 25.6 1.0

Copper binding site 4 out of 26 in 5fje

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Copper binding site 4 out of 26 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1126

b:31.2
occ:1.00
SG A:CYS26 2.2 28.4 1.0
SG A:CYS87 2.3 31.0 1.0
SG A:CYS62 2.4 30.1 1.0
CU A:CU11125 2.5 31.3 1.0
CU A:CU11127 2.8 29.3 1.0
CB A:CYS26 3.1 25.5 1.0
CD2 A:LEU58 3.2 32.1 1.0
CB A:CYS113 3.5 32.6 1.0
CB A:CYS87 3.7 30.4 1.0
CB A:CYS62 3.7 30.2 1.0
SG A:CYS113 3.7 29.6 1.0
CU A:CU11124 3.8 30.1 1.0
CD1 A:LEU58 4.3 32.2 1.0
CG A:LEU58 4.3 30.5 1.0
SG A:CYS110 4.4 26.3 1.0
CA A:CYS87 4.4 30.1 1.0
CA A:CYS26 4.5 28.7 1.0
CU A:CU11123 4.6 32.2 1.0
CA A:CYS110 4.7 30.8 1.0
CA A:CYS113 4.8 33.7 1.0
O A:ALA109 4.9 25.6 1.0
O A:SER22 5.0 31.3 1.0

Copper binding site 5 out of 26 in 5fje

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Copper binding site 5 out of 26 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1127

b:29.3
occ:1.00
SG A:CYS110 2.2 26.3 1.0
SG A:CYS26 2.2 28.4 1.0
CU A:CU11126 2.8 31.2 1.0
CU A:CU11128 2.9 26.4 1.0
CA A:CYS110 3.1 30.8 1.0
CB A:CYS26 3.2 25.5 1.0
CB A:CYS110 3.2 29.8 1.0
N A:CYS110 3.3 25.9 1.0
CD1 A:LEU58 3.4 32.2 1.0
CD2 A:LEU58 3.5 32.1 1.0
CG A:LEU58 3.7 30.5 1.0
C A:ALA109 3.7 25.2 1.0
CA A:CYS26 3.9 28.7 1.0
O A:ALA109 4.0 25.6 1.0
SG A:CYS87 4.2 31.0 1.0
O A:CYS106 4.2 28.1 1.0
CB A:ALA109 4.2 24.9 1.0
C A:CYS110 4.4 31.4 1.0
CB A:CYS87 4.5 30.4 1.0
CA A:ALA109 4.6 25.7 1.0
SG A:CYS106 4.7 27.1 1.0
CA A:CYS87 4.7 30.1 1.0
O A:CYS110 4.8 34.4 1.0
C A:CYS26 4.8 29.7 1.0
CB A:CYS113 4.8 32.6 1.0
SG A:CYS62 4.9 30.1 1.0
O A:CYS26 4.9 25.7 1.0
N A:CYS26 5.0 27.1 1.0
CU A:CU11129 5.0 32.2 1.0

Copper binding site 6 out of 26 in 5fje

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Copper binding site 6 out of 26 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1128

b:26.4
occ:1.00
SG A:CYS110 2.2 26.3 1.0
O A:CYS106 2.2 28.1 1.0
SG A:CYS106 2.2 27.1 1.0
CU A:CU11129 2.6 32.2 1.0
CU A:CU11127 2.9 29.3 1.0
C A:CYS106 3.0 29.2 1.0
CB A:CYS110 3.2 29.8 1.0
CB A:CYS106 3.3 31.9 1.0
CA A:CYS106 3.4 27.9 1.0
N A:CYS110 3.8 25.9 1.0
CA A:CYS110 4.0 30.8 1.0
N A:GLY107 4.0 29.8 1.0
CD1 A:LEU58 4.1 32.2 1.0
SG A:CYS90 4.3 28.8 1.0
CG A:LEU58 4.3 30.5 1.0
CB A:CYS90 4.4 30.6 1.0
CU A:CU11130 4.4 30.7 1.0
CB A:ALA109 4.4 24.9 1.0
CA A:GLY107 4.5 31.4 1.0
C A:ALA109 4.6 25.2 1.0
CG2 A:VAL29 4.7 38.5 1.0
SG A:CYS26 4.8 28.4 1.0
N A:CYS106 4.9 32.8 1.0
CA A:ALA109 5.0 25.7 1.0
CD2 A:LEU58 5.0 32.1 1.0

Copper binding site 7 out of 26 in 5fje

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Copper binding site 7 out of 26 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1129

b:32.2
occ:1.00
SG A:CYS106 2.1 27.1 1.0
SG A:CYS90 2.2 28.8 1.0
CU A:CU11128 2.6 26.4 1.0
CU A:CU11130 2.6 30.7 1.0
CB A:CYS106 3.2 31.9 1.0
CB A:CYS90 3.3 30.6 1.0
OG1 A:THR55 3.5 34.7 1.0
SG A:CYS94 3.8 27.2 1.0
SG A:CYS110 3.9 26.3 1.0
CG2 A:THR55 4.1 30.4 1.0
O A:CYS106 4.1 28.1 1.0
O A:CYS90 4.2 26.2 1.0
CB A:THR55 4.2 31.7 1.0
CG A:LEU58 4.2 30.5 1.0
C A:CYS106 4.3 29.2 1.0
CD1 A:LEU58 4.3 32.2 1.0
CA A:CYS106 4.3 27.9 1.0
C A:CYS90 4.4 27.5 1.0
CA A:CYS90 4.4 28.9 1.0
CA A:THR55 4.5 32.4 1.0
CB A:LEU58 4.7 33.0 1.0
CU A:CU11131 4.8 34.6 1.0
N A:GLY107 4.9 29.8 1.0
CU A:CU11127 5.0 29.3 1.0

Copper binding site 8 out of 26 in 5fje

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Copper binding site 8 out of 26 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1130

b:30.7
occ:1.00
O A:CYS90 2.1 26.2 1.0
SG A:CYS90 2.2 28.8 1.0
SG A:CYS94 2.2 27.2 1.0
CU A:CU11129 2.6 32.2 1.0
CU A:CU11131 2.9 34.6 1.0
C A:CYS90 2.9 27.5 1.0
CB A:CYS90 3.3 30.6 1.0
CB A:CYS94 3.3 31.7 1.0
CA A:CYS90 3.4 28.9 1.0
N A:CYS94 3.7 29.1 1.0
OG1 A:THR55 3.8 34.7 1.0
CA A:CYS94 4.0 30.3 1.0
N A:LYS91 4.0 27.6 1.0
SG A:CYS106 4.3 27.1 1.0
CU A:CU11128 4.4 26.4 1.0
CB A:CYS106 4.4 31.9 1.0
CB A:GLU93 4.5 38.0 1.0
CA A:LYS91 4.5 31.8 1.0
SG A:CYS51 4.6 48.2 1.0
C A:GLU93 4.7 34.3 1.0
N A:CYS90 4.9 30.5 1.0
N A:GLY107 4.9 29.8 1.0
C A:CYS106 4.9 29.2 1.0
C A:LYS91 5.0 35.2 1.0

Copper binding site 9 out of 26 in 5fje

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Copper binding site 9 out of 26 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1131

b:34.6
occ:1.00
SG A:CYS51 2.0 48.2 1.0
SG A:CYS94 2.2 27.2 1.0
CU A:CU11130 2.9 30.7 1.0
CU A:CU11133 3.1 32.3 1.0
CA A:CYS94 3.2 30.3 1.0
CB A:CYS51 3.3 44.6 1.0
CB A:CYS94 3.3 31.7 1.0
CU A:CU11132 3.4 34.8 1.0
N A:CYS94 3.5 29.1 1.0
SG A:CYS33 3.7 30.7 1.0
CA A:CYS51 4.0 42.5 1.0
C A:GLU93 4.0 34.3 1.0
CB A:CYS103 4.1 32.8 1.0
SG A:CYS103 4.1 33.0 1.0
OG1 A:THR55 4.2 34.7 1.0
O A:GLU93 4.3 36.0 1.0
O A:CYS90 4.3 26.2 1.0
CB A:GLU93 4.4 38.0 1.0
CA A:CYS103 4.5 31.5 1.0
SG A:CYS90 4.6 28.8 1.0
C A:CYS94 4.7 33.2 1.0
O A:CYS51 4.7 39.8 1.0
CU A:CU11134 4.8 29.8 1.0
CU A:CU11129 4.8 32.2 1.0
C A:CYS51 4.8 41.1 1.0
CA A:GLU93 4.9 34.8 1.0

Copper binding site 10 out of 26 in 5fje

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Copper binding site 10 out of 26 in the Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Cu(I)-CSP1 (Copper Storage Protein 1) From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1132

b:34.8
occ:1.00
SG A:CYS33 2.1 30.7 1.0
SG A:CYS103 2.3 33.0 1.0
CU A:CU11134 2.6 29.8 1.0
CU A:CU11133 2.7 32.3 1.0
CB A:CYS103 3.2 32.8 1.0
CB A:CYS33 3.2 27.3 1.0
CA A:CYS103 3.3 31.5 1.0
CU A:CU11131 3.4 34.6 1.0
N A:CYS103 3.5 31.9 1.0
CU A:CU11135 3.8 33.2 1.0
CA A:CYS33 3.9 29.3 1.0
C A:GLU102 3.9 29.4 1.0
SG A:CYS51 3.9 48.2 1.0
SD A:MET48 4.1 36.1 1.0
O A:CYS33 4.2 28.1 1.0
O A:GLU102 4.2 30.7 1.0
SG A:CYS94 4.3 27.2 1.0
SG A:CYS37 4.3 30.9 1.0
C A:CYS33 4.4 28.8 1.0
CB A:GLU102 4.5 27.6 1.0
ND1 A:HIS36 4.6 36.2 1.0
CB A:CYS51 4.6 44.6 1.0
C A:CYS103 4.7 33.8 1.0
CA A:GLU102 4.8 27.9 1.0
CB A:HIS36 4.9 33.0 1.0
CG A:HIS36 5.0 32.8 1.0

Reference:

N.Vita, S.Platsaki, A.Basle, S.J.Allen, N.G.Paterson, A.T.Crombie, J.C.Murrell, K.J.Waldron, C.Dennison. A Four-Helix Bundle Stores Copper For Methane Oxidation. Nature V. 525 140 2015.
ISSN: ISSN 0028-0836
PubMed: 26308900
DOI: 10.1038/NATURE14854
Page generated: Sun Dec 13 11:17:34 2020

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