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Copper in PDB 5fej: Copm in the Cu(I)-Bound Form

Protein crystallography data

The structure of Copm in the Cu(I)-Bound Form, PDB code: 5fej 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) 36.94 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.824, 86.082, 74.971, 90.00, 106.26, 90.00
R / Rfree (%) 21.1 / 25.9

Copper Binding Sites:

The binding sites of Copper atom in the Copm in the Cu(I)-Bound Form (pdb code 5fej). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Copm in the Cu(I)-Bound Form, PDB code: 5fej:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 5fej

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Copper binding site 1 out of 8 in the Copm in the Cu(I)-Bound Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:11.8
occ:1.00
ND1 A:HIS56 1.8 8.0 1.0
ND1 A:HIS57 1.8 10.0 1.0
CE1 A:HIS57 2.5 10.5 1.0
CE1 A:HIS56 2.7 8.1 1.0
CG A:HIS56 2.9 8.1 1.0
N A:HIS57 3.0 9.2 1.0
CG A:HIS57 3.0 10.7 1.0
SD A:MET53 3.1 9.2 1.0
C A:HIS56 3.2 8.7 1.0
CA A:HIS57 3.3 9.4 1.0
CB A:HIS56 3.4 9.0 1.0
O A:HOH311 3.5 12.2 1.0
O A:HIS56 3.6 11.7 1.0
CB A:HIS57 3.6 8.8 1.0
O A:MET53 3.7 9.9 1.0
NE2 A:HIS57 3.8 10.0 1.0
NE2 A:HIS56 3.8 8.2 1.0
OE1 A:GLN87 3.9 13.1 1.0
CA A:HIS56 3.9 8.4 1.0
CD2 A:HIS56 4.0 6.4 1.0
CD2 A:HIS57 4.0 9.9 1.0
CG A:MET53 4.0 10.0 1.0
CE1 A:HIS148 4.4 9.7 1.0
NE2 A:HIS148 4.6 10.1 1.0
CB A:ALA152 4.6 9.2 1.0
C A:MET53 4.6 9.6 1.0
NE2 A:GLN179 4.7 12.7 1.0
CE A:MET53 4.7 11.1 1.0
C A:HIS57 4.8 10.2 1.0
CA A:MET53 4.8 7.6 1.0
N A:HIS56 4.9 9.9 1.0

Copper binding site 2 out of 8 in 5fej

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Copper binding site 2 out of 8 in the Copm in the Cu(I)-Bound Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:10.3
occ:1.00
ND1 A:HIS148 1.8 10.1 1.0
ND1 A:HIS149 1.8 11.6 1.0
CE1 A:HIS149 2.5 9.9 1.0
CE1 A:HIS148 2.7 9.7 1.0
CG A:HIS148 2.9 9.4 1.0
N A:HIS149 2.9 10.2 1.0
CG A:HIS149 3.0 11.2 1.0
C A:HIS148 3.2 9.4 1.0
CA A:HIS149 3.2 9.3 1.0
O A:HOH311 3.3 12.2 1.0
SD A:MET145 3.4 10.1 1.0
CB A:HIS148 3.4 9.3 1.0
O A:MET145 3.6 9.5 1.0
CB A:HIS149 3.6 9.7 1.0
O A:HIS148 3.6 9.9 1.0
NE2 A:HIS149 3.7 7.6 1.0
NE2 A:HIS148 3.8 10.1 1.0
OE1 A:GLN179 3.8 10.8 1.0
CD2 A:HIS148 3.9 9.6 1.0
CA A:HIS148 3.9 9.8 1.0
CD2 A:HIS149 4.0 9.5 1.0
CG A:MET145 4.2 8.4 1.0
CE1 A:HIS56 4.3 8.1 1.0
CB A:ALA60 4.5 10.6 1.0
C A:MET145 4.5 8.6 1.0
C A:HIS149 4.7 10.9 1.0
NE2 A:HIS56 4.7 8.2 1.0
CA A:MET145 4.8 8.7 1.0
N A:HIS148 4.8 10.0 1.0
CD A:GLN179 4.9 12.1 1.0
NE2 A:GLN87 5.0 12.8 1.0

Copper binding site 3 out of 8 in 5fej

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Copper binding site 3 out of 8 in the Copm in the Cu(I)-Bound Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:15.8
occ:1.00
ND1 B:HIS57 1.8 13.7 1.0
ND1 B:HIS56 1.8 12.4 1.0
CE1 B:HIS57 2.6 13.3 1.0
CE1 B:HIS56 2.6 11.7 1.0
SD B:MET53 2.9 13.6 1.0
CG B:HIS56 3.0 11.7 1.0
CG B:HIS57 3.0 14.3 1.0
N B:HIS57 3.0 12.3 1.0
CA B:HIS57 3.2 12.0 1.0
C B:HIS56 3.2 12.5 1.0
O B:MET53 3.5 12.4 1.0
CB B:HIS56 3.5 11.9 1.0
O B:HIS56 3.5 13.6 1.0
O B:HOH302 3.5 15.1 1.0
CB B:HIS57 3.6 12.7 1.0
NE2 B:HIS57 3.7 13.6 1.0
NE2 B:HIS56 3.8 13.0 1.0
CD2 B:HIS57 4.0 12.6 1.0
OE1 B:GLN87 4.0 14.5 1.0
CG B:MET53 4.0 14.0 1.0
CD2 B:HIS56 4.0 11.2 1.0
CA B:HIS56 4.0 11.4 1.0
CE1 B:HIS148 4.4 12.7 1.0
CB B:ALA152 4.5 12.9 1.0
C B:MET53 4.5 12.5 1.0
CE B:MET53 4.5 16.5 1.0
NE2 B:HIS148 4.6 13.1 1.0
C B:HIS57 4.7 13.0 1.0
NE2 B:GLN179 4.7 13.3 1.0
CA B:MET53 4.8 10.8 1.0
N B:HIS56 4.8 11.9 1.0
CB B:MET53 5.0 11.9 1.0

Copper binding site 4 out of 8 in 5fej

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Copper binding site 4 out of 8 in the Copm in the Cu(I)-Bound Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu202

b:12.9
occ:1.00
ND1 B:HIS148 1.8 13.5 1.0
ND1 B:HIS149 1.8 13.4 1.0
CE1 B:HIS149 2.5 13.1 1.0
CE1 B:HIS148 2.7 12.7 1.0
CG B:HIS148 2.9 12.4 1.0
N B:HIS149 2.9 12.4 1.0
CG B:HIS149 3.0 12.1 1.0
O B:HOH302 3.1 15.1 1.0
CA B:HIS149 3.2 12.9 1.0
C B:HIS148 3.2 12.7 1.0
SD B:MET145 3.4 13.4 1.0
CB B:HIS148 3.4 11.5 1.0
O B:MET145 3.6 10.5 1.0
CB B:HIS149 3.6 11.5 1.0
O B:HIS148 3.7 12.9 1.0
NE2 B:HIS149 3.7 11.6 1.0
NE2 B:HIS148 3.8 13.1 1.0
CA B:HIS148 3.9 13.0 1.0
CD2 B:HIS148 4.0 13.2 1.0
CD2 B:HIS149 4.0 10.9 1.0
CG B:MET145 4.3 12.0 1.0
NE2 B:GLN179 4.3 13.3 1.0
CE1 B:HIS56 4.4 11.7 1.0
CB B:ALA60 4.5 13.6 1.0
C B:MET145 4.6 11.0 1.0
OE1 B:GLN179 4.6 15.6 1.0
NE2 B:HIS56 4.6 13.0 1.0
C B:HIS149 4.7 14.1 1.0
CD B:GLN179 4.8 13.2 1.0
CA B:MET145 4.8 10.1 1.0
N B:HIS148 4.9 12.2 1.0
CE B:MET145 4.9 12.6 1.0

Copper binding site 5 out of 8 in 5fej

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Copper binding site 5 out of 8 in the Copm in the Cu(I)-Bound Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:9.4
occ:1.00
ND1 C:HIS57 1.8 10.4 1.0
ND1 C:HIS56 1.8 12.2 1.0
CE1 C:HIS57 2.6 11.5 1.0
CE1 C:HIS56 2.6 11.6 1.0
CG C:HIS57 2.9 12.4 1.0
N C:HIS57 2.9 10.2 1.0
CG C:HIS56 3.0 11.2 1.0
SD C:MET53 3.1 12.6 1.0
CA C:HIS57 3.1 10.0 1.0
C C:HIS56 3.4 10.9 1.0
CB C:HIS57 3.4 11.2 1.0
CB C:HIS56 3.5 9.3 1.0
O C:MET53 3.6 10.3 1.0
NE2 C:HIS57 3.7 11.8 1.0
NE2 C:HIS56 3.8 11.6 1.0
O C:HIS56 3.8 12.2 1.0
NE2 C:GLN87 3.9 15.4 1.0
CD2 C:HIS57 3.9 12.0 1.0
CD2 C:HIS56 4.0 10.0 1.0
CG C:MET53 4.0 11.4 1.0
CA C:HIS56 4.1 9.6 1.0
CE1 C:HIS148 4.5 11.6 1.0
C C:HIS57 4.6 11.2 1.0
C C:MET53 4.6 10.8 1.0
CB C:ALA152 4.7 11.4 1.0
NE2 C:HIS148 4.7 12.0 1.0
CE C:MET53 4.7 15.3 1.0
CD C:GLN87 4.8 13.7 1.0
CA C:MET53 4.8 11.2 1.0
OE1 C:GLN87 5.0 15.2 1.0
N C:HIS56 5.0 9.4 1.0

Copper binding site 6 out of 8 in 5fej

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Copper binding site 6 out of 8 in the Copm in the Cu(I)-Bound Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu202

b:14.9
occ:1.00
ND1 C:HIS148 1.8 11.2 1.0
ND1 C:HIS149 1.8 11.3 1.0
CE1 C:HIS149 2.5 11.5 1.0
CE1 C:HIS148 2.6 11.6 1.0
CG C:HIS148 2.9 11.9 1.0
CG C:HIS149 3.0 11.4 1.0
N C:HIS149 3.0 11.8 1.0
SD C:MET145 3.2 12.3 1.0
CA C:HIS149 3.3 11.9 1.0
C C:HIS148 3.3 11.9 1.0
CB C:HIS148 3.4 11.6 1.0
O C:MET145 3.5 10.8 1.0
CB C:HIS149 3.7 12.1 1.0
O C:HIS148 3.7 11.6 1.0
NE2 C:HIS149 3.7 10.8 1.0
OE1 C:GLN179 3.8 16.2 1.0
NE2 C:HIS148 3.8 12.0 1.0
CD2 C:HIS148 3.9 12.1 1.0
CD2 C:HIS149 4.0 10.9 1.0
CA C:HIS148 4.0 12.4 1.0
CG C:MET145 4.0 10.3 1.0
CE1 C:HIS56 4.4 11.6 1.0
C C:MET145 4.5 10.5 1.0
CB C:ALA60 4.5 11.7 1.0
NE2 C:HIS56 4.6 11.6 1.0
CA C:MET145 4.7 9.5 1.0
C C:HIS149 4.7 12.7 1.0
CE C:MET145 4.9 10.7 1.0
N C:HIS148 4.9 11.6 1.0
OE1 C:GLN87 4.9 15.2 1.0
CD C:GLN179 5.0 17.1 1.0
CB C:MET145 5.0 10.4 1.0

Copper binding site 7 out of 8 in 5fej

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Copper binding site 7 out of 8 in the Copm in the Cu(I)-Bound Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu201

b:13.2
occ:1.00
ND1 D:HIS57 1.8 11.5 1.0
ND1 D:HIS56 1.8 12.6 1.0
CE1 D:HIS57 2.4 11.4 1.0
CE1 D:HIS56 2.7 12.2 1.0
CG D:HIS56 2.9 11.8 1.0
SD D:MET53 3.0 12.3 1.0
CG D:HIS57 3.0 12.5 1.0
N D:HIS57 3.0 10.8 1.0
C D:HIS56 3.3 12.0 1.0
CA D:HIS57 3.3 10.5 1.0
CB D:HIS56 3.4 11.4 1.0
NE2 D:HIS57 3.7 13.3 1.0
CB D:HIS57 3.7 11.2 1.0
O D:MET53 3.7 12.5 1.0
O D:HIS56 3.7 13.8 1.0
NE2 D:HIS56 3.8 12.8 1.0
CD2 D:HIS57 3.9 12.6 1.0
CD2 D:HIS56 4.0 11.8 1.0
CA D:HIS56 4.0 10.5 1.0
CG D:MET53 4.0 10.2 1.0
NE2 D:GLN87 4.1 12.2 1.0
CE1 D:HIS148 4.4 12.1 1.0
NE2 D:HIS148 4.5 12.5 1.0
CE D:MET53 4.6 13.9 1.0
CB D:ALA152 4.6 12.1 1.0
C D:MET53 4.7 12.2 1.0
C D:HIS57 4.8 11.3 1.0
N D:HIS56 4.9 12.3 1.0
CD D:GLN87 4.9 11.4 1.0
CA D:MET53 4.9 10.8 1.0
OE1 D:GLN87 4.9 13.7 1.0

Copper binding site 8 out of 8 in 5fej

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Copper binding site 8 out of 8 in the Copm in the Cu(I)-Bound Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Copm in the Cu(I)-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu202

b:10.7
occ:1.00
ND1 D:HIS149 1.8 11.8 1.0
ND1 D:HIS148 1.8 11.7 1.0
CE1 D:HIS149 2.5 12.2 1.0
CE1 D:HIS148 2.6 12.1 1.0
CG D:HIS148 3.0 12.0 1.0
CG D:HIS149 3.0 9.7 1.0
N D:HIS149 3.1 9.5 1.0
SD D:MET145 3.2 12.3 1.0
CA D:HIS149 3.3 10.4 1.0
C D:HIS148 3.4 10.5 1.0
O D:MET145 3.5 11.1 1.0
CB D:HIS148 3.5 11.4 1.0
CB D:HIS149 3.7 11.2 1.0
NE2 D:HIS149 3.7 11.9 1.0
O D:HIS148 3.7 11.5 1.0
NE2 D:HIS148 3.8 12.5 1.0
NE2 D:GLN179 3.9 17.4 1.0
CD2 D:HIS148 4.0 12.3 1.0
CD2 D:HIS149 4.0 9.6 1.0
CA D:HIS148 4.1 11.2 1.0
CG D:MET145 4.1 11.2 1.0
CE1 D:HIS56 4.5 12.2 1.0
C D:MET145 4.5 10.4 1.0
CB D:ALA60 4.6 10.5 1.0
NE2 D:HIS56 4.7 12.8 1.0
CA D:MET145 4.8 10.0 1.0
C D:HIS149 4.8 11.6 1.0
CE D:MET145 4.9 10.5 1.0
N D:HIS148 4.9 11.4 1.0
CD D:GLN179 4.9 16.2 1.0

Reference:

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
Page generated: Wed Jul 31 04:05:09 2024

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