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Copper in PDB 5n0k: Rat Ceruloplasmin Orthorhombic Form

Protein crystallography data

The structure of Rat Ceruloplasmin Orthorhombic Form, PDB code: 5n0k was solved by V.R.Samygina, A.V.Sokolov, G.Bourenkov, V.B.Vasilyev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.98 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.360, 103.810, 172.811, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.6

Other elements in 5n0k:

The structure of Rat Ceruloplasmin Orthorhombic Form also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Rat Ceruloplasmin Orthorhombic Form (pdb code 5n0k). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Rat Ceruloplasmin Orthorhombic Form, PDB code: 5n0k:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 5n0k

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Copper binding site 1 out of 9 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1102

b:40.8
occ:1.00
 NE2 A:HIS974 2.1 36.4 1.0
NE2 A:HIS1014 2.3 36.9 1.0
NE2 A:HIS162 2.3 44.3 1.0
O A:HOH1371 2.7 36.3 1.0
O A:HOH1377 2.9 52.0 1.0
CE1 A:HIS974 2.9 37.7 1.0
CD2 A:HIS162 3.0 42.3 1.0
CD2 A:HIS1014 3.2 37.3 1.0
CE1 A:HIS1014 3.2 36.1 1.0
CD2 A:HIS974 3.3 37.0 1.0
CE1 A:HIS162 3.5 44.3 1.0
CD2 A:LEU1012 3.9 35.1 1.0
CD2 A:HIS972 4.0 33.2 1.0
ND1 A:HIS974 4.1 38.2 1.0
CU A:CU1104 4.2 41.9 1.0
CG A:HIS162 4.2 42.6 1.0
ND1 A:HIS1014 4.3 37.2 1.0
CG A:HIS974 4.3 36.5 1.0
CG A:HIS1014 4.3 36.2 1.0
ND1 A:HIS162 4.4 44.5 1.0
NE2 A:HIS972 4.5 34.2 1.0
NE2 A:HIS101 4.8 37.6 1.0
CU A:CU1106 4.8 37.4 1.0
CG A:LEU1012 4.9 35.2 1.0
CD2 A:HIS101 5.0 37.4 1.0

Copper binding site 2 out of 9 in 5n0k

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Copper binding site 2 out of 9 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1103

b:30.2
occ:1.00
 SG A:CYS318 2.1 28.5 1.0
ND1 A:HIS275 2.1 30.1 1.0
ND1 A:HIS323 2.2 29.0 1.0
CG A:HIS275 3.1 29.6 1.0
CE1 A:HIS275 3.1 31.3 1.0
CB A:CYS318 3.1 30.3 1.0
CG A:HIS323 3.1 28.6 1.0
CE1 A:HIS323 3.1 28.8 1.0
CD1 A:LEU328 3.3 36.1 1.0
CB A:HIS275 3.4 29.0 1.0
CA A:HIS275 3.4 29.0 1.0
CB A:HIS323 3.4 28.8 1.0
O A:VAL274 3.7 29.0 1.0
CB A:ASN320 4.1 29.3 1.0
NE2 A:HIS275 4.2 30.6 1.0
CD2 A:HIS275 4.2 30.1 1.0
N A:HIS275 4.2 28.1 1.0
NE2 A:HIS323 4.2 29.8 1.0
CD2 A:HIS323 4.2 29.2 1.0
C A:VAL274 4.3 28.4 1.0
N A:SER276 4.3 28.1 1.0
C A:HIS275 4.4 28.4 1.0
CA A:CYS318 4.5 31.5 1.0
CG A:LEU328 4.6 35.5 1.0
CD2 A:PHE201 4.8 31.9 1.0
CG A:ASN320 4.8 29.4 1.0
ND2 A:ASN320 4.9 29.2 1.0
CA A:HIS323 4.9 29.6 1.0
CB A:LEU328 5.0 35.8 1.0

Copper binding site 3 out of 9 in 5n0k

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Copper binding site 3 out of 9 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1104

b:41.9
occ:1.00
 NE2 A:HIS972 2.0 34.2 1.0
NE2 A:HIS101 2.3 37.6 1.0
O A:HOH1219 2.6 40.5 1.0
CE1 A:HIS972 3.0 32.7 1.0
O A:HOH1371 3.1 36.3 1.0
CD2 A:HIS972 3.1 33.2 1.0
CD2 A:HIS101 3.1 37.4 1.0
CE1 A:HIS101 3.3 37.3 1.0
NE2 A:HIS974 3.4 36.4 1.0
CD2 A:HIS974 3.4 37.0 1.0
NE2 A:HIS103 3.4 37.5 1.0
CD2 A:HIS103 3.7 36.2 1.0
CE1 A:HIS974 3.7 37.7 1.0
CG A:HIS974 3.8 36.5 1.0
CE1 A:HIS103 3.9 36.9 1.0
ND1 A:HIS974 4.0 38.2 1.0
ND1 A:HIS972 4.1 33.2 1.0
CU A:CU1106 4.1 37.4 1.0
CG A:HIS972 4.2 32.8 1.0
CU A:CU1102 4.2 40.8 1.0
CG A:HIS103 4.2 36.5 1.0
OH A:TYR107 4.3 43.5 1.0
CG A:HIS101 4.3 38.4 1.0
ND1 A:HIS101 4.4 39.6 1.0
ND1 A:HIS103 4.4 36.9 1.0
CA A:HIS974 4.5 35.3 1.0
O A:ALA102 4.7 39.7 1.0
CB A:HIS974 4.7 36.5 1.0
CA A:HIS103 4.9 38.6 1.0
NE2 A:HIS160 4.9 38.8 1.0
N A:HIS974 5.0 34.7 1.0

Copper binding site 4 out of 9 in 5n0k

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Copper binding site 4 out of 9 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1105

b:29.7
occ:1.00
 ND1 A:HIS1020 2.1 27.8 1.0
ND1 A:HIS969 2.1 26.8 1.0
SG A:CYS1015 2.2 32.0 1.0
CE1 A:HIS1020 3.0 27.8 1.0
CG A:HIS1020 3.1 29.2 1.0
CG A:HIS969 3.1 27.5 1.0
CE1 A:HIS969 3.1 28.0 1.0
CB A:CYS1015 3.1 32.0 1.0
O A:LEU968 3.2 33.0 1.0
SD A:MET1025 3.3 32.1 1.0
CA A:HIS969 3.3 27.2 1.0
CB A:HIS969 3.4 27.0 1.0
CB A:HIS1020 3.4 30.6 1.0
C A:LEU968 3.9 30.2 1.0
CG1 A:VAL1017 4.0 30.8 1.0
N A:HIS969 4.0 27.4 1.0
NE2 A:HIS1020 4.2 28.7 1.0
CE A:MET1025 4.2 32.3 1.0
CD2 A:HIS1020 4.2 29.1 1.0
NE2 A:HIS969 4.2 28.8 1.0
CG2 A:VAL1017 4.2 31.1 1.0
CD2 A:HIS969 4.2 27.9 1.0
C A:HIS969 4.5 28.3 1.0
CA A:CYS1015 4.5 31.9 1.0
N A:THR970 4.6 29.1 1.0
CB A:VAL1017 4.6 30.5 1.0
CG A:MET1025 4.8 32.5 1.0
N A:VAL1017 4.9 29.8 1.0
CA A:HIS1020 4.9 31.9 1.0

Copper binding site 5 out of 9 in 5n0k

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Copper binding site 5 out of 9 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1106

b:37.4
occ:1.00
 NE2 A:HIS103 2.0 37.5 1.0
O A:HOH1371 2.1 36.3 1.0
NE2 A:HIS1016 2.1 33.2 1.0
NE2 A:HIS160 2.2 38.8 1.0
CE1 A:HIS103 2.8 36.9 1.0
CE1 A:HIS1016 3.1 33.2 1.0
CD2 A:HIS1016 3.1 31.8 1.0
CD2 A:HIS160 3.1 37.8 1.0
CE1 A:HIS160 3.2 36.8 1.0
CD2 A:HIS103 3.2 36.2 1.0
O A:HOH1377 3.5 52.0 1.0
ND1 A:HIS103 4.0 36.9 1.0
CU A:CU1104 4.1 41.9 1.0
CD1 A:ILE158 4.2 31.5 1.0
CG A:HIS103 4.2 36.5 1.0
ND1 A:HIS1016 4.2 33.2 1.0
ND1 A:HIS160 4.3 37.9 1.0
CG A:HIS160 4.3 37.4 1.0
CG A:HIS1016 4.3 32.0 1.0
CD2 A:HIS972 4.3 33.2 1.0
NE2 A:HIS972 4.3 34.2 1.0
CD2 A:HIS101 4.8 37.4 1.0
CU A:CU1102 4.8 40.8 1.0
CG1 A:ILE158 4.8 32.2 1.0
CG A:HIS972 4.9 32.8 1.0
CE1 A:HIS972 4.9 32.7 1.0

Copper binding site 6 out of 9 in 5n0k

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Copper binding site 6 out of 9 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1107

b:30.1
occ:1.00
 CD2 A:HIS679 2.1 26.7 1.0
SG A:CYS674 2.2 26.3 1.0
ND1 A:HIS631 2.2 25.4 1.0
SD A:MET684 2.9 36.3 1.0
CG A:HIS679 2.9 27.9 1.0
CB A:CYS674 3.1 27.2 1.0
CE1 A:HIS631 3.1 26.2 1.0
CG A:HIS631 3.2 25.1 1.0
CB A:HIS679 3.2 28.7 1.0
NE2 A:HIS679 3.3 27.4 1.0
CB A:HIS631 3.5 25.2 1.0
CA A:HIS631 3.5 25.2 1.0
CE A:MET684 3.8 36.6 1.0
CG2 A:THR676 3.8 27.9 1.0
O A:VAL630 4.1 29.2 1.0
ND1 A:HIS679 4.1 28.8 1.0
NE2 A:HIS631 4.3 26.2 1.0
CE1 A:HIS679 4.3 27.7 1.0
CD2 A:HIS631 4.3 26.4 1.0
N A:HIS631 4.4 26.0 1.0
OG1 A:THR676 4.4 31.1 1.0
CG A:MET684 4.4 34.3 1.0
C A:VAL630 4.5 27.2 1.0
CA A:CYS674 4.5 28.2 1.0
N A:GLY632 4.5 25.7 1.0
CB A:THR676 4.6 28.9 1.0
C A:HIS631 4.6 24.3 1.0
CA A:HIS679 4.8 29.2 1.0
CD1 A:ILE633 4.8 25.2 1.0
CB A:MET684 4.9 32.9 1.0

Copper binding site 7 out of 9 in 5n0k

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Copper binding site 7 out of 9 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1108

b:38.2
occ:1.00
 O A:HOH1226 2.0 35.1 1.0
OD2 A:ASP678 2.2 40.7 1.0
NE2 A:HIS596 2.2 33.3 1.0
O A:HOH1212 2.4 36.5 1.0
O A:HOH1343 2.5 28.8 1.0
CG A:ASP678 2.8 38.8 1.0
OD1 A:ASP678 2.8 42.9 1.0
CE1 A:HIS596 2.9 34.5 1.0
O A:HOH1388 3.0 38.3 1.0
CD2 A:HIS596 3.3 32.9 1.0
OE2 A:GLU965 3.9 36.6 1.0
ND1 A:HIS596 4.1 34.0 1.0
OE1 A:GLU591 4.2 40.2 1.0
CB A:ASP678 4.3 34.5 1.0
CG A:HIS596 4.4 32.9 1.0
OE2 A:GLU591 4.5 40.3 1.0
ND1 A:HIS679 4.7 28.8 1.0
CD A:GLU965 4.7 35.3 1.0
O A:ASP678 4.7 31.4 1.0
CD A:GLU591 4.8 40.9 1.0
C A:ASP678 4.9 31.3 1.0
CE1 A:HIS679 4.9 27.7 1.0

Copper binding site 8 out of 9 in 5n0k

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Copper binding site 8 out of 9 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1109

b:34.2
occ:1.00
 OD2 A:ASP1019 2.0 36.7 1.0
O A:HOH1218 2.1 35.0 1.0
NE2 A:HIS934 2.1 29.0 1.0
O A:HOH1252 2.1 35.2 1.0
O A:HOH1327 2.4 24.0 1.0
O A:HOH1372 2.6 35.4 1.0
CG A:ASP1019 2.9 36.5 1.0
CE1 A:HIS934 3.0 29.7 1.0
OD1 A:ASP1019 3.1 38.2 1.0
CD2 A:HIS934 3.1 28.7 1.0
OE1 A:GLU271 3.9 33.4 1.0
OE1 A:GLU929 3.9 46.1 1.0
ND1 A:HIS934 4.1 28.8 1.0
CG A:HIS934 4.2 28.5 1.0
CB A:ASP1019 4.3 33.7 1.0
CD A:GLU271 4.5 34.1 1.0
OE2 A:GLU271 4.6 38.5 1.0
OE2 A:GLU929 4.6 40.9 1.0
CD2 A:HIS1020 4.6 29.1 1.0
CD A:GLU929 4.7 43.7 1.0
O A:ASP1019 4.8 33.0 1.0
NE2 A:HIS1020 5.0 28.7 1.0

Copper binding site 9 out of 9 in 5n0k

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Copper binding site 9 out of 9 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1110

b:40.6
occ:1.00
 OD2 A:ASP292 1.9 31.7 1.0
NE2 A:HIS290 2.2 28.4 1.0
NZ A:LYS512 2.2 28.1 1.0
O A:HOH1386 2.3 26.0 1.0
CG A:ASP292 2.7 31.8 1.0
OD1 A:ASP292 2.9 31.9 1.0
CE1 A:HIS290 3.0 29.1 1.0
CD2 A:HIS290 3.2 27.8 1.0
CE A:LYS512 3.3 28.4 1.0
CA A:GLY459 3.3 34.2 1.0
O A:GLY459 3.7 36.8 1.0
O A:HOH1256 3.7 37.5 1.0
CD A:LYS512 3.7 28.6 1.0
O A:MET500 3.9 33.2 1.0
C A:GLY459 3.9 35.9 1.0
CB A:ASP292 4.1 32.4 1.0
ND1 A:HIS290 4.2 29.1 1.0
CG A:HIS290 4.3 28.2 1.0
CG A:MET500 4.4 48.1 1.0
CA A:ASP292 4.5 31.8 1.0
N A:GLY459 4.5 34.2 1.0
O A:THR291 4.6 29.6 1.0
CA A:MET500 4.7 39.1 1.0
C A:MET500 4.7 35.9 1.0
CB A:MET500 4.9 42.7 1.0
N A:ASP292 4.9 30.4 1.0
C A:THR291 4.9 30.4 1.0

Reference:

V.R.Samygina, A.V.Sokolov, G.Bourenkov, T.R.Schneider, V.A.Anashkin, S.O.Kozlov, N.N.Kolmakov, V.B.Vasilyev. Rat Ceruloplasmin: A New Labile Copper Binding Site and Zinc/Copper Mosaic. Metallomics V. 9 1828 2017.
ISSN: ESSN 1756-591X
PubMed: 29177316
DOI: 10.1039/C7MT00157F
Page generated: Wed Jul 31 04:42:48 2024

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