Atomistry » Copper » PDB 5luf-5nln » 5n0k
Atomistry »
  Copper »
    PDB 5luf-5nln »
      5n0k »

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

Go back to Copper Binding Sites List in 5n0k
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

Go back to Copper Binding Sites List in 5n0k
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

Go back to Copper Binding Sites List in 5n0k
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

Go back to Copper Binding Sites List in 5n0k
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

Go back to Copper Binding Sites List in 5n0k
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

Go back to Copper Binding Sites List in 5n0k
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

Go back to Copper Binding Sites List in 5n0k
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

Go back to Copper Binding Sites List in 5n0k
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

Go back to Copper Binding Sites List in 5n0k
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: Sun Dec 13 11:18:51 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy