Atomistry » Copper » PDB 5lww-5nlo » 5n0k
Atomistry »
  Copper »
    PDB 5lww-5nlo »
      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: Wed Jul 31 04:42:48 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy