Atomistry » Copper » PDB 4e9v-4hd7 » 4enz
Atomistry »
  Copper »
    PDB 4e9v-4hd7 »
      4enz »

Copper in PDB 4enz: Structure of Human Ceruloplasmin at 2.6 A Resolution

Enzymatic activity of Structure of Human Ceruloplasmin at 2.6 A Resolution

All present enzymatic activity of Structure of Human Ceruloplasmin at 2.6 A Resolution:
1.16.3.1;

Protein crystallography data

The structure of Structure of Human Ceruloplasmin at 2.6 A Resolution, PDB code: 4enz was solved by V.R.Samygina, A.V.Sokolov, G.Bourenkov, V.B.Vasilyev, H.Bartunik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.90 / 2.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 210.775, 210.775, 84.502, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 23.4

Other elements in 4enz:

The structure of Structure of Human Ceruloplasmin at 2.6 A Resolution also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Human Ceruloplasmin at 2.6 A Resolution (pdb code 4enz). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Structure of Human Ceruloplasmin at 2.6 A Resolution, PDB code: 4enz:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 4enz

Go back to Copper Binding Sites List in 4enz
Copper binding site 1 out of 6 in the Structure of Human Ceruloplasmin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Human Ceruloplasmin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1102

b:66.4
occ:1.00
 ND1 A:HIS324 1.9 62.1 1.0
ND1 A:HIS276 1.9 66.1 1.0
SG A:CYS319 2.1 67.6 1.0
CE1 A:HIS324 2.9 62.8 1.0
CE1 A:HIS276 2.9 65.5 1.0
CG A:HIS276 3.0 65.0 1.0
CG A:HIS324 3.0 66.0 1.0
CB A:CYS319 3.2 67.9 1.0
CD1 A:LEU329 3.2 66.1 1.0
CB A:HIS276 3.3 64.4 1.0
CA A:HIS276 3.4 63.5 1.0
CB A:HIS324 3.4 67.3 1.0
O A:VAL275 3.9 64.0 1.0
NE2 A:HIS324 4.0 62.6 1.0
NE2 A:HIS276 4.0 64.2 1.0
CD2 A:HIS276 4.1 64.2 1.0
CD2 A:HIS324 4.1 65.9 1.0
CB A:ASN321 4.1 65.6 1.0
N A:HIS276 4.2 62.0 1.0
N A:ALA277 4.3 63.0 1.0
C A:VAL275 4.4 62.7 1.0
C A:HIS276 4.4 62.5 1.0
CG A:LEU329 4.5 66.9 1.0
CA A:CYS319 4.5 68.5 1.0
ND2 A:ASN321 4.8 64.3 1.0
CD2 A:PHE202 4.8 62.9 1.0
CB A:LEU329 4.8 69.0 1.0
CG A:ASN321 4.8 65.3 1.0
CA A:HIS324 4.9 68.3 1.0

Copper binding site 2 out of 6 in 4enz

Go back to Copper Binding Sites List in 4enz
Copper binding site 2 out of 6 in the Structure of Human Ceruloplasmin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Human Ceruloplasmin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1103

b:59.3
occ:1.00
 NE2 A:HIS1020 2.0 47.7 1.0
NE2 A:HIS980 2.1 47.8 1.0
NE2 A:HIS163 2.1 58.1 1.0
O2 A:OXY1109 2.6 66.1 1.0
O1 A:OXY1109 2.7 66.2 1.0
CD2 A:HIS1020 2.9 49.4 1.0
CE1 A:HIS980 2.9 47.7 1.0
CD2 A:HIS163 2.9 59.6 1.0
CE1 A:HIS1020 3.0 49.1 1.0
CD2 A:HIS980 3.1 47.8 1.0
CE1 A:HIS163 3.2 58.9 1.0
CD2 A:LEU1018 4.0 52.5 1.0
CG A:HIS1020 4.1 52.2 1.0
ND1 A:HIS1020 4.1 47.9 1.0
ND1 A:HIS980 4.1 45.8 1.0
CG A:HIS163 4.2 58.9 1.0
CG A:HIS980 4.2 48.9 1.0
ND1 A:HIS163 4.2 56.9 1.0
CD2 A:HIS978 4.3 53.7 1.0
CU A:CU1104 4.5 60.7 1.0
NE2 A:HIS101 4.7 55.0 1.0
NE2 A:HIS978 4.9 55.8 1.0
CG A:LEU1018 4.9 53.7 1.0

Copper binding site 3 out of 6 in 4enz

Go back to Copper Binding Sites List in 4enz
Copper binding site 3 out of 6 in the Structure of Human Ceruloplasmin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Human Ceruloplasmin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1104

b:60.7
occ:1.00
 NE2 A:HIS101 2.1 55.0 1.0
NE2 A:HIS978 2.2 55.8 1.0
O2 A:OXY1109 2.3 66.1 1.0
CE1 A:HIS101 3.0 55.2 1.0
CD2 A:HIS978 3.1 53.7 1.0
CD2 A:HIS101 3.1 55.8 1.0
CE1 A:HIS978 3.1 56.1 1.0
O A:O1108 3.2 22.1 0.5
O1 A:OXY1109 3.3 66.2 1.0
NE2 A:HIS103 3.4 57.1 1.0
CD2 A:HIS103 3.5 60.9 1.0
NE2 A:HIS980 3.5 47.8 1.0
CD2 A:HIS980 3.6 47.8 1.0
CE1 A:HIS980 3.7 47.7 1.0
CE1 A:HIS103 3.8 56.7 1.0
CG A:HIS980 3.8 48.9 1.0
CG A:HIS103 3.9 60.0 1.0
ND1 A:HIS980 3.9 45.8 1.0
ND1 A:HIS103 4.0 55.5 1.0
ND1 A:HIS101 4.1 56.7 1.0
CG A:HIS101 4.2 57.9 1.0
ND1 A:HIS978 4.2 53.9 1.0
CG A:HIS978 4.3 53.0 1.0
CA A:HIS980 4.4 50.9 1.0
CU A:CU1105 4.4 62.6 1.0
CU A:CU1103 4.5 59.3 1.0
OH A:TYR107 4.5 62.3 1.0
CA A:HIS103 4.5 63.4 1.0
CB A:HIS980 4.6 51.0 1.0
O A:SER102 4.7 64.6 1.0
CB A:HIS103 4.8 62.6 1.0
O A:PHE979 4.9 53.3 1.0
N A:HIS980 5.0 50.9 1.0

Copper binding site 4 out of 6 in 4enz

Go back to Copper Binding Sites List in 4enz
Copper binding site 4 out of 6 in the Structure of Human Ceruloplasmin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Human Ceruloplasmin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1105

b:62.6
occ:1.00
 NE2 A:HIS103 1.7 57.1 1.0
NE2 A:HIS1022 1.8 53.2 1.0
NE2 A:HIS161 1.9 54.5 1.0
O1 A:OXY1109 2.4 66.2 1.0
CE1 A:HIS103 2.4 56.7 1.0
CE1 A:HIS1022 2.7 57.4 1.0
CE1 A:HIS161 2.8 55.8 1.0
CD2 A:HIS1022 2.8 53.9 1.0
CD2 A:HIS103 3.0 60.9 1.0
CD2 A:HIS161 3.0 57.5 1.0
O2 A:OXY1109 3.2 66.1 1.0
ND1 A:HIS103 3.6 55.5 1.0
ND1 A:HIS1022 3.9 55.0 1.0
CG A:HIS103 3.9 60.0 1.0
ND1 A:HIS161 3.9 55.9 1.0
CG A:HIS1022 3.9 53.6 1.0
CG A:HIS161 4.1 57.2 1.0
CD1 A:ILE159 4.1 49.4 1.0
CD2 A:HIS978 4.4 53.7 1.0
CU A:CU1104 4.4 60.7 1.0
NE2 A:HIS978 4.5 55.8 1.0
CD2 A:HIS101 4.7 55.8 1.0
CG1 A:ILE159 4.7 55.9 1.0

Copper binding site 5 out of 6 in 4enz

Go back to Copper Binding Sites List in 4enz
Copper binding site 5 out of 6 in the Structure of Human Ceruloplasmin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Human Ceruloplasmin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1106

b:61.5
occ:1.00
 ND1 A:HIS685 1.9 52.5 1.0
ND1 A:HIS637 2.0 59.6 1.0
SG A:CYS680 2.2 52.8 1.0
SD A:MET690 2.8 58.9 1.0
CE1 A:HIS685 2.8 55.3 1.0
CE1 A:HIS637 2.9 61.0 1.0
CG A:HIS685 2.9 54.0 1.0
CG A:HIS637 3.0 56.5 1.0
CB A:CYS680 3.2 53.5 1.0
OG1 A:THR682 3.3 61.4 1.0
CB A:HIS685 3.4 55.2 1.0
CB A:HIS637 3.4 56.7 1.0
CA A:HIS637 3.5 55.9 1.0
CE A:MET690 3.7 58.3 1.0
NE2 A:HIS685 4.0 54.8 1.0
CD2 A:HIS685 4.0 53.7 1.0
O A:VAL636 4.0 55.9 1.0
NE2 A:HIS637 4.0 58.9 1.0
CD2 A:HIS637 4.1 57.2 1.0
CG A:MET690 4.4 55.7 1.0
CG2 A:THR682 4.4 51.4 1.0
N A:HIS637 4.4 56.5 1.0
CB A:THR682 4.5 54.3 1.0
N A:GLY638 4.5 53.4 1.0
C A:HIS637 4.5 54.9 1.0
C A:VAL636 4.5 57.0 1.0
CA A:CYS680 4.5 52.6 1.0
CD1 A:ILE639 4.7 51.1 1.0
CA A:HIS685 4.9 55.5 1.0

Copper binding site 6 out of 6 in 4enz

Go back to Copper Binding Sites List in 4enz
Copper binding site 6 out of 6 in the Structure of Human Ceruloplasmin at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Human Ceruloplasmin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1107

b:62.7
occ:1.00
 ND1 A:HIS1026 2.0 53.9 1.0
ND1 A:HIS975 2.1 50.9 1.0
SG A:CYS1021 2.3 56.1 1.0
CE1 A:HIS1026 2.9 54.8 1.0
CG A:HIS1026 3.0 54.5 1.0
CE1 A:HIS975 3.0 50.4 1.0
O A:LEU974 3.1 54.7 1.0
CG A:HIS975 3.1 50.2 1.0
CB A:CYS1021 3.2 54.3 1.0
CB A:HIS1026 3.3 55.1 1.0
SD A:MET1031 3.3 62.0 1.0
CA A:HIS975 3.4 51.1 1.0
CB A:HIS975 3.5 50.5 1.0
CG1 A:VAL1023 3.7 53.6 1.0
C A:LEU974 3.9 53.5 1.0
NE2 A:HIS1026 4.1 53.6 1.0
CD2 A:HIS1026 4.1 53.1 1.0
N A:HIS975 4.1 51.6 1.0
NE2 A:HIS975 4.2 50.4 1.0
CD2 A:HIS975 4.2 48.4 1.0
CG2 A:VAL1023 4.4 52.8 1.0
C A:HIS975 4.5 51.2 1.0
CB A:VAL1023 4.6 54.4 1.0
CE A:MET1031 4.6 57.1 1.0
N A:THR976 4.6 50.5 1.0
CA A:CYS1021 4.6 54.2 1.0
CG A:MET1031 4.7 56.8 1.0
CA A:HIS1026 4.9 56.5 1.0

Reference:

V.R.Samygina, A.V.Sokolov, G.Bourenkov, M.V.Petoukhov, M.O.Pulina, E.T.Zakharova, V.B.Vasilyev, H.Bartunik, D.I.Svergun. Ceruloplasmin: Macromolecular Assemblies with Iron-Containing Acute Phase Proteins. Plos One V. 8 67145 2013.
ISSN: ESSN 1932-6203
PubMed: 23843990
DOI: 10.1371/JOURNAL.PONE.0067145
Page generated: Sun Dec 13 11:14:14 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