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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: Wed Jul 31 02:50:13 2024

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