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Copper in PDB 4ejx: Structure of Ceruloplasmin-Myeloperoxidase Complex

Enzymatic activity of Structure of Ceruloplasmin-Myeloperoxidase Complex

All present enzymatic activity of Structure of Ceruloplasmin-Myeloperoxidase Complex:
1.11.2.2; 1.16.3.1;

Protein crystallography data

The structure of Structure of Ceruloplasmin-Myeloperoxidase Complex, PDB code: 4ejx 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) 15.00 / 4.69
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 106.249, 106.249, 834.619, 90.00, 90.00, 120.00
R / Rfree (%) 36.6 / 40.1

Other elements in 4ejx:

The structure of Structure of Ceruloplasmin-Myeloperoxidase Complex also contains other interesting chemical elements:

Iron (Fe) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Ceruloplasmin-Myeloperoxidase Complex (pdb code 4ejx). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 7 binding sites of Copper where determined in the Structure of Ceruloplasmin-Myeloperoxidase Complex, PDB code: 4ejx:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7;

Copper binding site 1 out of 7 in 4ejx

Go back to Copper Binding Sites List in 4ejx
Copper binding site 1 out of 7 in the Structure of Ceruloplasmin-Myeloperoxidase Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Ceruloplasmin-Myeloperoxidase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1101

b:20.0
occ:1.00
 SG A:CYS319 1.6 20.0 1.0
ND1 A:HIS324 2.6 20.0 1.0
ND1 A:HIS276 2.7 20.0 1.0
CG A:HIS324 3.1 20.0 1.0
CB A:HIS324 3.2 20.0 1.0
CB A:CYS319 3.2 20.0 1.0
CD1 A:LEU329 3.3 20.0 1.0
CE1 A:HIS276 3.5 20.0 1.0
CB A:ASN321 3.5 20.0 1.0
CE1 A:HIS324 3.5 20.0 1.0
CG A:HIS276 3.6 20.0 1.0
CA A:HIS276 3.6 20.0 1.0
O A:VAL275 3.7 20.0 1.0
CB A:HIS276 3.9 20.0 1.0
CD2 A:HIS324 4.1 20.0 1.0
N A:ALA277 4.3 20.0 1.0
NE2 A:HIS324 4.3 20.0 1.0
CA A:CYS319 4.3 20.0 1.0
C A:VAL275 4.4 20.0 1.0
CG A:ASN321 4.4 20.0 1.0
N A:HIS276 4.4 20.0 1.0
CG A:LEU329 4.5 20.0 1.0
NE2 A:HIS276 4.5 20.0 1.0
N A:ASN321 4.5 20.0 1.0
C A:HIS276 4.6 20.0 1.0
CD2 A:HIS276 4.6 20.0 1.0
CA A:ASN321 4.6 20.0 1.0
ND2 A:ASN321 4.6 20.0 1.0
CA A:HIS324 4.7 20.0 1.0
C A:CYS319 4.8 20.0 1.0
CD2 A:LEU329 4.8 20.0 1.0
CB A:LEU329 4.9 20.0 1.0

Copper binding site 2 out of 7 in 4ejx

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Copper binding site 2 out of 7 in the Structure of Ceruloplasmin-Myeloperoxidase Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Ceruloplasmin-Myeloperoxidase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1102

b:20.0
occ:1.00
 NE2 A:HIS980 2.0 20.0 1.0
NE2 A:HIS1020 2.2 20.0 1.0
NE2 A:HIS163 2.4 20.0 1.0
CE1 A:HIS980 2.8 20.0 1.0
CD2 A:HIS1020 3.0 20.0 1.0
CD2 A:HIS980 3.1 20.0 1.0
CE1 A:HIS1020 3.2 20.0 1.0
CD2 A:HIS163 3.2 20.0 1.0
CD2 A:LEU1018 3.4 20.0 1.0
CE1 A:HIS163 3.4 20.0 1.0
ND1 A:HIS980 4.0 20.0 1.0
CU A:CU1104 4.1 20.0 1.0
CG A:HIS1020 4.1 20.0 1.0
CD2 A:HIS978 4.1 20.0 1.0
ND1 A:HIS1020 4.2 20.0 1.0
CG A:HIS980 4.2 20.0 1.0
CG A:HIS163 4.4 20.0 1.0
CG A:LEU1018 4.4 20.0 1.0
NE2 A:HIS101 4.4 20.0 1.0
ND1 A:HIS163 4.4 20.0 1.0
NE2 A:HIS978 4.6 20.0 1.0
CD2 A:HIS101 4.6 20.0 1.0
CU A:CU1103 4.8 20.0 1.0
CB A:LEU1018 4.9 20.0 1.0
NE2 A:HIS1022 5.0 20.0 1.0

Copper binding site 3 out of 7 in 4ejx

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Copper binding site 3 out of 7 in the Structure of Ceruloplasmin-Myeloperoxidase Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Ceruloplasmin-Myeloperoxidase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1103

b:20.0
occ:1.00
 NE2 A:HIS161 2.1 20.0 1.0
NE2 A:HIS103 2.1 20.0 1.0
NE2 A:HIS1022 2.3 20.0 1.0
CE1 A:HIS161 2.9 20.0 1.0
CE1 A:HIS103 3.0 20.0 1.0
CD2 A:HIS103 3.2 20.0 1.0
CD2 A:HIS1022 3.2 20.0 1.0
CD2 A:HIS161 3.3 20.0 1.0
CE1 A:HIS1022 3.3 20.0 1.0
CD1 A:ILE159 4.1 20.0 1.0
ND1 A:HIS161 4.1 20.0 1.0
CU A:CU1104 4.1 20.0 1.0
ND1 A:HIS103 4.2 20.0 1.0
CG A:HIS103 4.3 20.0 1.0
CG A:HIS161 4.3 20.0 1.0
NE2 A:HIS978 4.3 20.0 1.0
ND1 A:HIS1022 4.4 20.0 1.0
CG A:HIS1022 4.4 20.0 1.0
CD2 A:HIS101 4.4 20.0 1.0
CD2 A:HIS978 4.4 20.0 1.0
CU A:CU1102 4.8 20.0 1.0
NE2 A:HIS101 4.9 20.0 1.0
CE1 A:HIS978 5.0 20.0 1.0

Copper binding site 4 out of 7 in 4ejx

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Copper binding site 4 out of 7 in the Structure of Ceruloplasmin-Myeloperoxidase Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Ceruloplasmin-Myeloperoxidase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1104

b:20.0
occ:1.00
 NE2 A:HIS101 2.0 20.0 1.0
NE2 A:HIS978 2.3 20.0 1.0
CD2 A:HIS101 2.9 20.0 1.0
CE1 A:HIS101 3.0 20.0 1.0
NE2 A:HIS980 3.2 20.0 1.0
CE1 A:HIS978 3.2 20.0 1.0
CD2 A:HIS978 3.3 20.0 1.0
CD2 A:HIS980 3.3 20.0 1.0
CE1 A:HIS980 3.5 20.0 1.0
NE2 A:HIS103 3.6 20.0 1.0
CD2 A:HIS103 3.7 20.0 1.0
CG A:HIS980 3.7 20.0 1.0
ND1 A:HIS980 3.8 20.0 1.0
CG A:HIS101 4.0 20.0 1.0
ND1 A:HIS101 4.0 20.0 1.0
CU A:CU1102 4.1 20.0 1.0
CU A:CU1103 4.1 20.0 1.0
OH A:TYR107 4.3 20.0 1.0
CE1 A:HIS103 4.3 20.0 1.0
ND1 A:HIS978 4.3 20.0 1.0
CG A:HIS978 4.4 20.0 1.0
CG A:HIS103 4.4 20.0 1.0
O A:SER102 4.4 20.0 1.0
CA A:HIS980 4.5 20.0 1.0
CB A:HIS980 4.7 20.0 1.0
ND1 A:HIS103 4.8 20.0 1.0
O A:PHE979 4.8 20.0 1.0
C A:SER102 5.0 20.0 1.0

Copper binding site 5 out of 7 in 4ejx

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Copper binding site 5 out of 7 in the Structure of Ceruloplasmin-Myeloperoxidase Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Ceruloplasmin-Myeloperoxidase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1105

b:20.0
occ:1.00
 SG A:CYS680 1.9 20.0 1.0
ND1 A:HIS685 2.3 20.0 1.0
ND1 A:HIS637 2.8 20.0 1.0
SD A:MET690 2.9 20.0 1.0
CG A:HIS685 2.9 20.0 1.0
CB A:HIS685 3.1 20.0 1.0
CE1 A:HIS685 3.3 20.0 1.0
CB A:CYS680 3.3 20.0 1.0
CE1 A:HIS637 3.5 20.0 1.0
OG1 A:THR682 3.7 20.0 1.0
CG A:HIS637 3.7 20.0 1.0
CE A:MET690 3.8 20.0 1.0
CB A:THR682 3.8 20.0 1.0
CA A:HIS637 4.0 20.0 1.0
CD2 A:HIS685 4.0 20.0 1.0
CB A:HIS637 4.1 20.0 1.0
NE2 A:HIS685 4.2 20.0 1.0
CG A:MET690 4.2 20.0 1.0
CB A:MET690 4.5 20.0 1.0
NE2 A:HIS637 4.6 20.0 1.0
O A:VAL636 4.6 20.0 1.0
CA A:CYS680 4.6 20.0 1.0
CG2 A:THR682 4.6 20.0 1.0
CD1 A:ILE639 4.6 20.0 1.0
CA A:HIS685 4.6 20.0 1.0
N A:GLY638 4.7 20.0 1.0
CD2 A:HIS637 4.7 20.0 1.0
N A:HIS637 4.9 20.0 1.0
C A:CYS680 4.9 20.0 1.0
CA A:THR682 4.9 20.0 1.0
C A:HIS637 5.0 20.0 1.0
N A:THR682 5.0 20.0 1.0
C A:VAL636 5.0 20.0 1.0

Copper binding site 6 out of 7 in 4ejx

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Copper binding site 6 out of 7 in the Structure of Ceruloplasmin-Myeloperoxidase Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Ceruloplasmin-Myeloperoxidase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1106

b:20.0
occ:1.00
 SD A:MET1031 2.3 20.0 1.0
SG A:CYS1021 2.4 20.0 1.0
ND1 A:HIS975 2.5 20.0 1.0
CB A:CYS1021 2.6 20.0 1.0
CG A:HIS975 3.3 20.0 1.0
CE1 A:HIS975 3.3 20.0 1.0
ND1 A:HIS1026 3.3 20.0 1.0
CB A:HIS1026 3.5 20.0 1.0
CG A:MET1031 3.6 20.0 1.0
CB A:HIS975 3.6 20.0 1.0
CG A:HIS1026 3.7 20.0 1.0
CE A:MET1031 3.8 20.0 1.0
CA A:HIS975 4.0 20.0 1.0
CA A:CYS1021 4.1 20.0 1.0
NE2 A:HIS975 4.3 20.0 1.0
CD2 A:HIS975 4.3 20.0 1.0
CB A:MET1031 4.3 20.0 1.0
CE1 A:HIS1026 4.3 20.0 1.0
CD2 A:PHE901 4.7 20.0 1.0
O A:LEU974 4.7 20.0 1.0
CD2 A:HIS1026 4.8 20.0 1.0
N A:THR976 4.8 20.0 1.0
C A:CYS1021 4.8 20.0 1.0
N A:CYS1021 4.9 20.0 1.0
C A:HIS975 4.9 20.0 1.0
CA A:HIS1026 4.9 20.0 1.0

Copper binding site 7 out of 7 in 4ejx

Go back to Copper Binding Sites List in 4ejx
Copper binding site 7 out of 7 in the Structure of Ceruloplasmin-Myeloperoxidase Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Structure of Ceruloplasmin-Myeloperoxidase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1107

b:20.0
occ:0.50
 NE2 A:HIS940 2.4 20.0 1.0
CE1 A:HIS940 3.0 20.0 1.0
OD1 A:ASP1025 3.1 20.0 0.5
OE2 A:GLU935 3.5 20.0 1.0
OE2 A:GLU272 3.5 20.0 1.0
CD2 A:HIS940 3.5 20.0 1.0
CG A:ASP1025 3.7 20.0 0.5
ND1 A:HIS940 4.2 20.0 1.0
OD2 A:ASP1025 4.2 20.0 0.5
CD A:GLU935 4.4 20.0 1.0
OE1 A:GLU935 4.4 20.0 1.0
CD2 A:HIS1026 4.5 20.0 1.0
CG A:HIS940 4.5 20.0 1.0
CZ A:PHE748 4.5 20.0 1.0
CD A:GLU272 4.5 20.0 1.0
CB A:ASP1025 4.5 20.0 0.5
OE1 A:GLU272 4.7 20.0 1.0
CE1 A:PHE748 4.7 20.0 1.0
NE2 A:HIS1026 4.8 20.0 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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