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Copper in PDB 2j5w: Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites

Enzymatic activity of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites

All present enzymatic activity of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites:
1.16.3.1;

Protein crystallography data

The structure of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites, PDB code: 2j5w was solved by I.Bento, C.Peixoto, V.N.Zaitsev, P.F.Lindley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.52 / 2.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.140, 209.139, 82.752, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 22.6

Other elements in 2j5w:

The structure of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Sodium (Na) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites (pdb code 2j5w). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 7 binding sites of Copper where determined in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites, PDB code: 2j5w:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7;

Copper binding site 1 out of 7 in 2j5w

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Copper binding site 1 out of 7 in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu3046

b:44.0
occ:1.00
 ND1 A:HIS324 1.9 41.0 1.0
SG A:CYS319 1.9 46.3 1.0
ND1 A:HIS276 2.0 41.3 1.0
CE1 A:HIS324 2.9 41.6 1.0
CG A:HIS324 2.9 41.9 1.0
CE1 A:HIS276 2.9 42.3 1.0
CG A:HIS276 3.0 42.0 1.0
CB A:CYS319 3.1 46.4 1.0
CB A:HIS324 3.3 42.4 1.0
CA A:HIS276 3.4 40.9 1.0
CB A:HIS276 3.4 41.2 1.0
CD1 A:LEU329 3.5 47.0 1.0
O A:VAL275 3.9 40.5 1.0
NE2 A:HIS324 4.0 41.4 1.0
CD2 A:HIS324 4.0 43.0 1.0
NE2 A:HIS276 4.0 41.8 1.0
CB A:ASN321 4.0 41.2 1.0
CD2 A:HIS276 4.1 42.5 1.0
N A:HIS276 4.2 40.3 1.0
N A:ALA277 4.3 41.0 1.0
C A:VAL275 4.4 40.1 1.0
C A:HIS276 4.4 41.1 1.0
CA A:CYS319 4.5 46.3 1.0
CD2 A:PHE202 4.6 41.5 1.0
ND2 A:ASN321 4.6 38.0 1.0
CG A:ASN321 4.7 40.3 1.0
CG A:LEU329 4.7 46.2 1.0
CA A:HIS324 4.8 42.5 1.0

Copper binding site 2 out of 7 in 2j5w

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Copper binding site 2 out of 7 in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu3047

b:37.2
occ:1.00
 NE2 A:HIS980 2.0 29.3 1.0
NE2 A:HIS1020 2.0 29.0 1.0
NE2 A:HIS163 2.1 43.2 1.0
O A:HOH2338 2.6 17.6 0.5
O1 A:OXY3054 2.6 35.6 1.0
O2 A:OXY3054 2.8 34.9 1.0
CE1 A:HIS980 2.8 29.8 1.0
CE1 A:HIS1020 2.9 28.9 1.0
CD2 A:HIS163 3.0 43.0 1.0
CD2 A:HIS1020 3.0 29.8 1.0
CD2 A:HIS980 3.1 31.1 1.0
CE1 A:HIS163 3.2 43.1 1.0
CD2 A:LEU1018 3.9 33.2 1.0
O A:HOH2090 3.9 48.4 1.0
ND1 A:HIS980 4.0 30.8 1.0
CU A:CU3049 4.0 43.0 1.0
ND1 A:HIS1020 4.0 28.0 1.0
CD2 A:HIS978 4.1 37.4 1.0
CG A:HIS1020 4.1 31.1 1.0
CG A:HIS980 4.2 32.5 1.0
CG A:HIS163 4.2 42.2 1.0
ND1 A:HIS163 4.3 42.5 1.0
NE2 A:HIS101 4.4 41.6 1.0
NE2 A:HIS978 4.6 36.9 1.0
CD2 A:HIS101 4.7 42.0 1.0
O A:HOH2325 4.8 38.6 1.0
CG A:LEU1018 4.9 33.3 1.0
CU A:CU3048 5.0 40.1 1.0

Copper binding site 3 out of 7 in 2j5w

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Copper binding site 3 out of 7 in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu3048

b:40.1
occ:1.00
 NE2 A:HIS103 1.9 42.1 1.0
NE2 A:HIS161 2.1 39.0 1.0
NE2 A:HIS1022 2.2 31.8 1.0
O1 A:OXY3054 2.4 35.6 1.0
O2 A:OXY3054 2.6 34.9 1.0
CE1 A:HIS103 2.7 43.1 1.0
CD2 A:HIS103 3.0 44.0 1.0
CD2 A:HIS161 3.0 38.3 1.0
CE1 A:HIS161 3.1 38.0 1.0
CD2 A:HIS1022 3.2 32.8 1.0
CE1 A:HIS1022 3.2 33.0 1.0
ND1 A:HIS103 3.9 43.5 1.0
CG A:HIS103 4.1 44.1 1.0
CU A:CU3049 4.1 43.0 1.0
ND1 A:HIS161 4.2 36.7 1.0
CG A:HIS161 4.2 39.1 1.0
O A:HOH2338 4.2 17.6 0.5
CD1 A:ILE159 4.3 37.2 1.0
ND1 A:HIS1022 4.3 32.6 1.0
CG A:HIS1022 4.3 33.4 1.0
CD2 A:HIS978 4.3 37.4 1.0
NE2 A:HIS978 4.4 36.9 1.0
CD2 A:HIS101 4.4 42.0 1.0
CG1 A:ILE159 4.7 39.4 1.0
NE2 A:HIS101 4.7 41.6 1.0
O A:HOH2325 4.8 38.6 1.0
CU A:CU3047 5.0 37.2 1.0

Copper binding site 4 out of 7 in 2j5w

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Copper binding site 4 out of 7 in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu3049

b:43.0
occ:1.00
 NE2 A:HIS101 1.9 41.6 1.0
NE2 A:HIS978 2.0 36.9 1.0
O A:O3050 2.1 51.8 0.5
O2 A:OXY3054 2.3 34.9 1.0
CE1 A:HIS101 2.8 41.2 1.0
CD2 A:HIS101 2.9 42.0 1.0
CD2 A:HIS978 2.9 37.4 1.0
O A:HOH2337 3.0 31.2 0.5
CE1 A:HIS978 3.0 36.7 1.0
NE2 A:HIS980 3.3 29.3 1.0
NE2 A:HIS103 3.3 42.1 1.0
O1 A:OXY3054 3.3 35.6 1.0
CD2 A:HIS980 3.4 31.1 1.0
CD2 A:HIS103 3.6 44.0 1.0
CE1 A:HIS980 3.6 29.8 1.0
CG A:HIS980 3.8 32.5 1.0
CE1 A:HIS103 3.8 43.1 1.0
ND1 A:HIS980 3.9 30.8 1.0
ND1 A:HIS101 3.9 41.3 1.0
CG A:HIS101 4.0 41.5 1.0
CU A:CU3047 4.0 37.2 1.0
CU A:CU3048 4.1 40.1 1.0
CG A:HIS978 4.1 36.9 1.0
ND1 A:HIS978 4.1 36.0 1.0
CG A:HIS103 4.2 44.1 1.0
ND1 A:HIS103 4.3 43.5 1.0
CA A:HIS980 4.5 36.1 1.0
O A:SER102 4.6 42.8 1.0
OH A:TYR107 4.6 47.6 1.0
CB A:HIS980 4.7 35.3 1.0
CD2 A:HIS163 4.9 43.0 1.0
N A:HIS980 5.0 36.6 1.0

Copper binding site 5 out of 7 in 2j5w

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Copper binding site 5 out of 7 in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu3051

b:44.0
occ:1.00
 ND1 A:HIS685 2.0 37.3 1.0
SG A:CYS680 2.1 39.9 1.0
ND1 A:HIS637 2.1 39.2 1.0
SD A:MET690 2.9 42.1 1.0
CE1 A:HIS685 3.0 37.8 1.0
CE1 A:HIS637 3.0 38.8 1.0
CG A:HIS685 3.0 36.6 1.0
CG A:HIS637 3.1 38.7 1.0
CB A:CYS680 3.2 38.3 1.0
CB A:HIS685 3.4 37.3 1.0
CB A:HIS637 3.5 38.8 1.0
CA A:HIS637 3.5 38.7 1.0
CE A:MET690 3.8 39.6 1.0
O A:VAL636 3.8 40.5 1.0
NE2 A:HIS685 4.1 35.9 1.0
CB A:THR682 4.1 37.4 1.0
OG1 A:THR682 4.1 36.5 1.0
NE2 A:HIS637 4.1 38.7 1.0
CD2 A:HIS685 4.1 36.4 1.0
CD2 A:HIS637 4.2 38.5 1.0
N A:HIS637 4.4 39.3 1.0
C A:VAL636 4.4 40.0 1.0
CG A:MET690 4.4 38.6 1.0
CA A:CYS680 4.6 38.4 1.0
N A:GLY638 4.6 37.5 1.0
C A:HIS637 4.6 38.2 1.0
CA A:HIS685 4.9 37.5 1.0
CB A:MET690 4.9 37.3 1.0
CG2 A:THR682 4.9 36.2 1.0

Copper binding site 6 out of 7 in 2j5w

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Copper binding site 6 out of 7 in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu3052

b:41.3
occ:1.00
 ND1 A:HIS975 2.0 36.0 1.0
ND1 A:HIS1026 2.0 37.4 1.0
SG A:CYS1021 2.1 30.9 1.0
CE1 A:HIS1026 2.9 37.5 1.0
CE1 A:HIS975 2.9 36.7 1.0
CG A:HIS975 3.0 36.7 1.0
CG A:HIS1026 3.1 37.3 1.0
CB A:CYS1021 3.2 32.4 1.0
SD A:MET1031 3.3 40.5 1.0
CA A:HIS975 3.3 37.2 1.0
CB A:HIS975 3.4 37.2 1.0
O A:LEU974 3.5 39.0 1.0
CB A:HIS1026 3.5 37.1 1.0
CG2 A:VAL1023 3.9 36.1 1.0
NE2 A:HIS975 4.1 37.0 1.0
NE2 A:HIS1026 4.1 36.6 1.0
C A:LEU974 4.1 38.2 1.0
CD2 A:HIS975 4.1 37.4 1.0
N A:HIS975 4.1 37.8 1.0
CD2 A:HIS1026 4.2 36.5 1.0
CB A:VAL1023 4.3 35.9 1.0
CE A:MET1031 4.4 40.4 1.0
C A:HIS975 4.5 37.1 1.0
N A:THR976 4.5 36.8 1.0
CA A:CYS1021 4.6 32.7 1.0
CG A:MET1031 4.8 38.6 1.0

Copper binding site 7 out of 7 in 2j5w

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Copper binding site 7 out of 7 in the Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu3053

b:53.4
occ:0.50
 O A:HOH2327 2.2 45.6 1.0
NE2 A:HIS940 2.3 33.5 1.0
OD1 A:ASP1025 2.3 38.0 0.5
O A:HOH2295 2.4 40.8 1.0
O A:HOH2296 2.4 22.8 0.5
CE1 A:HIS940 3.1 33.2 1.0
CG A:ASP1025 3.3 37.7 0.5
CD2 A:HIS940 3.3 34.0 1.0
OE2 A:GLU272 3.4 45.1 1.0
OD2 A:ASP1025 3.6 39.2 0.5
OE2 A:GLU935 4.1 49.3 1.0
CD2 A:HIS1026 4.2 36.5 1.0
CD A:GLU272 4.2 44.8 1.0
ND1 A:HIS940 4.3 33.2 1.0
OE1 A:GLU272 4.4 45.0 1.0
CG A:HIS940 4.4 33.3 1.0
CB A:ASP1025 4.5 37.2 0.5
O A:HOH2326 4.5 45.5 1.0
NE2 A:HIS1026 4.6 36.6 1.0
O A:ASP1025 4.7 38.1 1.0
OE1 A:GLU935 4.8 50.7 1.0
CD A:GLU935 4.9 49.2 1.0
C A:ASP1025 4.9 37.4 1.0
CB A:ALA1029 5.0 36.9 1.0

Reference:

I.Bento, C.Peixoto, V.N.Zaitsev, P.F.Lindley. Ceruloplasmin Revisited: Structural and Functional Roles of Various Metal Cation-Binding Sites. Acta Crystallogr.,Sect.D V. 63 240 2007.
ISSN: ISSN 0907-4449
PubMed: 17242517
DOI: 10.1107/S090744490604947X
Page generated: Tue Jul 30 23:44:46 2024

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