Atomistry » Copper » PDB 2idq-2pp7 » 2j5w
Atomistry »
  Copper »
    PDB 2idq-2pp7 »
      2j5w »

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

Go back to Copper Binding Sites List in 2j5w
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

Go back to Copper Binding Sites List in 2j5w
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

Go back to Copper Binding Sites List in 2j5w
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

Go back to Copper Binding Sites List in 2j5w
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

Go back to Copper Binding Sites List in 2j5w
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

Go back to Copper Binding Sites List in 2j5w
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

Go back to Copper Binding Sites List in 2j5w
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

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