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Copper in PDB 1kcw: X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms

Enzymatic activity of X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms

All present enzymatic activity of X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms:
1.16.3.1;

Protein crystallography data

The structure of X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms, PDB code: 1kcw was solved by G.L.Card, 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) 12.00 / 3.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 213.920, 213.920, 85.630, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 28.6

Copper Binding Sites:

The binding sites of Copper atom in the X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms (pdb code 1kcw). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms, PDB code: 1kcw:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 1kcw

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Copper binding site 1 out of 8 in the X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1049

b:34.2
occ:1.00
 SG A:CYS319 2.0 30.4 1.0
ND1 A:HIS324 2.0 25.9 1.0
ND1 A:HIS276 2.1 45.2 1.0
CE1 A:HIS276 2.9 45.2 1.0
CG A:HIS324 3.0 25.9 1.0
CE1 A:HIS324 3.1 25.9 1.0
CG A:HIS276 3.1 45.2 1.0
CB A:HIS324 3.3 25.9 1.0
CB A:CYS319 3.3 30.4 1.0
CA A:HIS276 3.5 22.4 1.0
CB A:HIS276 3.5 45.2 1.0
CD1 A:LEU329 3.7 27.1 1.0
O A:VAL275 3.7 28.8 1.0
CB A:ASN321 4.0 33.6 1.0
NE2 A:HIS276 4.0 45.2 1.0
CD2 A:HIS276 4.2 45.2 1.0
CD2 A:HIS324 4.2 25.9 1.0
N A:HIS276 4.2 22.4 1.0
NE2 A:HIS324 4.2 25.9 1.0
C A:VAL275 4.3 28.8 1.0
N A:ALA277 4.5 41.3 1.0
C A:HIS276 4.5 22.4 1.0
ND2 A:ASN321 4.6 33.6 1.0
CG A:ASN321 4.6 33.6 1.0
CA A:CYS319 4.6 35.7 1.0
CD2 A:PHE202 4.8 16.5 1.0
CA A:HIS324 4.8 30.1 1.0
O A:CYS319 4.9 35.7 1.0
CG A:LEU329 4.9 27.1 1.0

Copper binding site 2 out of 8 in 1kcw

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Copper binding site 2 out of 8 in the X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1050

b:46.4
occ:1.00
 O A:O1057 1.9 6.9 1.0
NE2 A:HIS1020 2.1 46.2 1.0
NE2 A:HIS980 2.1 35.4 1.0
NE2 A:HIS163 2.1 27.9 1.0
CE1 A:HIS980 2.2 35.4 1.0
CE1 A:HIS1020 2.7 46.2 1.0
CD2 A:HIS163 3.0 27.9 1.0
CE1 A:HIS163 3.2 27.9 1.0
CD2 A:HIS1020 3.4 46.2 1.0
CD2 A:HIS980 3.5 35.4 1.0
ND1 A:HIS980 3.5 35.4 1.0
CU A:CU1051 3.7 44.8 1.0
ND1 A:HIS1020 4.0 46.2 1.0
CG A:HIS980 4.1 35.4 1.0
CU A:CU1052 4.2 31.1 1.0
CG A:HIS163 4.2 27.9 1.0
CD2 A:HIS978 4.3 40.5 1.0
ND1 A:HIS163 4.3 27.9 1.0
CG A:HIS1020 4.3 46.2 1.0
CE1 A:HIS161 4.6 26.7 1.0
CD2 A:LEU1018 4.6 9.9 1.0
CD2 A:HIS101 4.6 46.6 1.0
NE2 A:HIS101 4.7 46.6 1.0
NE2 A:HIS1022 4.9 33.5 1.0
NE2 A:HIS978 4.9 40.5 1.0
NE2 A:HIS161 4.9 26.7 1.0

Copper binding site 3 out of 8 in 1kcw

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Copper binding site 3 out of 8 in the X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1051

b:44.8
occ:1.00
 O A:O1057 1.9 6.9 1.0
NE2 A:HIS103 2.1 24.1 1.0
NE2 A:HIS1022 2.1 33.5 1.0
NE2 A:HIS161 2.1 26.7 1.0
CE1 A:HIS161 2.7 26.7 1.0
CE1 A:HIS103 2.9 24.1 1.0
CE1 A:HIS1022 3.0 33.5 1.0
CD2 A:HIS1022 3.2 33.5 1.0
CD2 A:HIS103 3.2 24.1 1.0
CD2 A:HIS161 3.5 26.7 1.0
CU A:CU1052 3.5 31.1 1.0
CU A:CU1050 3.7 46.4 1.0
CD2 A:HIS978 4.0 40.5 1.0
ND1 A:HIS161 4.0 26.7 1.0
NE2 A:HIS980 4.1 35.4 1.0
ND1 A:HIS1022 4.1 33.5 1.0
ND1 A:HIS103 4.1 24.1 1.0
NE2 A:HIS978 4.1 40.5 1.0
CG A:HIS1022 4.2 33.5 1.0
CG A:HIS103 4.3 24.1 1.0
CG A:HIS161 4.4 26.7 1.0
CD2 A:HIS101 4.5 46.6 1.0
CE1 A:HIS1020 4.6 46.2 1.0
NE2 A:HIS101 4.7 46.6 1.0
CG A:HIS978 4.7 40.5 1.0
CD2 A:HIS980 4.9 35.4 1.0
CE1 A:HIS978 4.9 40.5 1.0
CD2 A:HIS163 4.9 27.9 1.0
NE2 A:HIS1020 4.9 46.2 1.0

Copper binding site 4 out of 8 in 1kcw

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Copper binding site 4 out of 8 in the X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1052

b:31.1
occ:1.00
 NE2 A:HIS101 2.1 46.6 1.0
NE2 A:HIS978 2.1 40.5 1.0
O A:O1058 2.1 2.0 1.0
CD2 A:HIS980 2.3 35.4 1.0
NE2 A:HIS980 2.7 35.4 1.0
CD2 A:HIS101 2.9 46.6 1.0
CD2 A:HIS978 3.0 40.5 1.0
O A:O1057 3.1 6.9 1.0
CE1 A:HIS978 3.1 40.5 1.0
CE1 A:HIS101 3.2 46.6 1.0
CD2 A:HIS103 3.3 24.1 1.0
NE2 A:HIS103 3.3 24.1 1.0
CU A:CU1051 3.5 44.8 1.0
CG A:HIS980 3.7 35.4 1.0
CG A:HIS103 3.8 24.1 1.0
CE1 A:HIS103 3.8 24.1 1.0
CE1 A:HIS980 4.0 35.4 1.0
ND1 A:HIS103 4.0 24.1 1.0
CG A:HIS101 4.1 46.6 1.0
CG A:HIS978 4.1 40.5 1.0
CU A:CU1050 4.2 46.4 1.0
ND1 A:HIS978 4.2 40.5 1.0
ND1 A:HIS101 4.2 46.6 1.0
O A:SER102 4.2 51.8 1.0
ND1 A:HIS980 4.4 35.4 1.0
CA A:HIS980 4.5 26.3 1.0
NE2 A:HIS161 4.5 26.7 1.0
CA A:HIS103 4.5 53.7 1.0
CB A:HIS980 4.6 35.4 1.0
CB A:HIS103 4.7 24.1 1.0
C A:SER102 5.0 51.8 1.0

Copper binding site 5 out of 8 in 1kcw

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Copper binding site 5 out of 8 in the X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1053

b:34.5
occ:1.00
 SG A:CYS680 2.0 38.6 1.0
ND1 A:HIS685 2.1 19.6 1.0
ND1 A:HIS637 2.1 23.9 1.0
CG A:HIS637 2.8 23.9 1.0
CB A:HIS637 2.9 23.9 1.0
CG A:HIS685 3.0 19.6 1.0
SD A:MET690 3.1 37.1 1.0
CE1 A:HIS685 3.1 19.6 1.0
CB A:CYS680 3.2 38.6 1.0
CE1 A:HIS637 3.2 23.9 1.0
CB A:HIS685 3.3 19.6 1.0
CA A:HIS637 3.5 28.3 1.0
CE A:MET690 3.8 37.1 1.0
CD2 A:HIS637 4.1 23.9 1.0
OG1 A:THR682 4.2 12.8 1.0
O A:VAL636 4.2 27.0 1.0
CD2 A:HIS685 4.2 19.6 1.0
NE2 A:HIS685 4.2 19.6 1.0
CG2 A:THR682 4.2 12.8 1.0
NE2 A:HIS637 4.3 23.9 1.0
N A:HIS637 4.4 28.3 1.0
CG A:MET690 4.5 37.1 1.0
CA A:CYS680 4.5 17.7 1.0
N A:GLY638 4.6 29.6 1.0
C A:VAL636 4.6 27.0 1.0
C A:HIS637 4.6 28.3 1.0
CA A:HIS685 4.8 17.7 1.0
CB A:THR682 4.8 12.8 1.0
CB A:MET690 5.0 37.1 1.0
O A:THR682 5.0 15.2 1.0
CD1 A:ILE639 5.0 17.2 1.0

Copper binding site 6 out of 8 in 1kcw

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Copper binding site 6 out of 8 in the X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1054

b:61.6
occ:1.00
 OD2 A:ASP684 2.2 33.0 1.0
OD1 A:ASP684 2.4 33.0 1.0
NE2 A:HIS602 2.4 35.9 1.0
CE1 A:HIS602 2.5 35.9 1.0
CG A:ASP684 2.6 33.0 1.0
CD2 A:HIS602 3.8 35.9 1.0
ND1 A:HIS602 3.8 35.9 1.0
CB A:ASP684 4.1 33.0 1.0
OE2 A:GLU597 4.2 82.0 1.0
OE2 A:GLU971 4.5 46.6 1.0
CG A:HIS602 4.5 35.9 1.0
OE1 A:GLU971 4.6 46.6 1.0
CD A:GLU971 4.8 46.6 1.0

Copper binding site 7 out of 8 in 1kcw

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Copper binding site 7 out of 8 in the X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1055

b:33.5
occ:1.00
 SG A:CYS1021 2.0 28.4 1.0
ND1 A:HIS1026 2.1 32.3 1.0
ND1 A:HIS975 2.1 19.5 1.0
CB A:CYS1021 2.9 28.4 1.0
CG A:HIS1026 3.0 32.3 1.0
CE1 A:HIS975 3.0 19.5 1.0
CE1 A:HIS1026 3.1 32.3 1.0
O A:LEU974 3.1 37.2 1.0
CG A:HIS975 3.2 19.5 1.0
SD A:MET1031 3.2 32.1 1.0
CB A:HIS1026 3.2 32.3 1.0
CA A:HIS975 3.5 29.4 1.0
CB A:HIS975 3.5 19.5 1.0
CG1 A:VAL1023 4.0 25.6 1.0
C A:LEU974 4.1 37.2 1.0
CD2 A:HIS1026 4.2 32.3 1.0
NE2 A:HIS975 4.2 19.5 1.0
NE2 A:HIS1026 4.2 32.3 1.0
CG A:MET1031 4.3 32.1 1.0
CA A:CYS1021 4.3 23.5 1.0
CD2 A:HIS975 4.3 19.5 1.0
N A:HIS975 4.3 29.4 1.0
CG2 A:VAL1023 4.5 25.6 1.0
C A:HIS975 4.5 29.4 1.0
N A:THR976 4.6 27.3 1.0
CA A:HIS1026 4.8 22.6 1.0
CB A:VAL1023 4.8 25.6 1.0
CE A:MET1031 4.8 32.1 1.0
C A:CYS1021 4.9 23.5 1.0
CB A:MET1031 4.9 32.1 1.0
N A:VAL1023 5.0 20.5 1.0

Copper binding site 8 out of 8 in 1kcw

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Copper binding site 8 out of 8 in the X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of X-Ray Crystal Structure of Human Ceruloplasmin at 3.0 Angstroms within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1056

b:27.6
occ:1.00
 NE2 A:HIS940 2.1 28.3 1.0
OD2 A:ASP1025 2.1 77.3 1.0
CE1 A:HIS940 2.8 28.3 1.0
CG A:ASP1025 3.0 77.3 1.0
OD1 A:ASP1025 3.1 77.3 1.0
CD2 A:HIS940 3.3 28.3 1.0
OE2 A:GLU935 3.4 63.1 1.0
OE2 A:GLU272 4.0 36.9 1.0
ND1 A:HIS940 4.1 28.3 1.0
CG A:HIS940 4.3 28.3 1.0
CB A:ASP1025 4.4 77.3 1.0
CD A:GLU935 4.5 63.1 1.0
OE1 A:GLU272 4.7 36.9 1.0
CD A:GLU272 4.8 36.9 1.0
CD2 A:HIS1026 4.9 32.3 1.0
CB A:LYS938 4.9 41.2 1.0
CG2 A:ILE972 4.9 39.6 1.0

Reference:

I.Zaitseva, V.Zaitsev, G.Card, K.Moshkov, B.Bax, A.Ralph, P.Lindley. The X-Ray Structure of Human Serum Ceruloplasmin at 3.1 Angstrom: Nature of the Copper Centres. J.Biol.Inorg.Chem. V. 1 15 1996.
ISSN: ISSN 0949-8257
Page generated: Tue Jul 30 22:10:46 2024

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