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Copper in PDB 1id2: Crystal Structure of Amicyanin From Paracoccus Versutus (Thiobacillus Versutus)

Protein crystallography data

The structure of Crystal Structure of Amicyanin From Paracoccus Versutus (Thiobacillus Versutus), PDB code: 1id2 was solved by A.Romero, H.Nar, A.Messerschmidt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.15
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 87.400, 87.400, 38.200, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / n/a

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Amicyanin From Paracoccus Versutus (Thiobacillus Versutus) (pdb code 1id2). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of Amicyanin From Paracoccus Versutus (Thiobacillus Versutus), PDB code: 1id2:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 1id2

Go back to Copper Binding Sites List in 1id2
Copper binding site 1 out of 3 in the Crystal Structure of Amicyanin From Paracoccus Versutus (Thiobacillus Versutus)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Amicyanin From Paracoccus Versutus (Thiobacillus Versutus) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu107

b:21.8
occ:1.00
ND1 A:HIS54 2.0 18.4 1.0
SG A:CYS93 2.0 11.2 1.0
ND1 A:HIS96 2.2 20.0 1.0
SD A:MET99 2.9 19.8 1.0
CE1 A:HIS54 2.9 7.3 1.0
CB A:CYS93 3.0 10.2 1.0
CG A:HIS54 3.1 12.3 1.0
CG A:HIS96 3.2 18.1 1.0
CE1 A:HIS96 3.2 20.6 1.0
CB A:HIS96 3.4 14.4 1.0
CB A:HIS54 3.6 5.8 1.0
CA A:HIS54 3.7 3.9 1.0
CE A:MET99 3.8 6.3 1.0
O A:PRO53 3.9 16.7 1.0
NE2 A:HIS54 4.1 9.2 1.0
CD2 A:HIS54 4.2 12.7 1.0
CD2 A:HIS96 4.4 27.5 1.0
NE2 A:HIS96 4.4 17.8 1.0
CG A:MET99 4.4 17.9 1.0
CA A:CYS93 4.4 20.8 1.0
N A:HIS96 4.6 13.5 1.0
CA A:HIS96 4.6 10.1 1.0
N A:HIS54 4.6 15.4 1.0
CG A:PRO95 4.6 17.6 1.0
C A:PRO53 4.7 17.2 1.0
N A:ASN55 4.7 12.6 1.0
C A:HIS54 4.8 10.0 1.0
O A:HIS96 4.8 15.0 1.0
CB A:MET99 4.8 21.1 1.0
C A:CYS93 4.9 13.9 1.0
CD A:PRO95 4.9 20.0 1.0

Copper binding site 2 out of 3 in 1id2

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Copper binding site 2 out of 3 in the Crystal Structure of Amicyanin From Paracoccus Versutus (Thiobacillus Versutus)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Amicyanin From Paracoccus Versutus (Thiobacillus Versutus) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu107

b:18.1
occ:1.00
ND1 B:HIS96 2.1 9.5 1.0
ND1 B:HIS54 2.2 39.3 1.0
SG B:CYS93 2.2 14.2 1.0
SD B:MET99 2.7 14.6 1.0
CE1 B:HIS54 3.1 26.2 1.0
CE1 B:HIS96 3.1 11.7 1.0
CB B:CYS93 3.2 3.1 1.0
CG B:HIS96 3.2 11.4 1.0
CG B:HIS54 3.2 28.7 1.0
CB B:HIS96 3.5 20.8 1.0
CB B:HIS54 3.6 10.7 1.0
CA B:HIS54 3.6 5.7 1.0
CE B:MET99 3.6 4.5 1.0
O B:PRO53 3.9 13.8 1.0
NE2 B:HIS54 4.2 13.1 1.0
NE2 B:HIS96 4.3 10.7 1.0
CG B:MET99 4.3 4.5 1.0
CD2 B:HIS96 4.3 15.3 1.0
CD2 B:HIS54 4.3 16.8 1.0
N B:HIS96 4.4 17.1 1.0
CG B:PRO95 4.5 9.4 1.0
CA B:HIS96 4.5 7.2 1.0
CA B:CYS93 4.6 6.7 1.0
N B:HIS54 4.6 5.8 1.0
N B:ASN55 4.7 13.1 1.0
C B:PRO53 4.7 14.1 1.0
C B:HIS54 4.7 8.3 1.0
CB B:MET99 4.7 12.2 1.0
O B:HIS96 4.8 13.6 1.0
CD B:PRO95 4.9 20.1 1.0

Copper binding site 3 out of 3 in 1id2

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Copper binding site 3 out of 3 in the Crystal Structure of Amicyanin From Paracoccus Versutus (Thiobacillus Versutus)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Amicyanin From Paracoccus Versutus (Thiobacillus Versutus) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu107

b:21.3
occ:1.00
ND1 C:HIS54 1.9 24.8 1.0
ND1 C:HIS96 2.0 17.8 1.0
SG C:CYS93 2.2 12.2 1.0
CE1 C:HIS54 2.9 5.5 1.0
SD C:MET99 2.9 11.8 1.0
CE1 C:HIS96 3.0 19.0 1.0
CG C:HIS54 3.0 12.8 1.0
CG C:HIS96 3.1 6.2 1.0
CB C:CYS93 3.1 2.0 1.0
CB C:HIS96 3.5 3.1 1.0
CB C:HIS54 3.5 8.8 1.0
CA C:HIS54 3.6 10.7 1.0
O C:PRO53 3.8 14.2 1.0
CE C:MET99 3.9 2.0 1.0
NE2 C:HIS54 4.0 12.4 1.0
CD2 C:HIS54 4.1 5.6 1.0
NE2 C:HIS96 4.2 15.3 1.0
CD2 C:HIS96 4.2 14.3 1.0
CG C:MET99 4.3 5.5 1.0
N C:HIS96 4.5 12.6 1.0
CG C:PRO95 4.5 3.6 1.0
CA C:HIS96 4.6 12.6 1.0
CA C:CYS93 4.6 17.5 1.0
N C:HIS54 4.6 7.2 1.0
C C:PRO53 4.6 13.9 1.0
N C:ASN55 4.7 8.4 1.0
C C:HIS54 4.7 7.0 1.0
O C:HIS96 4.8 18.7 1.0
CD C:PRO95 4.8 6.8 1.0
CB C:MET99 4.9 22.7 1.0

Reference:

A.Romero, H.Nar, R.Huber, A.Messerschmidt, A.P.Kalverda, G.W.Canters, R.Durley, F.S.Mathews. Crystal Structure Analysis and Refinement at 2.15 A Resolution of Amicyanin, A Type I Blue Copper Protein, From Thiobacillus Versutus. J.Mol.Biol. V. 236 1196 1994.
ISSN: ISSN 0022-2836
PubMed: 8120896
DOI: 10.1016/0022-2836(94)90021-3
Page generated: Thu Sep 3 15:59:42 2020
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