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Copper in PDB 2w88: Plastocyanin Variant with N-Terminal Methionine - Open Structure

Protein crystallography data

The structure of Plastocyanin Variant with N-Terminal Methionine - Open Structure, PDB code: 2w88 was solved by P.B.Crowley, P.M.Matias, A.R.Khan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 110.43 / 2.89
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 127.700, 127.700, 94.990, 90.00, 90.00, 120.00
R / Rfree (%) 19.433 / 22.285

Other elements in 2w88:

The structure of Plastocyanin Variant with N-Terminal Methionine - Open Structure also contains other interesting chemical elements:

Zinc (Zn) 7 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Plastocyanin Variant with N-Terminal Methionine - Open Structure (pdb code 2w88). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Plastocyanin Variant with N-Terminal Methionine - Open Structure, PDB code: 2w88:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 2w88

Go back to Copper Binding Sites List in 2w88
Copper binding site 1 out of 3 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu106

b:26.8
occ:1.00
ND1 A:HIS92 2.1 29.5 1.0
ND1 A:HIS39 2.1 27.2 1.0
SG A:CYS89 2.3 28.9 1.0
SD A:MET97 2.3 28.4 1.0
CE1 A:HIS92 3.0 30.7 1.0
CE1 A:HIS39 3.0 26.8 1.0
CG A:HIS92 3.1 30.2 1.0
CG A:HIS39 3.1 27.5 1.0
CE A:MET97 3.3 28.1 1.0
CB A:CYS89 3.4 29.2 1.0
CB A:HIS92 3.5 30.1 1.0
CB A:HIS39 3.5 27.8 1.0
CA A:HIS39 3.9 27.8 1.0
O A:PRO38 3.9 28.6 1.0
CG A:MET97 3.9 29.6 1.0
NE2 A:HIS92 4.1 30.5 1.0
NE2 A:HIS39 4.1 26.5 1.0
CD2 A:HIS92 4.2 30.3 1.0
CD2 A:HIS39 4.2 27.1 1.0
N A:HIS92 4.4 30.0 1.0
CB A:MET97 4.4 29.9 1.0
CA A:HIS92 4.6 30.2 1.0
C A:PRO38 4.7 28.4 1.0
N A:HIS39 4.7 28.1 1.0
CA A:CYS89 4.8 29.1 1.0

Copper binding site 2 out of 3 in 2w88

Go back to Copper Binding Sites List in 2w88
Copper binding site 2 out of 3 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu106

b:24.6
occ:1.00
ND1 C:HIS39 2.0 26.8 1.0
ND1 C:HIS92 2.1 29.8 1.0
SG C:CYS89 2.3 26.7 1.0
SD C:MET97 2.3 28.6 1.0
CE1 C:HIS39 2.9 28.4 1.0
CE1 C:HIS92 3.0 30.3 1.0
CG C:HIS92 3.1 29.1 1.0
CG C:HIS39 3.1 28.1 1.0
CE C:MET97 3.3 28.1 1.0
CB C:HIS92 3.4 28.6 1.0
CB C:CYS89 3.4 27.4 1.0
CB C:HIS39 3.6 28.1 1.0
CG C:MET97 3.9 29.3 1.0
CA C:HIS39 3.9 28.0 1.0
O C:PRO38 4.0 27.8 1.0
NE2 C:HIS39 4.1 29.1 1.0
NE2 C:HIS92 4.1 28.5 1.0
CD2 C:HIS92 4.2 28.5 1.0
CD2 C:HIS39 4.2 28.8 1.0
N C:HIS92 4.4 28.6 1.0
CB C:MET97 4.5 28.8 1.0
CA C:HIS92 4.5 28.9 1.0
N C:HIS39 4.7 28.1 1.0
C C:PRO38 4.7 28.1 1.0
CA C:CYS89 4.8 27.3 1.0
CB C:PRO91 4.9 27.7 1.0
CD2 C:LEU14 5.0 26.0 1.0

Copper binding site 3 out of 3 in 2w88

Go back to Copper Binding Sites List in 2w88
Copper binding site 3 out of 3 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu106

b:23.8
occ:1.00
ND1 B:HIS39 2.1 26.3 1.0
ND1 B:HIS92 2.1 27.5 1.0
SG B:CYS89 2.3 27.1 1.0
SD B:MET97 2.3 27.1 1.0
CE1 B:HIS92 3.0 27.7 1.0
CE1 B:HIS39 3.0 25.5 1.0
CG B:HIS39 3.1 25.9 1.0
CG B:HIS92 3.1 27.3 1.0
CE B:MET97 3.3 25.9 1.0
CB B:CYS89 3.3 26.4 1.0
CB B:HIS39 3.4 26.0 1.0
CB B:HIS92 3.5 27.8 1.0
CA B:HIS39 3.8 26.4 1.0
CG B:MET97 3.9 27.0 1.0
O B:PRO38 3.9 26.0 1.0
NE2 B:HIS92 4.1 26.9 1.0
NE2 B:HIS39 4.2 24.7 1.0
CD2 B:HIS39 4.2 25.0 1.0
CD2 B:HIS92 4.2 26.3 1.0
N B:HIS92 4.4 28.2 1.0
CB B:MET97 4.4 26.4 1.0
CA B:HIS92 4.6 28.2 1.0
N B:HIS39 4.7 26.3 1.0
C B:PRO38 4.7 26.2 1.0
CA B:CYS89 4.7 26.7 1.0
CD B:PRO91 4.9 27.9 1.0

Reference:

P.B.Crowley, P.M.Matias, A.R.Khan, M.Roessle, D.I.Svergun. Metal-Mediated Self-Assembly of A Beta-Sandwich Protein. Chemistry V. 15 12672 2009.
ISSN: ISSN 0947-6539
PubMed: 19834935
DOI: 10.1002/CHEM.200901410
Page generated: Sun Dec 13 11:07:19 2020

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