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Copper in PDB 2q5b: High Resolution Structure of Plastocyanin From Phormidium Laminosum

Protein crystallography data

The structure of High Resolution Structure of Plastocyanin From Phormidium Laminosum, PDB code: 2q5b was solved by R.Fromme, Y.S.Bukhman-Deruyter, I.Grotjohann, H.Mi, P.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.99 / 1.45
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.329, 84.329, 90.536, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21

Other elements in 2q5b:

The structure of High Resolution Structure of Plastocyanin From Phormidium Laminosum also contains other interesting chemical elements:

Potassium (K) 5 atoms
Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the High Resolution Structure of Plastocyanin From Phormidium Laminosum (pdb code 2q5b). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the High Resolution Structure of Plastocyanin From Phormidium Laminosum, PDB code: 2q5b:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 2q5b

Go back to Copper Binding Sites List in 2q5b
Copper binding site 1 out of 3 in the High Resolution Structure of Plastocyanin From Phormidium Laminosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of High Resolution Structure of Plastocyanin From Phormidium Laminosum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu106

b:13.1
occ:1.00
ND1 A:HIS39 2.1 10.7 1.0
ND1 A:HIS92 2.1 11.4 1.0
SG A:CYS89 2.2 10.3 1.0
SD A:MET97 2.6 11.0 1.0
CE1 A:HIS39 2.9 10.5 1.0
CE1 A:HIS92 3.0 12.1 1.0
CG A:HIS92 3.1 11.0 1.0
CG A:HIS39 3.2 9.4 1.0
CB A:CYS89 3.2 10.2 1.0
CB A:HIS92 3.4 11.2 1.0
CE A:MET97 3.4 12.0 1.0
CB A:HIS39 3.6 9.2 1.0
O A:PRO38 3.7 12.2 1.0
CA A:HIS39 3.7 9.8 1.0
CG A:MET97 4.0 10.4 1.0
NE2 A:HIS39 4.1 12.2 1.0
NE2 A:HIS92 4.2 12.8 1.0
CD2 A:HIS92 4.2 12.0 1.0
CD2 A:HIS39 4.2 10.5 1.0
N A:HIS92 4.2 11.4 1.0
CA A:HIS92 4.4 11.5 1.0
C A:PRO38 4.5 12.0 1.0
CB A:MET97 4.5 11.1 1.0
N A:HIS39 4.5 10.1 1.0
CA A:CYS89 4.7 9.2 1.0
CB A:PRO91 4.7 13.3 1.0
N A:ASN40 4.9 9.0 1.0
C A:HIS39 4.9 9.3 1.0

Copper binding site 2 out of 3 in 2q5b

Go back to Copper Binding Sites List in 2q5b
Copper binding site 2 out of 3 in the High Resolution Structure of Plastocyanin From Phormidium Laminosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of High Resolution Structure of Plastocyanin From Phormidium Laminosum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu106

b:14.6
occ:1.00
ND1 B:HIS39 2.0 11.6 1.0
ND1 B:HIS92 2.1 15.0 1.0
SG B:CYS89 2.3 12.1 1.0
SD B:MET97 2.6 12.6 1.0
CE1 B:HIS39 2.9 12.0 1.0
CE1 B:HIS92 3.0 15.9 1.0
CG B:HIS92 3.1 14.5 1.0
CG B:HIS39 3.1 11.9 1.0
CB B:CYS89 3.2 11.9 1.0
CB B:HIS92 3.4 14.7 1.0
CE B:MET97 3.4 13.9 1.0
CB B:HIS39 3.5 11.6 1.0
CA B:HIS39 3.8 12.0 1.0
O B:PRO38 3.9 13.2 1.0
CG B:MET97 3.9 12.7 1.0
NE2 B:HIS39 4.1 11.7 1.0
NE2 B:HIS92 4.1 15.7 1.0
CD2 B:HIS92 4.2 15.2 1.0
CD2 B:HIS39 4.2 11.3 1.0
N B:HIS92 4.4 14.9 1.0
CB B:MET97 4.4 13.1 1.0
CA B:HIS92 4.5 14.7 1.0
N B:HIS39 4.6 12.3 1.0
CA B:CYS89 4.6 11.6 1.0
CG B:PRO91 4.6 16.0 1.0
C B:PRO38 4.6 13.3 1.0
N B:ASN40 4.9 10.7 1.0
C B:HIS39 4.9 11.6 1.0

Copper binding site 3 out of 3 in 2q5b

Go back to Copper Binding Sites List in 2q5b
Copper binding site 3 out of 3 in the High Resolution Structure of Plastocyanin From Phormidium Laminosum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of High Resolution Structure of Plastocyanin From Phormidium Laminosum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu106

b:13.0
occ:1.00
ND1 C:HIS39 2.0 11.6 1.0
ND1 C:HIS92 2.1 12.1 1.0
SG C:CYS89 2.2 11.4 1.0
SD C:MET97 2.6 11.9 1.0
CE1 C:HIS39 2.9 12.3 1.0
CE1 C:HIS92 3.0 13.8 1.0
CG C:HIS92 3.1 12.6 1.0
CG C:HIS39 3.1 10.6 1.0
CB C:CYS89 3.2 9.9 1.0
CE C:MET97 3.3 12.9 1.0
CB C:HIS92 3.4 12.1 1.0
CB C:HIS39 3.6 11.4 1.0
O C:PRO38 3.8 13.5 1.0
CA C:HIS39 3.8 12.0 1.0
CG C:MET97 3.9 10.6 1.0
NE2 C:HIS39 4.1 11.3 1.0
NE2 C:HIS92 4.2 14.0 1.0
CD2 C:HIS39 4.2 11.4 1.0
CD2 C:HIS92 4.2 14.5 1.0
N C:HIS92 4.2 12.7 1.0
CB C:MET97 4.4 11.0 1.0
CA C:HIS92 4.4 12.1 1.0
C C:PRO38 4.6 14.0 1.0
N C:HIS39 4.6 12.3 1.0
CA C:CYS89 4.7 10.1 1.0
CB C:PRO91 4.9 13.6 1.0
N C:ASN40 4.9 10.6 1.0
C C:HIS39 4.9 11.8 1.0

Reference:

Y.S.Bukhman-Deruyter, R.Fromme, I.Grotjohann, B.Schlarb-Ridley, H.Mi, P.Fromme. Plastocyanin at High Resolution From Phormidium Laminosum and the Double Mutant D44A, D45A To Be Published.
Page generated: Sun Dec 13 11:06:47 2020

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