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Copper in PDB 1f56: Spinach Plantacyanin

Protein crystallography data

The structure of Spinach Plantacyanin, PDB code: 1f56 was solved by O.Einsle, Z.Mehrabian, R.Nalbandyan, A.Messerschmidt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.500, 41.832, 158.300, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 21.3

Copper Binding Sites:

The binding sites of Copper atom in the Spinach Plantacyanin (pdb code 1f56). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Spinach Plantacyanin, PDB code: 1f56:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 1f56

Go back to Copper Binding Sites List in 1f56
Copper binding site 1 out of 3 in the Spinach Plantacyanin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Spinach Plantacyanin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu92

b:21.9
occ:1.00
ND1 A:HIS79 2.0 16.5 1.0
ND1 A:HIS34 2.0 13.2 1.0
SG A:CYS74 2.2 14.2 1.0
SD A:MET84 2.7 22.5 1.0
CG A:HIS79 3.0 13.4 1.0
CE1 A:HIS79 3.0 14.6 1.0
CG A:HIS34 3.0 8.0 1.0
CE1 A:HIS34 3.0 16.8 1.0
CB A:CYS74 3.1 11.4 1.0
CB A:HIS79 3.3 11.8 1.0
CB A:HIS34 3.3 10.9 1.0
CE A:MET84 3.6 20.3 1.0
CA A:HIS34 3.7 18.6 1.0
O A:GLN33 4.0 19.4 1.0
NE2 A:HIS79 4.1 18.7 1.0
CD2 A:HIS79 4.1 12.7 1.0
NE2 A:HIS34 4.1 14.9 1.0
CD2 A:HIS34 4.1 13.7 1.0
CG A:MET84 4.3 25.8 1.0
CD2 A:PHE76 4.5 16.2 1.0
CA A:CYS74 4.5 12.9 1.0
N A:ASN35 4.6 16.8 1.0
CB A:MET84 4.7 25.5 1.0
N A:HIS34 4.7 14.9 1.0
CB A:PHE76 4.7 15.3 1.0
C A:HIS34 4.7 16.9 1.0
CA A:HIS79 4.8 14.8 1.0
C A:GLN33 4.8 21.7 1.0
CG A:PHE76 4.8 12.5 1.0
CZ A:PHE9 5.0 32.4 1.0

Copper binding site 2 out of 3 in 1f56

Go back to Copper Binding Sites List in 1f56
Copper binding site 2 out of 3 in the Spinach Plantacyanin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Spinach Plantacyanin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu92

b:19.3
occ:1.00
ND1 B:HIS79 2.0 11.2 1.0
ND1 B:HIS34 2.1 17.5 1.0
SG B:CYS74 2.2 15.2 1.0
SD B:MET84 2.8 18.8 1.0
CG B:HIS79 3.0 15.4 1.0
CG B:HIS34 3.0 13.1 1.0
CE1 B:HIS79 3.0 11.9 1.0
CE1 B:HIS34 3.1 16.2 1.0
CB B:CYS74 3.2 9.3 1.0
CB B:HIS79 3.3 14.1 1.0
CB B:HIS34 3.3 17.7 1.0
CE B:MET84 3.6 13.5 1.0
CA B:HIS34 3.7 13.2 1.0
O B:GLN33 4.0 12.6 1.0
CD2 B:HIS79 4.1 15.9 1.0
NE2 B:HIS79 4.1 16.0 1.0
CD2 B:HIS34 4.2 21.7 1.0
NE2 B:HIS34 4.2 25.4 1.0
CG B:MET84 4.3 22.0 1.0
CB B:PHE76 4.4 13.2 1.0
CD2 B:PHE76 4.6 19.3 1.0
CA B:CYS74 4.6 15.1 1.0
N B:ASN35 4.6 11.0 1.0
CG B:PHE76 4.7 14.6 1.0
N B:HIS34 4.7 13.6 1.0
CA B:HIS79 4.7 15.9 1.0
C B:HIS34 4.7 15.3 1.0
CB B:MET84 4.7 16.2 1.0
C B:GLN33 4.7 14.1 1.0

Copper binding site 3 out of 3 in 1f56

Go back to Copper Binding Sites List in 1f56
Copper binding site 3 out of 3 in the Spinach Plantacyanin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Spinach Plantacyanin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu92

b:19.0
occ:1.00
ND1 C:HIS79 2.0 24.0 1.0
ND1 C:HIS34 2.0 12.3 1.0
SG C:CYS74 2.2 18.3 1.0
SD C:MET84 2.6 18.4 1.0
CE1 C:HIS79 2.9 22.2 1.0
CG C:HIS79 3.0 18.5 1.0
CE1 C:HIS34 3.0 12.9 1.0
CG C:HIS34 3.0 15.7 1.0
CB C:CYS74 3.2 15.7 1.0
CB C:HIS79 3.3 14.6 1.0
CB C:HIS34 3.4 13.4 1.0
CE C:MET84 3.4 20.6 1.0
CA C:HIS34 3.8 11.8 1.0
CG C:MET84 4.0 25.2 1.0
NE2 C:HIS79 4.1 20.6 1.0
CD2 C:HIS79 4.1 24.4 1.0
NE2 C:HIS34 4.1 13.2 1.0
CD2 C:HIS34 4.1 13.2 1.0
O C:GLN33 4.2 20.7 1.0
CB C:PHE76 4.4 11.5 1.0
CB C:MET84 4.4 12.1 1.0
CA C:CYS74 4.6 14.3 1.0
CG C:PHE76 4.6 14.1 1.0
N C:ASN35 4.7 11.1 1.0
CA C:HIS79 4.7 15.6 1.0
N C:HIS34 4.8 14.2 1.0
C C:HIS34 4.8 17.1 1.0
CD1 C:PHE76 4.9 14.9 1.0
C C:GLN33 4.9 17.5 1.0

Reference:

O.Einsle, Z.Mehrabian, R.Nalbandyan, A.Messerschmidt. Crystal Structure of Plantacyanin, A Basic Blue Cupredoxin From Spinach. J.Biol.Inorg.Chem. V. 5 666 2000.
ISSN: ISSN 0949-8257
PubMed: 11085657
DOI: 10.1007/S007750000154
Page generated: Sun Dec 13 10:58:46 2020

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