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Copper in PDB 4r0o: Crystal Structure of Pegylated Plastocyanin at 4.2 A Resolution

Protein crystallography data

The structure of Crystal Structure of Pegylated Plastocyanin at 4.2 A Resolution, PDB code: 4r0o was solved by G.Cattani, L.Vogeley, P.B.Crowley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.03 / 4.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.140, 116.140, 172.140, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Pegylated Plastocyanin at 4.2 A Resolution (pdb code 4r0o). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of Pegylated Plastocyanin at 4.2 A Resolution, PDB code: 4r0o:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 4r0o

Go back to Copper Binding Sites List in 4r0o
Copper binding site 1 out of 4 in the Crystal Structure of Pegylated Plastocyanin at 4.2 A Resolution


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 Pegylated Plastocyanin at 4.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:0.0
occ:1.00
ND1 A:HIS39 1.9 0.9 1.0
ND1 A:HIS92 2.0 0.6 1.0
SD A:MET97 2.3 0.7 1.0
SG A:CYS89 2.4 0.5 1.0
CE1 A:HIS39 2.6 0.5 1.0
CE1 A:HIS92 2.7 0.5 1.0
CG A:HIS92 3.1 0.9 1.0
CB A:CYS89 3.1 0.5 1.0
CG A:HIS39 3.1 0.3 1.0
CE A:MET97 3.2 0.8 1.0
CB A:HIS92 3.6 0.4 1.0
CB A:HIS39 3.7 0.6 1.0
NE2 A:HIS39 3.8 0.9 1.0
NE2 A:HIS92 3.9 0.0 1.0
CG A:MET97 3.9 0.6 1.0
CD2 A:HIS92 4.0 0.3 1.0
CD2 A:HIS39 4.1 0.7 1.0
CA A:HIS39 4.1 0.8 1.0
O A:PRO38 4.1 0.8 1.0
CB A:MET97 4.4 0.1 1.0
CA A:CYS89 4.6 0.8 1.0
N A:HIS92 4.7 0.6 1.0
CD2 A:LEU14 4.7 0.9 1.0
CA A:HIS92 4.8 0.5 1.0
C A:PRO38 4.9 0.7 1.0
N A:HIS39 4.9 0.6 1.0

Copper binding site 2 out of 4 in 4r0o

Go back to Copper Binding Sites List in 4r0o
Copper binding site 2 out of 4 in the Crystal Structure of Pegylated Plastocyanin at 4.2 A Resolution


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 Pegylated Plastocyanin at 4.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:0.8
occ:1.00
ND1 B:HIS39 1.9 77.7 1.0
ND1 B:HIS92 2.0 0.3 1.0
SD B:MET97 2.2 0.8 1.0
SG B:CYS89 2.3 0.1 1.0
CE1 B:HIS39 2.6 84.2 1.0
CE1 B:HIS92 2.9 0.6 1.0
CB B:CYS89 2.9 0.6 1.0
CG B:HIS92 3.1 0.5 1.0
CE B:MET97 3.1 0.6 1.0
CG B:HIS39 3.1 82.4 1.0
CB B:HIS92 3.6 0.3 1.0
CB B:HIS39 3.8 89.3 1.0
CG B:MET97 3.8 0.3 1.0
NE2 B:HIS39 3.8 85.8 1.0
NE2 B:HIS92 4.0 0.7 1.0
CD2 B:HIS39 4.1 85.1 1.0
CD2 B:HIS92 4.1 0.8 1.0
CA B:HIS39 4.2 96.2 1.0
O B:PRO38 4.2 95.5 1.0
CB B:MET97 4.3 0.3 1.0
CA B:CYS89 4.4 0.3 1.0
N B:HIS92 4.7 1.0 1.0
CA B:HIS92 4.7 0.1 1.0
CD2 B:LEU14 4.8 0.6 1.0
C B:PRO38 5.0 0.3 1.0
N B:HIS39 5.0 0.7 1.0

Copper binding site 3 out of 4 in 4r0o

Go back to Copper Binding Sites List in 4r0o
Copper binding site 3 out of 4 in the Crystal Structure of Pegylated Plastocyanin at 4.2 A Resolution


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 Pegylated Plastocyanin at 4.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:1.0
occ:1.00
ND1 C:HIS92 2.0 0.6 1.0
ND1 C:HIS39 2.1 96.6 1.0
SG C:CYS89 2.2 0.2 1.0
SD C:MET97 2.4 0.4 1.0
CB C:CYS89 2.8 0.4 1.0
CE1 C:HIS92 2.8 0.2 1.0
CE1 C:HIS39 2.8 99.2 1.0
CG C:HIS92 3.0 0.8 1.0
CG C:HIS39 3.3 99.2 1.0
CE C:MET97 3.3 99.6 1.0
CB C:HIS92 3.4 0.5 1.0
CB C:HIS39 3.8 0.4 1.0
CG C:MET97 3.9 0.0 1.0
NE2 C:HIS92 4.0 0.8 1.0
NE2 C:HIS39 4.1 95.2 1.0
CD2 C:HIS92 4.1 0.0 1.0
CA C:HIS39 4.1 0.5 1.0
O C:PRO38 4.2 0.2 1.0
CD2 C:HIS39 4.3 93.6 1.0
CB C:MET97 4.3 1.0 1.0
CA C:CYS89 4.3 0.9 1.0
N C:HIS92 4.4 0.8 1.0
CA C:HIS92 4.6 0.8 1.0
C C:CYS89 4.8 98.0 1.0
CD2 C:LEU14 4.9 1.0 1.0
C C:PRO38 4.9 0.6 1.0
N C:HIS39 5.0 0.4 1.0

Copper binding site 4 out of 4 in 4r0o

Go back to Copper Binding Sites List in 4r0o
Copper binding site 4 out of 4 in the Crystal Structure of Pegylated Plastocyanin at 4.2 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Pegylated Plastocyanin at 4.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu201

b:0.8
occ:1.00
ND1 D:HIS39 2.0 87.5 1.0
ND1 D:HIS92 2.0 0.3 1.0
SG D:CYS89 2.2 0.5 1.0
SD D:MET97 2.3 0.8 1.0
CE1 D:HIS39 2.7 91.8 1.0
CE1 D:HIS92 2.9 0.8 1.0
CB D:CYS89 2.9 0.6 1.0
CG D:HIS92 3.0 0.9 1.0
CG D:HIS39 3.2 91.2 1.0
CE D:MET97 3.2 0.9 1.0
CB D:HIS92 3.5 0.4 1.0
CB D:HIS39 3.8 0.0 1.0
CG D:MET97 3.8 0.5 1.0
NE2 D:HIS39 3.9 92.8 1.0
NE2 D:HIS92 4.0 0.0 1.0
CD2 D:HIS92 4.1 0.0 1.0
CD2 D:HIS39 4.1 91.4 1.0
CA D:HIS39 4.2 1.0 1.0
CB D:MET97 4.2 0.1 1.0
O D:PRO38 4.3 0.2 1.0
CA D:CYS89 4.4 0.7 1.0
N D:HIS92 4.5 0.9 1.0
CA D:HIS92 4.6 0.4 1.0
CD2 D:LEU14 4.7 0.6 1.0
C D:CYS89 5.0 94.6 1.0

Reference:

G.Cattani, L.Vogeley, P.B.Crowley. Structure of A Pegylated Protein Reveals A Highly Porous Double-Helical Assembly. Nat.Chem. V. 7 823 2015.
ISSN: ISSN 1755-4330
PubMed: 26391082
DOI: 10.1038/NCHEM.2342
Page generated: Sun Dec 13 11:15:44 2020

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