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Copper in PDB 2c9p: Cu(I)Cu(II)-Copc at pH 4.5

Protein crystallography data

The structure of Cu(I)Cu(II)-Copc at pH 4.5, PDB code: 2c9p was solved by L.Zhang, M.Koay, M.J.Maher, Z.Xiao, A.G.Wedd, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.25
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.510, 104.510, 55.519, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 26.4

Copper Binding Sites:

The binding sites of Copper atom in the Cu(I)Cu(II)-Copc at pH 4.5 (pdb code 2c9p). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Cu(I)Cu(II)-Copc at pH 4.5, PDB code: 2c9p:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2c9p

Go back to Copper Binding Sites List in 2c9p
Copper binding site 1 out of 6 in the Cu(I)Cu(II)-Copc at pH 4.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cu(I)Cu(II)-Copc at pH 4.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1103

b:40.9
occ:1.00
SD A:MET46 2.2 32.0 1.0
SD B:MET40 2.3 28.8 1.0
SD A:MET43 2.4 34.7 1.0
SD B:MET51 2.5 37.3 1.0
CE A:MET46 3.3 29.2 1.0
CE A:MET43 3.3 37.5 1.0
CG A:MET43 3.4 33.8 1.0
CG B:MET51 3.4 25.4 1.0
CE B:MET51 3.4 48.8 1.0
CE B:MET40 3.4 32.0 1.0
CG A:MET46 3.5 29.4 1.0
CG B:MET40 3.5 31.1 1.0
CB B:MET40 3.7 31.9 1.0
CB A:MET46 3.8 32.4 1.0
SD B:MET43 4.6 34.0 1.0
CB B:MET51 4.8 24.6 1.0
CB A:MET43 4.8 35.2 1.0

Copper binding site 2 out of 6 in 2c9p

Go back to Copper Binding Sites List in 2c9p
Copper binding site 2 out of 6 in the Cu(I)Cu(II)-Copc at pH 4.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cu(I)Cu(II)-Copc at pH 4.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1104

b:59.2
occ:1.00
NE2 A:HIS1 2.0 66.2 1.0
ND1 A:HIS91 2.2 33.7 1.0
O A:HOH2004 2.3 42.5 1.0
CD2 A:HIS1 2.9 59.8 1.0
CE1 A:HIS1 3.0 70.8 1.0
CG A:HIS91 3.1 41.0 1.0
CE1 A:HIS91 3.2 46.0 1.0
CB A:HIS91 3.3 40.2 1.0
N A:HIS91 4.0 42.3 1.0
ND1 A:HIS1 4.1 63.0 1.0
CG A:HIS1 4.1 59.7 1.0
CA A:HIS91 4.2 40.5 1.0
CD2 A:HIS91 4.2 44.1 1.0
NE2 A:HIS91 4.3 31.0 1.0
O A:HOH2003 4.3 46.2 1.0
CG2 A:THR90 4.9 49.4 1.0
O A:HIS91 5.0 36.7 1.0

Copper binding site 3 out of 6 in 2c9p

Go back to Copper Binding Sites List in 2c9p
Copper binding site 3 out of 6 in the Cu(I)Cu(II)-Copc at pH 4.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cu(I)Cu(II)-Copc at pH 4.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1105

b:37.6
occ:1.00
SD B:MET46 2.2 33.8 1.0
SD A:MET51 2.3 32.3 1.0
SD B:MET43 2.4 34.0 1.0
SD A:MET40 2.4 34.8 1.0
CG B:MET43 3.2 24.0 1.0
CE B:MET43 3.3 33.0 1.0
CE A:MET40 3.3 47.5 1.0
CE A:MET51 3.3 47.4 1.0
CE B:MET46 3.4 40.1 1.0
CG A:MET51 3.4 33.9 1.0
CG B:MET46 3.5 41.9 1.0
CG A:MET40 3.6 38.8 1.0
CB A:MET40 3.7 34.8 1.0
CB B:MET46 3.8 39.0 1.0
SD A:MET43 4.5 34.7 1.0
CB B:MET43 4.6 28.5 1.0
CB A:MET51 4.8 31.0 1.0

Copper binding site 4 out of 6 in 2c9p

Go back to Copper Binding Sites List in 2c9p
Copper binding site 4 out of 6 in the Cu(I)Cu(II)-Copc at pH 4.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cu(I)Cu(II)-Copc at pH 4.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1103

b:58.5
occ:1.00
NE2 B:HIS1 2.0 58.2 1.0
ND1 B:HIS91 2.2 36.9 1.0
O B:HOH2003 2.7 36.9 1.0
CE1 B:HIS1 2.9 61.4 1.0
CD2 B:HIS1 3.0 53.4 1.0
CG B:HIS91 3.1 33.9 1.0
CB B:HIS91 3.2 32.4 1.0
CE1 B:HIS91 3.3 28.4 1.0
N B:HIS91 3.9 35.1 1.0
ND1 B:HIS1 4.1 55.9 1.0
CG B:HIS1 4.1 54.4 1.0
CA B:HIS91 4.2 33.2 1.0
CD2 B:HIS91 4.3 31.9 1.0
NE2 B:HIS91 4.3 42.3 1.0
CG2 B:THR90 4.7 33.8 1.0
O B:HIS91 4.9 30.5 1.0

Copper binding site 5 out of 6 in 2c9p

Go back to Copper Binding Sites List in 2c9p
Copper binding site 5 out of 6 in the Cu(I)Cu(II)-Copc at pH 4.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cu(I)Cu(II)-Copc at pH 4.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1103

b:39.2
occ:1.00
SD C:MET46 2.3 31.9 1.0
SD C:MET43 2.3 32.6 1.0
CE C:MET43 3.2 42.0 1.0
CG C:MET43 3.3 34.3 1.0
CE C:MET46 3.4 35.4 1.0
CG C:MET46 3.5 35.8 1.0
CB C:MET46 3.9 29.7 1.0
CB C:MET43 4.7 37.6 1.0

Copper binding site 6 out of 6 in 2c9p

Go back to Copper Binding Sites List in 2c9p
Copper binding site 6 out of 6 in the Cu(I)Cu(II)-Copc at pH 4.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cu(I)Cu(II)-Copc at pH 4.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1104

b:69.2
occ:1.00
NE2 C:HIS1 2.1 66.7 1.0
ND1 C:HIS91 2.4 39.9 1.0
O C:HOH2002 2.7 52.2 1.0
CE1 C:HIS1 3.0 63.3 1.0
CD2 C:HIS1 3.1 62.3 1.0
CG C:HIS91 3.2 37.7 1.0
CB C:HIS91 3.3 35.0 1.0
CE1 C:HIS91 3.5 42.3 1.0
ND1 C:HIS1 4.1 63.7 1.0
N C:HIS91 4.2 41.3 1.0
CG C:HIS1 4.2 62.9 1.0
CA C:HIS91 4.4 35.5 1.0
CD2 C:HIS91 4.4 49.2 1.0
NE2 C:HIS91 4.5 50.0 1.0
CG2 C:THR90 5.0 42.1 1.0

Reference:

L.Zhang, M.Koay, M.J.Maher, Z.Xiao, A.G.Wedd. Intermolecular Transfer of Copper Ions From the Copc Protein of Pseudomonas Syringae. Crystal Structures of Fully Loaded Cu(I)Cu(II) Forms. J.Am.Chem.Soc. V. 128 5834 2006.
ISSN: ISSN 0002-7863
PubMed: 16637653
DOI: 10.1021/JA058528X
Page generated: Wed Oct 28 14:18:49 2020
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