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Copper in PDB 3e12: CU2+ Substituted Aquifex Aeolicus KDO8PS in Complex with KDO8P

Enzymatic activity of CU2+ Substituted Aquifex Aeolicus KDO8PS in Complex with KDO8P

All present enzymatic activity of CU2+ Substituted Aquifex Aeolicus KDO8PS in Complex with KDO8P:
2.5.1.55;

Protein crystallography data

The structure of CU2+ Substituted Aquifex Aeolicus KDO8PS in Complex with KDO8P, PDB code: 3e12 was solved by D.L.Gatti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.30 / 1.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.747, 84.747, 160.309, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 19.6

Copper Binding Sites:

The binding sites of Copper atom in the CU2+ Substituted Aquifex Aeolicus KDO8PS in Complex with KDO8P (pdb code 3e12). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the CU2+ Substituted Aquifex Aeolicus KDO8PS in Complex with KDO8P, PDB code: 3e12:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 3e12

Go back to Copper Binding Sites List in 3e12
Copper binding site 1 out of 2 in the CU2+ Substituted Aquifex Aeolicus KDO8PS in Complex with KDO8P


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of CU2+ Substituted Aquifex Aeolicus KDO8PS in Complex with KDO8P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu270

b:14.7
occ:0.70
NE2 A:HIS185 2.0 18.2 1.0
OE1 A:GLU222 2.1 19.9 1.0
OD2 A:ASP233 2.2 36.5 1.0
SG A:CYS11 2.2 19.3 1.0
CD A:GLU222 2.8 20.0 1.0
CE1 A:HIS185 2.8 19.8 1.0
OE2 A:GLU222 2.9 18.7 1.0
O4 A:KD0268 3.0 21.6 0.9
CD2 A:HIS185 3.2 20.1 1.0
CG A:ASP233 3.3 26.8 1.0
CB A:CYS11 3.3 17.1 1.0
CB A:ASP233 3.8 23.3 1.0
NE2 A:GLN237 3.9 27.6 0.4
ND1 A:HIS185 4.0 18.7 1.0
CA A:CYS11 4.1 16.4 1.0
C4 A:KD0268 4.1 23.1 0.9
NZ A:LYS46 4.2 18.0 1.0
CG A:HIS185 4.2 16.9 1.0
CG A:GLU222 4.3 19.4 1.0
C2 A:KD0268 4.3 22.6 0.9
NZ A:LYS41 4.3 15.8 1.0
O2 A:KD0268 4.4 22.3 0.9
OD1 A:ASP233 4.4 33.2 1.0
C1 A:KD0268 4.5 24.1 0.9
CD A:GLN237 4.5 25.3 0.4
OE1 A:GLN237 4.5 30.0 0.4
O1 A:KD0268 4.7 21.8 0.9
CG2 A:THR184 4.7 20.0 1.0
C3 A:KD0268 4.8 23.2 0.9
CB A:GLU222 4.8 18.0 1.0
O6 A:KD0268 4.9 23.2 0.9
O3 A:KD0268 4.9 27.7 0.9
C A:CYS11 4.9 17.0 1.0
OG A:SER232 5.0 20.7 0.5

Copper binding site 2 out of 2 in 3e12

Go back to Copper Binding Sites List in 3e12
Copper binding site 2 out of 2 in the CU2+ Substituted Aquifex Aeolicus KDO8PS in Complex with KDO8P


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of CU2+ Substituted Aquifex Aeolicus KDO8PS in Complex with KDO8P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu270

b:18.1
occ:0.80
NE2 B:HIS185 2.1 19.8 1.0
OE1 B:GLU222 2.2 22.3 1.0
SG B:CYS11 2.3 20.5 1.0
OD2 B:ASP233 2.5 35.3 1.0
CD B:GLU222 2.8 20.4 1.0
OE2 B:GLU222 2.9 22.2 1.0
CE1 B:HIS185 2.9 19.8 1.0
O4 B:KD0268 3.0 22.2 0.9
CD2 B:HIS185 3.2 21.9 1.0
CB B:CYS11 3.3 19.4 1.0
OE1 B:GLN237 3.3 24.6 0.4
CG B:ASP233 3.5 28.3 1.0
CB B:ASP233 3.7 25.4 1.0
ND1 B:HIS185 4.1 19.8 1.0
CA B:CYS11 4.1 18.5 1.0
C4 B:KD0268 4.1 23.3 0.9
NZ B:LYS46 4.2 17.6 1.0
CG B:HIS185 4.2 17.9 1.0
C2 B:KD0268 4.3 25.8 0.9
CG B:GLU222 4.3 21.4 1.0
O2 B:KD0268 4.4 23.2 0.9
CD B:GLN237 4.4 20.9 0.4
NZ B:LYS41 4.4 18.8 1.0
C1 B:KD0268 4.5 25.9 0.9
NE2 B:GLN188 4.5 38.6 0.5
OD1 B:ASP233 4.6 31.2 1.0
CG2 B:THR184 4.6 18.4 1.0
O1 B:KD0268 4.7 22.4 0.9
C3 B:KD0268 4.8 25.5 0.9
CB B:GLU222 4.8 20.2 1.0
NE2 B:GLN237 4.8 22.8 0.4
O3 B:KD0268 4.9 25.1 0.9
O6 B:KD0268 4.9 24.2 0.9
OG B:SER232 5.0 23.9 0.5
C B:CYS11 5.0 18.9 1.0

Reference:

F.Kona, P.Tao, P.Martin, X.Xu, D.L.Gatti. Electronic Structure of the Metal Center in the Cd(2+), Zn(2+), and Cu(2+) Substituted Forms of KDO8P Synthase: Implications For Catalysis. Biochemistry V. 48 3610 2009.
ISSN: ISSN 0006-2960
PubMed: 19228070
DOI: 10.1021/BI801955H
Page generated: Wed Oct 28 14:23:41 2020
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