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Zinc in PDB 2a21: Aquifex Aeolicus KDO8PS in Complex with Pep, PO4, and ZN2+

Enzymatic activity of Aquifex Aeolicus KDO8PS in Complex with Pep, PO4, and ZN2+

All present enzymatic activity of Aquifex Aeolicus KDO8PS in Complex with Pep, PO4, and ZN2+:
2.5.1.55;

Protein crystallography data

The structure of Aquifex Aeolicus KDO8PS in Complex with Pep, PO4, and ZN2+, PDB code: 2a21 was solved by F.Kona, X.Xu, J.Lu, P.Martin, D.L.Gatti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.86 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.527, 84.527, 159.752, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 21

Zinc Binding Sites:

The binding sites of Zinc atom in the Aquifex Aeolicus KDO8PS in Complex with Pep, PO4, and ZN2+ (pdb code 2a21). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Aquifex Aeolicus KDO8PS in Complex with Pep, PO4, and ZN2+, PDB code: 2a21:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2a21

Go back to Zinc Binding Sites List in 2a21
Zinc binding site 1 out of 2 in the Aquifex Aeolicus KDO8PS in Complex with Pep, PO4, and ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Aquifex Aeolicus KDO8PS in Complex with Pep, PO4, and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1270

b:33.5
occ:0.50
OE1 A:GLU1222 1.9 36.6 1.0
OD1 A:ASP1233 2.0 48.1 1.0
NE2 A:HIS1185 2.4 27.9 1.0
CD A:GLU1222 2.5 37.0 1.0
OE2 A:GLU1222 2.5 37.0 1.0
SG A:CYS1011 2.5 36.9 1.0
O A:HOH176 2.7 44.4 1.0
CE1 A:HIS1185 3.1 26.9 1.0
CG A:ASP1233 3.2 46.2 1.0
CD2 A:HIS1185 3.5 28.0 1.0
CB A:CYS1011 3.5 30.4 1.0
CB A:ASP1233 3.9 43.0 1.0
CG A:GLU1222 3.9 35.0 1.0
OD2 A:ASP1233 4.1 47.6 1.0
ND1 A:HIS1185 4.3 25.5 1.0
NZ A:LYS1046 4.3 29.0 1.0
CA A:CYS1011 4.3 29.2 1.0
O1 A:PEP1268 4.4 27.1 1.0
CG A:HIS1185 4.5 24.6 1.0
C1 A:PEP1268 4.5 26.8 1.0
NZ A:LYS1041 4.7 23.2 1.0
O2' A:PEP1268 4.8 25.6 1.0
CB A:GLU1222 4.8 29.8 1.0
CE A:LYS1046 5.0 28.9 1.0

Zinc binding site 2 out of 2 in 2a21

Go back to Zinc Binding Sites List in 2a21
Zinc binding site 2 out of 2 in the Aquifex Aeolicus KDO8PS in Complex with Pep, PO4, and ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Aquifex Aeolicus KDO8PS in Complex with Pep, PO4, and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2270

b:39.1
occ:0.50
OD1 B:ASP2233 1.9 52.0 1.0
OE1 B:GLU2222 1.9 41.3 1.0
CD B:GLU2222 2.4 37.8 1.0
OE2 B:GLU2222 2.4 39.5 1.0
NE2 B:HIS2185 2.4 32.5 1.0
SG B:CYS2011 2.5 38.2 1.0
CE1 B:HIS2185 2.9 31.6 1.0
CG B:ASP2233 3.0 50.9 1.0
CB B:CYS2011 3.5 34.0 1.0
O B:HOH224 3.5 44.5 1.0
CD2 B:HIS2185 3.6 31.8 1.0
CB B:ASP2233 3.8 48.9 1.0
CG B:GLU2222 3.9 37.4 1.0
OD2 B:ASP2233 4.0 50.2 1.0
ND1 B:HIS2185 4.1 29.7 1.0
NZ B:LYS2046 4.2 28.1 1.0
CA B:CYS2011 4.3 31.4 1.0
O1 B:PEP2268 4.4 29.6 1.0
CG B:HIS2185 4.4 30.4 1.0
C1 B:PEP2268 4.5 30.5 1.0
O B:HOH299 4.7 48.5 1.0
CB B:GLU2222 4.7 33.0 1.0
NZ B:LYS2041 4.7 26.7 1.0
O2' B:PEP2268 4.8 24.7 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 Dec 16 03:16:27 2020

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