Zinc in PDB 2a21: 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;

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

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 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 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

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