Zinc in PDB 2a2i: Aquifex Aeolicus KDO8PS in Complex with Pep, A5P, ZN2+

All present enzymatic activity of Aquifex Aeolicus KDO8PS in Complex with Pep, A5P, ZN2+:
2.5.1.55;

The structure of Aquifex Aeolicus KDO8PS in Complex with Pep, A5P, ZN2+, PDB code: 2a2i 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)	25.47 / 1.95
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.272, 84.272, 159.844, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 22.9

The binding sites of Zinc atom in the Aquifex Aeolicus KDO8PS in Complex with Pep, A5P, ZN2+ (pdb code 2a2i). 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, A5P, ZN2+, PDB code: 2a2i:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Aquifex Aeolicus KDO8PS in Complex with Pep, A5P, 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, A5P, ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1270 b:57.8 occ:0.50 OE1 A:GLU1222 2.0 58.1 1.0 OD1 A:ASP1233 2.2 64.0 1.0 SG A:CYS1011 2.4 54.5 1.0 OE2 A:GLU1222 2.5 56.9 1.0 NE2 A:HIS1185 2.5 51.3 1.0 CD A:GLU1222 2.5 57.1 1.0 O3 A:A5P1269 3.0 77.5 1.0 CG A:ASP1233 3.2 63.1 1.0 CE1 A:HIS1185 3.2 50.4 1.0 CB A:CYS1011 3.4 48.1 1.0 CD2 A:HIS1185 3.7 49.1 1.0 NZ A:LYS1046 3.9 47.9 1.0 OD2 A:ASP1233 3.9 64.2 1.0 CG A:GLU1222 4.0 53.8 1.0 CA A:CYS1011 4.1 47.4 1.0 CB A:ASP1233 4.1 61.9 1.0 O1 A:PEP1268 4.2 53.8 1.0 C1 A:PEP1268 4.2 53.3 1.0 C3 A:A5P1269 4.4 77.6 1.0 ND1 A:HIS1185 4.4 49.5 1.0 O2' A:PEP1268 4.5 51.6 1.0 NZ A:LYS1041 4.6 39.0 1.0 CE A:LYS1046 4.6 45.3 1.0 CG A:HIS1185 4.7 48.0 1.0 O2 A:A5P1269 4.7 80.6 1.0 C2 A:PEP1268 4.8 52.4 1.0 C A:CYS1011 4.9 48.5 1.0 CB A:GLU1222 4.9 47.9 1.0 O A:CYS1011 5.0 49.6 1.0 O4 A:A5P1269 5.0 78.7 1.0

Zinc binding site 2 out of 2 in the Aquifex Aeolicus KDO8PS in Complex with Pep, A5P, 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, A5P, ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2270 b:57.1 occ:0.50 OD2 B:ASP2233 2.1 71.8 1.0 OE2 B:GLU2222 2.2 59.2 1.0 OE1 B:GLU2222 2.2 57.9 1.0 SG B:CYS2011 2.3 50.2 1.0 CD B:GLU2222 2.5 56.2 1.0 NE2 B:HIS2185 2.5 57.5 1.0 CE1 B:HIS2185 3.1 57.0 1.0 O2 B:A5P2269 3.2 78.1 1.0 CB B:CYS2011 3.2 48.2 1.0 CG B:ASP2233 3.3 70.1 1.0 CD2 B:HIS2185 3.7 55.6 1.0 O3 B:A5P2269 3.7 81.8 1.0 CG B:GLU2222 4.0 54.2 1.0 CA B:CYS2011 4.1 46.3 1.0 NZ B:LYS2046 4.1 41.7 1.0 CB B:ASP2233 4.1 67.7 1.0 O1 B:PEP2268 4.3 54.3 1.0 OD1 B:ASP2233 4.3 70.1 1.0 ND1 B:HIS2185 4.3 56.1 1.0 C2 B:A5P2269 4.3 78.8 1.0 C1 B:PEP2268 4.4 55.5 1.0 NZ B:LYS2041 4.6 44.8 1.0 C3 B:A5P2269 4.6 78.9 1.0 OG B:SER2232 4.6 69.7 1.0 CG B:HIS2185 4.7 53.7 1.0 CE B:LYS2046 4.7 41.4 1.0 O2' B:PEP2268 4.7 52.4 1.0 C B:CYS2011 4.8 45.5 1.0 C2 B:PEP2268 4.8 53.6 1.0 CB B:GLU2222 4.9 49.3 1.0 NE2 B:GLN2188 4.9 75.6 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