Zinc in PDB 1oj7: Structural Genomics, Unknown Function Crystal Structure of E. Coli K-12 Yqhd

The structure of Structural Genomics, Unknown Function Crystal Structure of E. Coli K-12 Yqhd, PDB code: 1oj7 was solved by G.Sulzenbacher, S.Perrier, V.Roig-Zamboni, F.Pagot, S.Grisel, A.Salamoni, C.Valencia, C.Bignon, R.Vincentelli, M.Tegoni, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.00 / 2.0
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	237.925, 237.925, 66.744, 90.00, 90.00, 120.00
R / Rfree (%)	14.5 / 16.4

The structure of Structural Genomics, Unknown Function Crystal Structure of E. Coli K-12 Yqhd also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Structural Genomics, Unknown Function Crystal Structure of E. Coli K-12 Yqhd (pdb code 1oj7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structural Genomics, Unknown Function Crystal Structure of E. Coli K-12 Yqhd, PDB code: 1oj7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structural Genomics, Unknown Function Crystal Structure of E. Coli K-12 Yqhd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Genomics, Unknown Function Crystal Structure of E. Coli K-12 Yqhd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1389 b:38.3 occ:1.00 O5N B:NZQ1388 1.7 47.8 1.0 OD1 B:ASP194 2.0 37.0 1.0 NE2 B:HIS267 2.1 31.5 1.0 NE2 B:HIS281 2.1 31.8 1.0 NE2 B:HIS198 2.6 38.5 1.0 C5N B:NZQ1388 2.8 47.7 1.0 CG B:ASP194 2.9 34.3 1.0 OD2 B:ASP194 2.9 35.2 1.0 CD2 B:HIS267 3.0 31.0 1.0 CD2 B:HIS281 3.0 31.6 1.0 CE1 B:HIS281 3.2 32.0 1.0 CE1 B:HIS267 3.2 32.7 1.0 CD2 B:HIS198 3.3 38.0 1.0 C6N B:NZQ1388 3.4 49.1 1.0 CE1 B:HIS198 3.5 38.8 1.0 O6N B:NZQ1388 3.7 49.7 1.0 CD1 B:LEU285 3.8 30.3 1.0 C4N B:NZQ1388 4.0 49.2 1.0 CG B:HIS267 4.2 31.3 1.0 CG B:HIS281 4.2 32.4 1.0 ND1 B:HIS267 4.2 30.2 1.0 ND1 B:HIS281 4.2 32.6 1.0 CB B:ASP194 4.3 33.1 1.0 CG B:HIS198 4.4 35.2 1.0 ND1 B:HIS198 4.5 37.0 1.0 O B:HOH2418 4.6 55.4 1.0 O B:ASP194 4.6 31.7 1.0 N1N B:NZQ1388 4.7 47.3 1.0 CA B:ASP194 4.7 32.9 1.0 CG B:LEU285 4.8 30.9 1.0 CD2 B:LEU285 4.9 30.9 1.0

Zinc binding site 2 out of 3 in the Structural Genomics, Unknown Function Crystal Structure of E. Coli K-12 Yqhd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Genomics, Unknown Function Crystal Structure of E. Coli K-12 Yqhd within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1388 b:41.3 occ:1.00 NE2 C:HIS267 2.1 34.3 1.0 OD1 C:ASP194 2.2 38.9 1.0 NE2 C:HIS281 2.2 36.3 1.0 NE2 C:HIS198 2.3 43.4 1.0 O2 C:BO31390 2.4 59.0 1.0 O3 C:BO31390 2.5 58.6 1.0 B C:BO31390 2.8 58.8 1.0 CG C:ASP194 3.0 37.4 1.0 OD2 C:ASP194 3.0 42.1 1.0 CD2 C:HIS198 3.0 40.6 1.0 CD2 C:HIS267 3.1 34.5 1.0 CE1 C:HIS281 3.1 37.7 1.0 CE1 C:HIS267 3.1 33.4 1.0 CD2 C:HIS281 3.2 35.9 1.0 CE1 C:HIS198 3.5 44.5 1.0 CD1 C:LEU285 4.1 31.6 1.0 O1 C:BO31390 4.1 60.8 1.0 ND1 C:HIS267 4.2 33.5 1.0 CG C:HIS267 4.2 32.1 1.0 CG C:HIS198 4.2 37.6 1.0 ND1 C:HIS281 4.3 37.2 1.0 CG C:HIS281 4.3 36.9 1.0 CB C:ASP194 4.4 34.2 1.0 ND1 C:HIS198 4.4 42.4 1.0 O C:ASP194 4.8 31.6 1.0 CA C:ASP194 4.9 33.2 1.0

Zinc binding site 3 out of 3 in the Structural Genomics, Unknown Function Crystal Structure of E. Coli K-12 Yqhd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Genomics, Unknown Function Crystal Structure of E. Coli K-12 Yqhd within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1389 b:41.3 occ:1.00 O5N D:NZQ1388 1.9 46.8 1.0 OD1 D:ASP194 2.0 37.8 1.0 NE2 D:HIS281 2.1 36.1 1.0 NE2 D:HIS267 2.1 32.8 1.0 NE2 D:HIS198 2.6 40.0 1.0 CG D:ASP194 2.9 36.7 1.0 C5N D:NZQ1388 2.9 48.5 1.0 CD2 D:HIS267 3.0 34.4 1.0 CD2 D:HIS281 3.0 37.5 1.0 OD2 D:ASP194 3.0 37.2 1.0 CE1 D:HIS267 3.1 34.0 1.0 CE1 D:HIS281 3.2 35.6 1.0 CD2 D:HIS198 3.3 38.1 1.0 CE1 D:HIS198 3.5 40.8 1.0 C6N D:NZQ1388 3.5 49.2 1.0 CD1 D:LEU285 3.7 36.2 1.0 O6N D:NZQ1388 3.9 49.6 1.0 CG D:HIS267 4.1 34.1 1.0 CG D:HIS281 4.2 37.6 1.0 C4N D:NZQ1388 4.2 50.9 1.0 ND1 D:HIS267 4.2 33.3 1.0 ND1 D:HIS281 4.2 37.8 1.0 CB D:ASP194 4.3 36.3 1.0 CG D:HIS198 4.4 36.7 1.0 ND1 D:HIS198 4.5 39.1 1.0 O D:HOH2283 4.7 52.1 1.0 O D:ASP194 4.7 34.7 1.0 CA D:ASP194 4.7 35.5 1.0 CG D:LEU285 4.8 36.0 1.0 N1N D:NZQ1388 4.8 49.5 1.0 CD2 D:LEU285 4.9 36.7 1.0

G.Sulzenbacher, K.Alvarez, R.H.H.Van-Den-Heuvel, C.Versluis, S.Spinelli, V.Campanacci, C.Valencia, C.Cambillau, H.Eklund, M.Tegoni. Crystal Structure of E.Coli Alcohol Dehydrogenase Yqhd: Evidence of A Covalently Modified Nadp Coenzyme J.Mol.Biol. V. 342 489 2004.
ISSN: ISSN 0022-2836
PubMed: 15327949
DOI: 10.1016/J.JMB.2004.07.034