Zinc in PDB 1vcv: Structure of 2-Deoxyribose-5-Phosphate Aldolase From Pyrobaculum Aerophilum

All present enzymatic activity of Structure of 2-Deoxyribose-5-Phosphate Aldolase From Pyrobaculum Aerophilum:
4.1.2.4;

The structure of Structure of 2-Deoxyribose-5-Phosphate Aldolase From Pyrobaculum Aerophilum, PDB code: 1vcv was solved by H.Sakuraba, T.Ohshima, H.Tsuge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.07 / 2.00
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	84.540, 84.540, 112.620, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 24.1

The binding sites of Zinc atom in the Structure of 2-Deoxyribose-5-Phosphate Aldolase From Pyrobaculum Aerophilum (pdb code 1vcv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of 2-Deoxyribose-5-Phosphate Aldolase From Pyrobaculum Aerophilum, PDB code: 1vcv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of 2-Deoxyribose-5-Phosphate Aldolase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of 2-Deoxyribose-5-Phosphate Aldolase From Pyrobaculum Aerophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:37.2 occ:1.00 OD2 A:ASP211 2.4 34.6 1.0 CG A:ASP211 2.9 30.2 1.0 OD1 A:ASP211 3.1 29.0 1.0 O A:HOH1046 3.3 56.8 1.0 CG A:ARG214 3.8 36.1 1.0 CD A:ARG214 3.9 40.6 1.0 CB A:ASP211 4.0 27.0 1.0 NE A:ARG214 4.2 46.5 1.0 CB A:ALA213 4.4 27.7 1.0 CB A:ARG214 4.6 30.4 1.0 N A:ARG214 4.9 28.7 1.0

Zinc binding site 2 out of 2 in the Structure of 2-Deoxyribose-5-Phosphate Aldolase From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of 2-Deoxyribose-5-Phosphate Aldolase From Pyrobaculum Aerophilum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:29.1 occ:1.00 OD1 B:ASP211 2.0 25.2 1.0 CG B:ASP211 2.8 24.7 1.0 OD2 B:ASP211 3.1 20.8 1.0 CB B:ASP211 4.2 22.6 1.0 O B:HOH1083 4.3 32.5 1.0 CB B:ALA213 4.5 23.7 1.0 CD B:ARG214 4.5 42.1 1.0 CG B:ARG214 4.7 37.3 1.0

H.Sakuraba, K.Yoneda, K.Yoshihara, K.Satoh, R.Kawakami, Y.Uto, H.Tsuge, K.Takahashi, H.Hori, T.Ohshima. Sequential Aldol Condensation Catalyzed By Hyperthermophilic 2-Deoxy-D-Ribose-5-Phosphate Aldolase Appl.Environ.Microbiol. V. 73 7427 2007.
ISSN: ISSN 0099-2240
PubMed: 17905878
DOI: 10.1128/AEM.01101-07