Atomistry » Zinc » PDB 1r22-1rad » 1vcv
Atomistry »
  Zinc »
    PDB 1r22-1rad »
      1vcv »

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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 1vcv

Go back to Zinc Binding Sites List in 1vcv
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 1vcv

Go back to Zinc Binding Sites List in 1vcv
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

Reference:

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
Page generated: Fri Sep 25 23:53:35 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy