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Zinc in PDB 3eb9: Crystal Structure of 6-Phosphogluconolactonase From Trypanosoma Brucei Complexed with Citrate

Enzymatic activity of Crystal Structure of 6-Phosphogluconolactonase From Trypanosoma Brucei Complexed with Citrate

All present enzymatic activity of Crystal Structure of 6-Phosphogluconolactonase From Trypanosoma Brucei Complexed with Citrate:
3.1.1.17;

Protein crystallography data

The structure of Crystal Structure of 6-Phosphogluconolactonase From Trypanosoma Brucei Complexed with Citrate, PDB code: 3eb9 was solved by L.Poggi, M.Delarue, N.Duclert-Savatier, V.Stoven, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.58 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.460, 87.210, 64.790, 90.00, 96.53, 90.00
R / Rfree (%) 19.5 / 24.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 6-Phosphogluconolactonase From Trypanosoma Brucei Complexed with Citrate (pdb code 3eb9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of 6-Phosphogluconolactonase From Trypanosoma Brucei Complexed with Citrate, PDB code: 3eb9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3eb9

Go back to Zinc Binding Sites List in 3eb9
Zinc binding site 1 out of 2 in the Crystal Structure of 6-Phosphogluconolactonase From Trypanosoma Brucei Complexed with Citrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 6-Phosphogluconolactonase From Trypanosoma Brucei Complexed with Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:27.6
occ:1.00
OD1 A:ASP98 1.9 23.3 1.0
NE2 A:HIS56 2.0 22.1 1.0
NE2 A:HIS97 2.0 23.4 1.0
O A:HOH304 2.6 23.6 1.0
CE1 A:HIS56 2.9 22.2 1.0
CG A:ASP98 2.9 22.4 1.0
CE1 A:HIS97 3.0 23.2 1.0
CD2 A:HIS56 3.0 21.3 1.0
CD2 A:HIS97 3.0 23.3 1.0
OD2 A:ASP98 3.4 24.3 1.0
ND1 A:HIS56 4.0 22.8 1.0
ND1 A:HIS97 4.1 24.0 1.0
CG A:HIS56 4.1 21.5 1.0
CB A:ASP98 4.1 19.9 1.0
CG A:HIS97 4.2 21.8 1.0
O A:HOH305 4.6 46.4 1.0
O A:HOH364 4.9 32.5 1.0

Zinc binding site 2 out of 2 in 3eb9

Go back to Zinc Binding Sites List in 3eb9
Zinc binding site 2 out of 2 in the Crystal Structure of 6-Phosphogluconolactonase From Trypanosoma Brucei Complexed with Citrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of 6-Phosphogluconolactonase From Trypanosoma Brucei Complexed with Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:24.2
occ:1.00
OD1 B:ASP98 2.0 26.0 1.0
NE2 B:HIS97 2.1 18.5 1.0
NE2 B:HIS56 2.2 26.3 1.0
O B:HOH319 2.8 28.4 1.0
CG B:ASP98 3.0 25.2 1.0
CD2 B:HIS56 3.0 25.8 1.0
CD2 B:HIS97 3.0 18.4 1.0
CE1 B:HIS97 3.1 18.4 1.0
CE1 B:HIS56 3.3 25.7 1.0
OD2 B:ASP98 3.3 24.4 1.0
CG B:HIS97 4.2 19.2 1.0
ND1 B:HIS97 4.2 20.2 1.0
CG B:HIS56 4.2 23.8 1.0
CB B:ASP98 4.2 21.7 1.0
ND1 B:HIS56 4.3 25.5 1.0
O B:HOH444 4.9 46.3 1.0
O B:HOH269 4.9 48.0 1.0

Reference:

N.Duclert-Savatier, L.Poggi, E.Miclet, P.Lopes, J.Ouazzani, N.Chevalier, M.Nilges, M.Delarue, V.Stoven. Insights Into the Enzymatic Mechanism of 6-Phosphogluconolactonase From Trypanosoma Brucei Using Structural Data and Molecular Dynamics Simulation. J.Mol.Biol. V. 388 1009 2009.
ISSN: ISSN 0022-2836
PubMed: 19345229
DOI: 10.1016/J.JMB.2009.03.063
Page generated: Wed Dec 16 04:15:27 2020

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