Atomistry » Magnesium » PDB 5t2v-5tfb » 5t8g
Atomistry »
  Magnesium »
    PDB 5t2v-5tfb »
      5t8g »

Magnesium in PDB 5t8g: Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid:
2.3.3.9;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid, PDB code: 5t8g was solved by H.-L.Huang, J.C.Sacchetiini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.01 / 2.04
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.850, 78.850, 224.934, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid (pdb code 5t8g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid, PDB code: 5t8g:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5t8g

Go back to Magnesium Binding Sites List in 5t8g
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:21.3
occ:1.00
 O08 A:4Z0804 2.0 24.2 1.0
OD2 A:ASP462 2.0 23.9 1.0
O A:HOH1045 2.1 22.6 1.0
O10 A:4Z0804 2.1 27.0 1.0
O A:HOH996 2.1 18.8 1.0
OE2 A:GLU434 2.1 22.5 1.0
C06 A:4Z0804 2.7 26.9 1.0
C07 A:4Z0804 2.7 23.6 1.0
CG A:ASP462 3.0 24.1 1.0
CD A:GLU434 3.1 21.9 1.0
OE1 A:GLU434 3.5 19.2 1.0
CB A:ASP462 3.5 19.5 1.0
NZ A:LYS399 3.9 21.4 1.0
NH1 A:ARG339 4.0 21.8 1.0
O09 A:4Z0804 4.0 23.3 1.0
OD1 A:ASP462 4.1 22.3 1.0
OD2 A:ASP274 4.2 26.9 1.0
C05 A:4Z0804 4.2 26.2 1.0
OD2 A:ASP633 4.2 29.1 1.0
CB A:ALA635 4.4 19.8 1.0
CG A:GLU434 4.4 19.9 1.0
N A:ASP462 4.4 18.3 1.0
OD1 A:ASP633 4.5 27.7 1.0
CA A:ASP462 4.5 21.1 1.0
OE1 A:GLU273 4.5 21.7 1.0
CB A:GLU434 4.7 22.6 1.0
CG A:ASP633 4.8 27.0 1.0
CZ A:ARG339 4.9 24.6 1.0
CG A:ASP274 4.9 25.1 1.0
C04 A:4Z0804 4.9 26.5 1.0
NH2 A:ARG339 5.0 22.9 1.0

Magnesium binding site 2 out of 3 in 5t8g

Go back to Magnesium Binding Sites List in 5t8g
Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:40.2
occ:1.00
 O A:HOH1054 1.9 41.8 1.0
O A:HOH1048 2.0 37.1 1.0
O A:HOH1365 2.2 40.7 1.0
O A:HOH1457 2.3 50.4 1.0
O A:HOH961 2.3 41.2 1.0
NE2 A:HIS235 2.4 33.5 1.0
CE1 A:HIS235 3.1 32.1 1.0
CD2 A:HIS235 3.5 30.7 1.0
O A:HOH1287 4.0 46.0 1.0
ND1 A:HIS235 4.3 29.9 1.0
OD1 A:ASN234 4.4 28.9 1.0
CG A:HIS235 4.5 31.2 1.0
OD2 A:ASP559 4.6 34.1 1.0
CB A:ASP559 4.7 31.0 1.0
O A:HIS556 5.0 28.3 1.0
O A:HOH1458 5.0 58.6 1.0

Magnesium binding site 3 out of 3 in 5t8g

Go back to Magnesium Binding Sites List in 5t8g
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mycobacterium Tuberculosis Malate Synthase in Complex with 2-Oxo-4-((Thiophene-2-Carbonyl)Oxy)Butanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:24.5
occ:1.00
 OG1 A:THR482 3.1 27.8 1.0
NE A:ARG479 3.2 32.9 1.0
NE1 A:TRP589 3.2 33.7 1.0
N A:ARG479 3.3 22.6 1.0
CB A:VAL478 3.6 22.8 1.0
CG A:ARG479 3.7 28.8 1.0
CB A:THR482 3.8 26.8 1.0
CB A:ARG479 3.9 21.6 1.0
CA A:VAL478 4.0 21.8 1.0
CG2 A:THR482 4.0 25.7 1.0
NH2 A:ARG479 4.0 35.3 1.0
CZ A:ARG479 4.1 39.5 1.0
CD A:ARG479 4.1 29.5 1.0
CG1 A:VAL478 4.1 23.5 1.0
C A:VAL478 4.1 26.3 1.0
CE2 A:TRP589 4.2 33.2 1.0
CA A:ARG479 4.2 26.2 1.0
CD1 A:TRP589 4.2 37.3 1.0
CZ2 A:TRP589 4.4 33.8 1.0
CG2 A:VAL478 4.8 23.8 1.0
O A:HOH1182 4.8 34.0 1.0
O A:ARG479 5.0 26.8 1.0

Reference:

H.L.Huang, I.V.Krieger, M.K.Parai, V.B.Gawandi, J.C.Sacchettini. Mycobacterium Tuberculosis Malate Synthase Structures with Fragments Reveal A Portal For Substrate/Product Exchange. J. Biol. Chem. V. 291 27421 2016.
ISSN: ESSN 1083-351X
PubMed: 27738104
DOI: 10.1074/JBC.M116.750877
Page generated: Mon Sep 30 04:46:10 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy