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Magnesium in PDB 4g5y: Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase in A Ternary Complex with Atp and N,N-Dimethylthiophene-3- Sulfonamide

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase in A Ternary Complex with Atp and N,N-Dimethylthiophene-3- Sulfonamide

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase in A Ternary Complex with Atp and N,N-Dimethylthiophene-3- Sulfonamide:
6.3.2.1;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase in A Ternary Complex with Atp and N,N-Dimethylthiophene-3- Sulfonamide, PDB code: 4g5y was solved by A.Ciulli, H.L.Silvestre, T.L.Blundell, C.Abell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.57 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.260, 71.060, 81.650, 90.00, 99.35, 90.00
R / Rfree (%) 15.8 / 20.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase in A Ternary Complex with Atp and N,N-Dimethylthiophene-3- Sulfonamide (pdb code 4g5y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase in A Ternary Complex with Atp and N,N-Dimethylthiophene-3- Sulfonamide, PDB code: 4g5y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4g5y

Go back to Magnesium Binding Sites List in 4g5y
Magnesium binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase in A Ternary Complex with Atp and N,N-Dimethylthiophene-3- Sulfonamide


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 Pantothenate Synthetase in A Ternary Complex with Atp and N,N-Dimethylthiophene-3- Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:43.9
occ:1.00
 O A:HOH672 1.8 32.2 1.0
O A:HOH674 2.0 44.2 1.0
O2B A:ATP401 2.1 34.1 1.0
O3G A:ATP401 2.2 37.5 1.0
O A:HOH682 2.3 54.9 1.0
O1A A:ATP401 2.7 47.0 1.0
PB A:ATP401 3.3 34.9 1.0
PG A:ATP401 3.4 41.3 1.0
O3B A:ATP401 3.5 45.4 1.0
OD2 A:ASP161 3.6 33.1 1.0
OD1 A:ASP161 3.7 24.0 1.0
O3A A:ATP401 3.9 38.1 1.0
CG A:ASP161 3.9 28.9 1.0
PA A:ATP401 3.9 33.0 1.0
O A:HOH677 4.0 50.9 1.0
NH2 A:ARG198 4.1 45.5 1.0
NZ A:LYS160 4.1 42.2 1.0
O1G A:ATP401 4.3 43.1 1.0
O A:HOH640 4.4 41.3 1.0
O5' A:ATP401 4.4 30.6 1.0
O A:HOH661 4.5 46.8 1.0
O2G A:ATP401 4.5 44.8 1.0
O1B A:ATP401 4.6 29.2 1.0
CE A:MET40 4.8 34.0 1.0
CZ A:ARG198 4.9 77.5 1.0
O A:HOH683 4.9 49.1 1.0

Magnesium binding site 2 out of 2 in 4g5y

Go back to Magnesium Binding Sites List in 4g5y
Magnesium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Pantothenate Synthetase in A Ternary Complex with Atp and N,N-Dimethylthiophene-3- Sulfonamide


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 Pantothenate Synthetase in A Ternary Complex with Atp and N,N-Dimethylthiophene-3- Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:44.3
occ:1.00
 O1B B:ATP401 2.0 42.0 1.0
O B:HOH689 2.1 47.2 1.0
O B:HOH691 2.2 39.4 1.0
O3G B:ATP401 2.2 39.6 1.0
O B:HOH690 2.2 46.4 1.0
O2A B:ATP401 2.6 50.7 1.0
PB B:ATP401 3.1 46.9 1.0
PG B:ATP401 3.4 39.6 1.0
O3B B:ATP401 3.5 37.8 1.0
C1 B:GOL405 3.6 39.7 0.5
O3A B:ATP401 3.7 39.8 1.0
PA B:ATP401 3.8 38.8 1.0
OD2 B:ASP161 3.8 26.9 1.0
OD1 B:ASP161 3.9 23.6 1.0
O B:HOH658 4.1 40.7 1.0
NH2 B:ARG198 4.1 50.3 1.0
CG B:ASP161 4.2 28.7 1.0
O2G B:ATP401 4.3 46.4 1.0
O5' B:ATP401 4.4 33.3 1.0
NZ B:LYS160 4.4 55.6 1.0
O B:HOH693 4.4 38.9 1.0
O1G B:ATP401 4.4 37.6 1.0
O2B B:ATP401 4.4 46.9 1.0
CE B:MET40 4.5 40.0 1.0
O1 B:GOL405 4.5 24.8 0.5
C2 B:GOL405 4.6 18.5 0.5
CE B:LYS160 4.8 39.5 1.0
C3 B:GOL405 4.9 62.0 0.5

Reference:

H.L.Silvestre, T.L.Blundell, C.Abell, A.Ciulli. Integrated Biophysical Approach to Fragment Screening and Validation For Fragment-Based Lead Discovery. Proc.Natl.Acad.Sci.Usa V. 110 12984 2013.
ISSN: ISSN 0027-8424
PubMed: 23872845
DOI: 10.1073/PNAS.1304045110
Page generated: Mon Aug 11 13:07:53 2025

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