Magnesium in PDB 6h59: Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound:
2.7.8.11;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound, PDB code: 6h59 was solved by K.Grave, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.62 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.986, 115.080, 45.472, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound (pdb code 6h59). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound, PDB code: 6h59:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6h59

Go back to Magnesium Binding Sites List in 6h59
Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound


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 Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:26.6
occ:1.00
OD1 A:ASP93 1.9 21.6 1.0
O A:HOH401 2.0 26.7 1.0
O A:HOH407 2.0 21.4 1.0
OD1 A:ASP89 2.1 17.3 0.7
O A:HOH402 2.1 20.7 1.0
O A:ASP89 2.3 15.6 0.3
O A:ASP89 2.3 13.7 0.7
OD1 A:ASP89 2.5 17.6 0.3
OD2 A:ASP89 2.6 24.3 0.3
CG A:ASP89 2.6 17.5 0.3
CG A:ASP93 2.6 20.3 1.0
OD2 A:ASP68 2.8 44.5 1.0
OD2 A:ASP93 2.9 24.3 1.0
CG A:ASP89 3.1 18.4 0.7
C A:ASP89 3.1 13.8 0.7
C A:ASP89 3.1 13.7 0.3
HA A:ASP89 3.4 14.4 0.7
HA A:ASP89 3.5 15.2 0.3
H A:ASP93 3.6 14.8 1.0
CA A:ASP89 3.6 12.0 0.7
CA A:ASP89 3.6 12.7 0.3
CB A:ASP89 3.7 14.2 0.3
CB A:ASP89 3.7 13.9 0.7
HB3 A:ASP89 3.8 16.8 0.7
CG A:ASP68 3.8 41.5 1.0
CB A:ASP93 3.9 15.1 1.0
N A:ASP93 4.0 12.4 1.0
HB2 A:CYS92 4.0 14.7 1.0
OD2 A:ASP89 4.0 14.6 0.7
OD1 A:ASP68 4.0 27.7 1.0
HA A:ALA90 4.1 14.5 1.0
O16 A:FQT309 4.1 24.1 1.0
O A:HOH417 4.1 30.5 1.0
HB2 A:ASP89 4.2 17.0 0.3
N A:ALA90 4.2 11.4 1.0
HA A:ASP93 4.2 16.0 1.0
HB2 A:ASP93 4.3 18.1 1.0
O A:HOH440 4.3 48.9 1.0
CA A:ASP93 4.3 13.3 1.0
HB3 A:ASP89 4.4 17.0 0.3
O17 A:FQT309 4.4 39.5 1.0
HH12 A:ARG152 4.4 38.2 1.0
O A:HOH412 4.5 27.2 1.0
O B:HOH411 4.5 28.2 1.0
HG23 A:THR34 4.6 13.1 1.0
MG A:MG302 4.6 27.7 1.0
HB3 A:ASP93 4.6 18.1 1.0
CA A:ALA90 4.6 12.1 1.0
HB2 A:ASP89 4.6 16.8 0.7
NH1 A:ARG152 4.7 31.9 1.0
HH11 A:ARG152 4.8 38.2 1.0
C A:CYS92 4.8 10.9 1.0
CB A:CYS92 4.8 12.3 1.0
HB3 A:CYS92 4.9 14.7 1.0
H A:ALA90 4.9 13.6 0.3
H A:ALA90 4.9 13.6 0.7
P15 A:FQT309 4.9 35.1 1.0

Magnesium binding site 2 out of 4 in 6h59

Go back to Magnesium Binding Sites List in 6h59
Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound


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 Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:27.7
occ:1.00
O16 A:FQT309 1.9 24.1 1.0
OD1 A:ASP68 2.1 27.7 1.0
OD1 A:ASP71 2.1 18.5 1.0
OD2 A:ASP89 2.1 14.6 0.7
O12 A:FQT309 2.2 24.0 1.0
O A:ASP68 2.3 25.7 1.0
OD2 A:ASP89 2.5 24.3 0.3
CG A:ASP68 2.8 41.5 1.0
CG A:ASP71 3.0 18.1 1.0
CG A:ASP89 3.0 18.4 0.7
P15 A:FQT309 3.1 35.1 1.0
OD1 A:ASP89 3.2 17.3 0.7
OD2 A:ASP71 3.2 21.7 1.0
H091 A:FQT309 3.3 22.8 1.0
P11 A:FQT309 3.3 22.1 1.0
OD2 A:ASP68 3.4 44.5 1.0
O14 A:FQT309 3.5 31.6 1.0
C A:ASP68 3.5 21.6 1.0
H A:GLY72 3.6 18.3 1.0
CG A:ASP89 3.6 17.5 0.3
H041 A:FQT309 3.7 16.3 1.0
O17 A:FQT309 3.8 39.5 1.0
O A:HOH401 3.8 26.7 1.0
CB A:ASP68 3.9 24.6 1.0
HA A:ASP68 3.9 25.3 1.0
H031 A:FQT309 4.0 14.0 1.0
CA A:ASP68 4.0 21.1 1.0
HB3 A:ASP68 4.1 29.6 1.0
C09 A:FQT309 4.2 19.0 1.0
HB2 A:ASP89 4.2 17.0 0.3
N A:GLY72 4.2 15.3 1.0
O18 A:FQT309 4.3 44.0 1.0
H A:ASP71 4.3 21.3 1.0
O10 A:FQT309 4.3 20.4 1.0
H191 A:FQT309 4.4 55.7 1.0
OD1 A:ASP89 4.4 17.6 0.3
CB A:ASP71 4.4 17.6 1.0
O13 A:FQT309 4.4 27.6 1.0
H192 A:FQT309 4.5 55.7 1.0
O A:HOH402 4.5 20.7 1.0
HA A:MET69 4.5 27.4 1.0
C04 A:FQT309 4.5 13.6 1.0
CB A:ASP89 4.5 13.9 0.7
H092 A:FQT309 4.5 22.8 1.0
CB A:ASP89 4.5 14.2 0.3
HA3 A:GLY72 4.6 25.7 1.0
MG A:MG301 4.6 26.6 1.0
N A:MET69 4.6 20.7 1.0
C03 A:FQT309 4.6 11.7 1.0
C19 A:FQT309 4.6 46.4 1.0
HG1 A:THR34 4.6 16.0 1.0
HB2 A:ASP68 4.7 29.6 1.0
HB2 A:ASP89 4.7 16.8 0.7
HB3 A:ASP89 4.8 16.8 0.7
O A:HOH421 4.8 22.5 1.0
HB2 A:ASP71 4.8 21.1 1.0
N A:ASP71 4.8 17.8 1.0
CA A:GLY72 4.9 21.4 1.0
C A:ASP71 4.9 14.7 1.0
CA A:MET69 5.0 22.8 1.0
CA A:ASP71 5.0 15.0 1.0
HB3 A:ASP71 5.0 21.1 1.0

Magnesium binding site 3 out of 4 in 6h59

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Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound


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 Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:31.2
occ:1.00
O B:ASP68 1.8 24.2 1.0
O13 B:FQT307 2.0 28.4 1.0
OD1 B:ASP71 2.1 21.4 1.0
O17 B:FQT307 2.1 41.8 1.0
OD1 B:ASP68 2.1 28.4 1.0
O B:HOH402 2.2 30.9 1.0
CG B:ASP68 2.9 38.5 1.0
P15 B:FQT307 2.9 55.5 1.0
C B:ASP68 3.0 19.7 1.0
CG B:ASP71 3.0 19.7 1.0
P11 B:FQT307 3.1 29.8 1.0
O14 B:FQT307 3.2 56.2 1.0
H B:GLY72 3.3 21.0 1.0
O18 B:FQT307 3.3 48.9 1.0
OD2 B:ASP71 3.4 23.2 1.0
HA B:ASP68 3.5 27.3 1.0
CA B:ASP68 3.6 22.8 1.0
CB B:ASP68 3.7 25.4 1.0
OD2 B:ASP68 3.7 50.5 1.0
H091 B:FQT307 3.7 27.4 1.0
HB3 B:ASP68 3.8 30.4 1.0
O B:HOH406 3.9 30.3 1.0
HA B:MET69 3.9 28.8 1.0
H B:ASP71 3.9 21.5 1.0
OD1 B:ASP89 4.0 24.9 1.0
N B:GLY72 4.0 17.5 1.0
N B:MET69 4.1 24.0 1.0
O B:HOH405 4.1 29.2 1.0
O12 B:FQT307 4.2 37.5 1.0
O10 B:FQT307 4.2 31.9 1.0
O16 B:FQT307 4.3 58.1 1.0
C09 B:FQT307 4.4 22.9 1.0
CA B:MET69 4.4 24.0 1.0
HA3 B:GLY72 4.4 26.9 1.0
CB B:ASP71 4.4 22.2 1.0
H041 B:FQT307 4.4 20.0 1.0
O B:HOH408 4.5 33.1 1.0
N B:ASP71 4.5 17.9 1.0
HB2 B:ASP68 4.5 30.4 1.0
O B:HOH456 4.6 24.9 1.0
C19 B:FQT307 4.6 60.4 1.0
C B:MET69 4.6 23.1 1.0
H092 B:FQT307 4.6 27.4 1.0
H192 B:FQT307 4.7 72.4 1.0
CA B:GLY72 4.8 22.4 1.0
H B:LEU70 4.8 23.5 1.0
CA B:ASP71 4.8 15.3 1.0
H B:MET69 4.8 28.8 1.0
H031 B:FQT307 4.9 18.0 1.0
C B:ASP71 4.9 17.9 1.0
CG B:ASP89 4.9 28.6 1.0
N B:LEU70 4.9 19.6 1.0
HB2 B:ASP71 4.9 26.7 1.0
HB3 B:ASP71 4.9 26.7 1.0

Magnesium binding site 4 out of 4 in 6h59

Go back to Magnesium Binding Sites List in 6h59
Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) with Cdp-Dag Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:26.8
occ:1.00
OD2 B:ASP89 2.0 31.3 1.0
O B:HOH449 2.1 39.9 1.0
O B:HOH435 2.1 27.3 1.0
O B:HOH408 2.2 33.1 1.0
O B:HOH405 2.2 29.2 1.0
OD2 B:ASP93 2.2 27.1 1.0
OD1 B:ASP93 2.9 21.7 1.0
CG B:ASP93 3.0 21.1 1.0
CG B:ASP89 3.1 28.6 1.0
O17 B:FQT307 3.6 41.8 1.0
OD1 B:ASP89 3.6 24.9 1.0
O16 B:FQT307 3.7 58.1 1.0
O B:ASP89 3.7 12.8 1.0
HA B:ALA90 3.9 17.2 1.0
C B:ASP89 4.1 17.1 1.0
O B:HOH402 4.1 30.9 1.0
CB B:ASP89 4.2 17.0 1.0
HB3 B:ASP89 4.2 20.4 1.0
P15 B:FQT307 4.3 55.5 1.0
OD2 B:ASP68 4.4 50.5 1.0
CB B:ASP93 4.4 17.6 1.0
H092 B:FQT307 4.5 27.4 1.0
O B:HOH424 4.5 17.2 1.0
N B:ALA90 4.5 13.4 1.0
HB2 B:ASP93 4.6 21.2 1.0
CA B:ALA90 4.7 14.3 1.0
CA B:ASP89 4.7 15.8 1.0
O A:HOH433 4.7 41.0 1.0
HH11 B:ARG152 4.8 36.5 1.0
HB3 B:ASP93 4.9 21.2 1.0
HA B:ASP89 4.9 18.9 1.0
H B:ASP93 4.9 16.2 1.0
H091 B:FQT307 4.9 27.4 1.0
O B:HOH406 4.9 30.3 1.0
HB2 B:ASP89 5.0 20.4 1.0

Reference:

K.Grave, M.D.Bennett, M.Hogbom. Structure Ofmycobacterium Tuberculosisphosphatidylinositol Phosphate Synthase Reveals Mechanism of Substrate Binding and Metal Catalysis. Commun Biol V. 2 175 2019.
ISSN: ESSN 2399-3642
PubMed: 31098408
DOI: 10.1038/S42003-019-0427-1
Page generated: Mon Dec 14 22:47:31 2020

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