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Manganese in PDB 6h5a: Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate:
2.7.8.11;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate, PDB code: 6h5a 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) 45.70 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.067, 77.941, 100.823, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate (pdb code 6h5a). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate, PDB code: 6h5a:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 6h5a

Go back to Manganese Binding Sites List in 6h5a
Manganese binding site 1 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:22.3
occ:1.00
 O A:ASP68 2.1 21.3 1.0
OD2 A:ASP89 2.1 20.3 1.0
O A:HOH440 2.1 23.4 1.0
OD1 A:ASP71 2.1 24.8 1.0
OD1 A:ASP68 2.1 22.4 1.0
O A:HOH445 2.1 21.0 1.0
CG A:ASP71 3.1 21.9 1.0
C A:ASP68 3.1 23.2 1.0
CG A:ASP89 3.2 21.9 1.0
CG A:ASP68 3.3 24.7 1.0
HA A:ASP68 3.3 30.8 1.0
HG1 A:THR34 3.5 25.7 1.0
CA A:ASP68 3.6 25.6 1.0
OD2 A:ASP71 3.6 25.8 1.0
OD1 A:ASP89 3.6 22.5 1.0
H A:ASP71 3.7 30.8 1.0
MN A:MN302 3.9 27.3 1.0
O B:HOH434 3.9 25.6 1.0
HB3 A:ASP71 3.9 30.0 1.0
O A:HOH443 4.0 24.1 1.0
CB A:ASP68 4.0 20.3 1.0
O A:HOH451 4.0 28.9 1.0
CB A:ASP71 4.1 24.9 1.0
HA A:MET69 4.2 29.1 1.0
OD2 A:ASP68 4.2 23.0 1.0
O A:HOH431 4.2 35.3 1.0
OA1 A:FLC305 4.2 25.7 1.0
OG1 A:THR34 4.2 21.4 1.0
N A:MET69 4.3 26.8 1.0
HB2 A:ASP89 4.4 24.0 1.0
H A:GLY72 4.4 28.5 1.0
CB A:ASP89 4.4 20.0 1.0
HB3 A:ASP68 4.5 24.5 1.0
N A:ASP71 4.5 25.6 1.0
CA A:MET69 4.6 24.2 1.0
HB2 A:ASP68 4.8 24.5 1.0
H A:LEU70 4.8 26.8 1.0
HG23 A:THR34 4.8 22.9 1.0
O A:HOH403 4.8 32.9 1.0
HB2 A:ASP71 4.8 30.0 1.0
CA A:ASP71 4.9 29.1 1.0
C A:MET69 4.9 23.7 1.0
HD1 B:PHE222 4.9 37.2 1.0
HA A:THR34 4.9 30.0 1.0
HA A:ASP89 4.9 22.6 1.0
N A:LEU70 5.0 22.3 1.0

Manganese binding site 2 out of 7 in 6h5a

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Manganese binding site 2 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:27.3
occ:1.00
 OA2 A:FLC305 2.2 25.1 1.0
OD2 A:ASP93 2.2 20.6 1.0
OD2 A:ASP68 2.2 23.0 1.0
OD1 A:ASP89 2.2 22.5 1.0
OD1 A:ASP93 2.5 23.1 1.0
OD1 A:ASP68 2.6 22.4 1.0
CG A:ASP93 2.7 20.1 1.0
CG A:ASP68 2.7 24.7 1.0
OA1 A:FLC305 2.8 25.7 1.0
CAC A:FLC305 2.8 25.7 1.0
CG A:ASP89 3.2 21.9 1.0
OD2 A:ASP89 3.5 20.3 1.0
O A:HOH427 3.5 23.1 1.0
O A:HOH440 3.8 23.4 1.0
MN A:MN301 3.9 22.3 1.0
O A:HOH451 3.9 28.9 1.0
HH12 A:ARG152 4.0 28.7 1.0
O A:ASP89 4.2 20.1 1.0
CB A:ASP68 4.2 20.3 1.0
HH22 A:ARG9 4.3 31.2 0.4
CB A:ASP93 4.3 17.2 1.0
CA A:FLC305 4.3 23.0 1.0
MN A:MN303 4.4 25.1 1.0
O A:HOH442 4.5 25.1 1.0
NH1 A:ARG152 4.5 23.9 1.0
HB3 A:ASP68 4.5 24.5 1.0
CB A:ASP89 4.5 20.0 1.0
O A:HOH406 4.5 21.7 1.0
HB2 A:ASP93 4.6 20.7 1.0
O A:HOH403 4.6 32.9 1.0
OB2 A:FLC305 4.6 25.1 1.0
HB2 A:ASP68 4.6 24.5 1.0
HB3 A:ASP93 4.6 20.7 1.0
C A:ASP89 4.6 22.4 1.0
CBC A:FLC305 4.6 30.9 1.0
CB A:FLC305 4.7 23.5 1.0
HB3 A:ASP89 4.7 24.0 1.0
HH11 A:ARG152 4.8 28.7 1.0
O A:HOH464 4.8 23.1 1.0
HA A:ALA90 4.9 22.2 1.0
HH22 A:ARG152 4.9 28.2 1.0
HA A:ASP89 5.0 22.6 1.0

Manganese binding site 3 out of 7 in 6h5a

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Manganese binding site 3 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:25.1
occ:1.00
 OHB A:FLC306 1.9 25.3 1.0
OHB A:FLC305 2.1 32.5 1.0
CB A:FLC305 2.2 23.5 1.0
O A:HOH427 2.3 23.1 1.0
O A:HOH464 2.3 23.1 1.0
OA2 A:FLC306 2.4 25.7 1.0
OA2 A:FLC305 2.5 25.1 1.0
MN A:MN304 2.8 24.6 1.0
CB A:FLC306 2.9 20.5 1.0
CA A:FLC305 2.9 23.0 1.0
CAC A:FLC305 3.0 25.7 1.0
CAC A:FLC306 3.1 24.5 1.0
CA A:FLC306 3.2 22.6 1.0
CBC A:FLC305 3.2 30.9 1.0
CBC A:FLC306 3.4 23.8 1.0
OB1 A:FLC305 3.6 27.5 1.0
OB2 A:FLC306 3.6 27.4 1.0
CG A:FLC305 3.7 25.9 1.0
O A:HOH406 3.7 21.7 1.0
OA1 A:FLC306 4.1 27.1 1.0
OA1 A:FLC305 4.1 25.7 1.0
O A:HOH441 4.2 23.9 1.0
OD2 A:ASP93 4.2 20.6 1.0
CG A:FLC306 4.2 25.6 1.0
OB2 A:FLC305 4.3 25.1 1.0
OB1 A:FLC306 4.4 25.4 1.0
MN A:MN302 4.4 27.3 1.0
OD1 A:ASP89 4.4 22.5 1.0
O A:HOH405 4.5 32.4 1.0
OG2 A:FLC305 4.5 38.0 1.0
CGC A:FLC305 4.6 30.5 1.0
OG1 A:FLC306 4.6 26.6 1.0
O B:HOH452 4.7 23.5 1.0
HA A:ALA90 4.8 22.2 1.0
HB2 A:ALA90 4.9 20.1 1.0
CGC A:FLC306 5.0 28.9 1.0

Manganese binding site 4 out of 7 in 6h5a

Go back to Manganese Binding Sites List in 6h5a
Manganese binding site 4 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:24.6
occ:1.00
 OHB A:FLC305 1.9 32.5 1.0
OHB A:FLC306 2.0 25.3 1.0
OG1 A:FLC306 2.1 26.6 1.0
OB1 A:FLC305 2.1 27.5 1.0
OG2 A:FLC305 2.2 38.0 1.0
OB2 A:FLC306 2.2 27.4 1.0
CB A:FLC306 2.3 20.5 1.0
CB A:FLC305 2.4 23.5 1.0
CBC A:FLC305 2.5 30.9 1.0
CBC A:FLC306 2.6 23.8 1.0
MN A:MN303 2.8 25.1 1.0
CGC A:FLC305 2.9 30.5 1.0
CGC A:FLC306 2.9 28.9 1.0
CG A:FLC305 3.0 25.9 1.0
CG A:FLC306 3.1 25.6 1.0
CA A:FLC306 3.7 22.6 1.0
OB2 A:FLC305 3.8 25.1 1.0
HD3 A:ARG152 3.8 27.9 1.0
O A:HOH406 3.8 21.7 1.0
OB1 A:FLC306 3.9 25.4 1.0
CA A:FLC305 3.9 23.0 1.0
HB3 A:ARG152 3.9 35.3 1.0
OG1 A:FLC305 4.0 37.6 1.0
OA2 A:FLC306 4.1 25.7 1.0
O A:HOH438 4.1 24.6 1.0
OG2 A:FLC306 4.1 28.4 1.0
O A:HOH408 4.2 36.9 1.0
OA2 A:FLC305 4.2 25.1 1.0
HH11 A:ARG152 4.4 28.7 1.0
CAC A:FLC306 4.4 24.5 1.0
HB2 A:ARG152 4.5 35.3 1.0
CAC A:FLC305 4.6 25.7 1.0
CB A:ARG152 4.7 29.4 1.0
CD A:ARG152 4.7 23.2 1.0
O A:HOH464 4.8 23.1 1.0
HD3 A:PRO153 4.8 31.2 1.0
O A:HOH427 4.8 23.1 1.0
HZ3 A:LYS135 4.9 48.1 1.0
HD2 A:ARG152 4.9 27.9 1.0
O A:HOH420 5.0 27.6 1.0

Manganese binding site 5 out of 7 in 6h5a

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Manganese binding site 5 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:37.9
occ:0.73
 OA2 B:FLC304 2.1 39.1 0.8
OE1 B:GLU151 2.2 43.8 1.0
O B:HOH441 2.2 44.2 1.0
OB1 B:FLC304 2.2 31.1 0.8
OHB B:FLC304 2.4 34.7 0.8
HOB B:FLC304 2.9 41.7 0.8
CBC B:FLC304 3.0 33.2 0.8
CB B:FLC304 3.1 32.1 0.8
CAC B:FLC304 3.2 32.5 0.8
CD B:GLU151 3.3 41.3 1.0
HE3 B:LYS135 3.4 34.0 1.0
HH12 B:ARG195 3.7 35.2 1.0
CA B:FLC304 3.7 35.6 0.8
OE2 B:GLU151 3.9 43.4 1.0
HD3 B:LYS135 4.0 34.7 1.0
OG1 B:FLC304 4.1 34.9 0.8
HB3 B:GLU151 4.2 40.3 1.0
HA2 B:FLC304 4.2 42.8 0.8
OB2 B:FLC304 4.2 28.9 0.8
HD2 B:LYS135 4.2 34.7 1.0
OA1 B:FLC304 4.2 36.9 0.8
CE B:LYS135 4.3 28.3 1.0
CG B:GLU151 4.4 37.8 1.0
HG2 B:GLU151 4.4 45.4 1.0
CD B:LYS135 4.4 28.9 1.0
HZ2 B:LYS135 4.5 38.9 1.0
CG B:FLC304 4.5 35.2 0.8
NH1 B:ARG195 4.5 29.3 1.0
HA1 B:FLC304 4.5 42.8 0.8
CGC B:FLC304 4.7 33.9 0.8
HH11 B:ARG195 4.7 35.2 1.0
CB B:GLU151 4.8 33.5 1.0
NZ B:LYS135 4.9 32.4 1.0
HG2 B:FLC304 5.0 42.2 0.8
HE2 B:LYS135 5.0 34.0 1.0

Manganese binding site 6 out of 7 in 6h5a

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Manganese binding site 6 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:47.9
occ:0.81
 OD1 B:ASP68 2.0 52.5 1.0
OD1 B:ASP71 2.1 51.5 1.0
OD2 B:ASP89 2.2 45.0 1.0
O B:HOH402 2.2 45.5 1.0
O B:ASP68 2.2 54.2 1.0
CG B:ASP68 2.7 51.8 1.0
OD2 B:ASP68 3.1 55.6 1.0
CG B:ASP71 3.1 50.4 1.0
CG B:ASP89 3.3 35.7 1.0
C B:ASP68 3.3 52.0 1.0
O B:HOH404 3.5 39.9 1.0
MN B:MN303 3.5 47.7 0.7
OD1 B:ASP89 3.7 38.1 1.0
CB B:ASP68 3.8 49.5 1.0
OD2 B:ASP71 3.8 53.3 1.0
HA B:ASP68 3.8 57.7 1.0
HB3 B:ASP71 3.8 52.5 1.0
CA B:ASP68 3.9 48.1 1.0
CB B:ASP71 4.1 43.7 1.0
HA B:MET69 4.1 65.6 1.0
HB3 B:ASP68 4.1 59.4 1.0
H B:ASP71 4.2 49.9 1.0
N B:MET69 4.3 49.0 1.0
HB2 B:ASP89 4.4 34.1 1.0
H B:GLY72 4.4 47.0 1.0
CB B:ASP89 4.5 28.4 1.0
HB2 B:ASP68 4.5 59.4 1.0
O B:HOH403 4.6 25.7 1.0
OG1 B:THR34 4.6 29.0 1.0
CA B:MET69 4.7 54.6 1.0
HB2 B:ASP71 4.8 52.5 1.0
N B:ASP71 4.8 41.6 1.0
HG23 B:THR34 4.9 37.7 1.0
HG1 B:THR34 4.9 34.9 1.0

Manganese binding site 7 out of 7 in 6h5a

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Manganese binding site 7 out of 7 in the Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Mycobacterium Tuberculosis Phosphatidylinositol Phosphate Synthase (PGSA1) in Complex with Manganese and Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:47.7
occ:0.66
 O B:HOH403 2.0 25.7 1.0
OD2 B:ASP68 2.1 55.6 1.0
O B:HOH404 2.2 39.9 1.0
OD1 B:ASP89 2.3 38.1 1.0
OD1 B:ASP93 2.3 28.8 1.0
OD2 B:ASP93 2.3 31.8 1.0
CG B:ASP93 2.7 28.6 1.0
CG B:ASP89 3.0 35.7 1.0
CG B:ASP68 3.1 51.8 1.0
OD2 B:ASP89 3.2 45.0 1.0
OD1 B:ASP68 3.4 52.5 1.0
MN B:MN302 3.5 47.9 0.8
O B:ASP89 3.9 20.5 1.0
CB B:ASP93 4.2 23.6 1.0
HH12 B:ARG152 4.2 42.4 1.0
HH11 B:ARG152 4.2 42.4 1.0
NH1 B:ARG152 4.4 35.3 1.0
C B:ASP89 4.4 25.0 1.0
CB B:ASP68 4.4 49.5 1.0
CB B:ASP89 4.4 28.4 1.0
HB3 B:ASP68 4.5 59.4 1.0
HB2 B:ASP93 4.5 28.3 1.0
O B:HOH402 4.6 45.5 1.0
HB3 B:ASP93 4.6 28.3 1.0
H B:ASP93 4.7 26.5 1.0
O B:HOH411 4.7 33.8 1.0
HA B:ALA90 4.7 26.7 1.0
HA B:ASP89 4.8 29.1 1.0
HB2 B:ASP68 4.8 59.4 1.0
CA B:ASP89 4.8 24.2 1.0
HB3 B:ASP89 4.8 34.1 1.0
HA B:ASP93 4.9 27.9 1.0
O B:HOH438 5.0 35.9 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: Sun Oct 6 04:50:17 2024

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