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Magnesium in PDB 5xd5: Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate, PDB code: 5xd5 was solved by S.M.Arif, U.Varshney, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.26 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.050, 64.440, 103.040, 90.00, 102.59, 90.00
R / Rfree (%) 16.6 / 20.5

Other elements in 5xd5:

The structure of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate (pdb code 5xd5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate, PDB code: 5xd5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5xd5

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Magnesium binding site 1 out of 8 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate


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 Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:19.8
occ:1.00
 F B:F411 1.9 19.2 1.0
O1G B:ATP401 1.9 22.5 1.0
O B:HOH588 2.0 18.8 1.0
OE2 B:GLU85 2.1 19.9 1.0
O B:LYS65 2.1 19.1 1.0
OE2 B:GLU127 2.2 21.4 1.0
CD B:GLU127 3.0 21.7 1.0
CD B:GLU85 3.1 19.6 1.0
MG B:MG408 3.1 21.9 1.0
PG B:ATP401 3.2 24.1 1.0
C B:LYS65 3.3 20.2 1.0
OE1 B:GLU127 3.4 19.9 1.0
OE1 B:GLU85 3.4 20.9 1.0
MG B:MG410 3.5 23.8 1.0
O3G B:ATP401 3.6 23.3 1.0
NH2 B:ARG55 3.8 23.9 1.0
CA B:GLY66 3.8 21.9 1.0
O3B B:ATP401 4.0 27.2 1.0
N B:GLY66 4.0 21.1 1.0
OE1 B:GLU81 4.0 19.7 1.0
NZ B:LYS65 4.2 26.0 1.0
F B:F412 4.3 21.9 1.0
N B:LYS65 4.3 19.5 1.0
O2G B:ATP401 4.3 28.2 1.0
CG B:GLU127 4.3 22.1 1.0
CA B:LYS65 4.4 19.4 1.0
CG B:GLU85 4.4 19.5 1.0
O B:HOH540 4.5 20.8 1.0
CD B:LYS65 4.6 22.3 1.0
CG B:LYS65 4.7 19.3 1.0
CD B:GLU81 4.8 20.3 1.0
CZ B:ARG55 4.8 22.8 1.0
F B:F413 4.8 22.1 1.0
CD B:ARG55 4.9 20.0 1.0
O1 B:PO4402 4.9 39.9 1.0
CE B:LYS65 5.0 25.6 1.0

Magnesium binding site 2 out of 8 in 5xd5

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Magnesium binding site 2 out of 8 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate


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 Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:21.9
occ:1.00
 F B:F411 1.9 19.2 1.0
F B:F412 2.0 21.9 1.0
OE1 B:GLU81 2.1 19.7 1.0
O B:HOH613 2.1 21.8 1.0
OE1 B:GLU127 2.1 19.9 1.0
OE2 B:GLU85 2.1 19.9 1.0
CD B:GLU127 3.0 21.7 1.0
MG B:MG410 3.1 23.8 1.0
CD B:GLU81 3.1 20.3 1.0
MG B:MG407 3.1 19.8 1.0
CD B:GLU85 3.1 19.6 1.0
OE2 B:GLU127 3.4 21.4 1.0
CG B:GLU85 3.4 19.5 1.0
OE2 B:GLU81 3.5 19.5 1.0
MG B:MG409 3.6 23.9 1.0
F B:F413 4.0 22.1 1.0
O B:LYS65 4.0 19.1 1.0
OE2 B:GLU84 4.1 25.8 1.0
O1 B:PO4402 4.3 39.9 1.0
OE1 B:GLU85 4.3 20.9 1.0
O B:HOH571 4.3 23.0 1.0
CG B:GLU127 4.4 22.1 1.0
CG B:GLU81 4.4 20.3 1.0
O B:HOH590 4.4 24.4 1.0
CA B:GLY66 4.5 21.9 1.0
O3G B:ATP401 4.6 23.3 1.0
O1G B:ATP401 4.6 22.5 1.0
O B:HOH588 4.7 18.8 1.0
CB B:GLU127 4.7 22.7 1.0
CB B:GLU81 4.7 18.3 1.0
C B:LYS65 4.8 20.2 1.0
CB B:GLU85 4.9 19.3 1.0

Magnesium binding site 3 out of 8 in 5xd5

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Magnesium binding site 3 out of 8 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate


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 Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg409

b:23.9
occ:1.00
 F B:F413 2.0 22.1 1.0
F B:F412 2.0 21.9 1.0
O B:HOH571 2.0 23.0 1.0
O B:HOH606 2.1 22.1 1.0
O B:HOH531 2.1 23.7 1.0
OE2 B:GLU81 2.2 19.5 1.0
MG B:MG410 3.0 23.8 1.0
CD B:GLU81 3.2 20.3 1.0
OE1 B:GLU81 3.5 19.7 1.0
MG B:MG408 3.6 21.9 1.0
F B:F411 3.8 19.2 1.0
O1 B:PO4402 3.9 39.9 1.0
O2 B:PO4402 4.0 39.4 1.0
NH1 B:ARG80 4.0 22.6 1.0
N B:LYS67 4.0 21.6 1.0
OE2 B:GLU84 4.1 25.8 1.0
O B:HOH672 4.2 35.9 1.0
O B:LYS67 4.3 23.6 1.0
O B:HOH613 4.4 21.8 1.0
O B:HOH761 4.4 36.7 1.0
CG B:GLU81 4.5 20.3 1.0
CA B:GLY66 4.6 21.9 1.0
P B:PO4402 4.6 35.2 1.0
O3G B:ATP401 4.6 23.3 1.0
C B:GLY66 4.7 23.1 1.0
NH2 B:ARG80 4.7 22.8 1.0
CZ B:ARG80 4.8 21.9 1.0
CA B:LYS67 4.8 23.6 1.0
CB B:LYS67 4.9 24.5 1.0
OD1 B:ASP69 4.9 34.6 1.0
OE1 B:GLU127 5.0 19.9 1.0
C B:LYS67 5.0 24.1 1.0

Magnesium binding site 4 out of 8 in 5xd5

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Magnesium binding site 4 out of 8 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate


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 Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg410

b:23.8
occ:1.00
 F B:F413 1.9 22.1 1.0
O1 B:PO4402 1.9 39.9 1.0
F B:F411 1.9 19.2 1.0
O3G B:ATP401 2.0 23.3 1.0
F B:F412 2.0 21.9 1.0
MG B:MG409 3.0 23.9 1.0
MG B:MG408 3.1 21.9 1.0
PG B:ATP401 3.2 24.1 1.0
P B:PO4402 3.3 35.2 1.0
OE1 B:GLU127 3.5 19.9 1.0
MG B:MG407 3.5 19.8 1.0
O B:HOH531 3.6 23.7 1.0
NZ B:LYS67 3.6 28.3 1.0
O1G B:ATP401 3.6 22.5 1.0
OE2 B:GLU127 3.7 21.4 1.0
O2 B:PO4402 3.8 39.4 1.0
CD B:GLU127 4.0 21.7 1.0
CA B:GLY66 4.0 21.9 1.0
OE2 B:GLU81 4.0 19.5 1.0
O4 B:PO4402 4.1 40.5 1.0
O3B B:ATP401 4.1 27.2 1.0
OE1 B:GLU81 4.1 19.7 1.0
CE B:LYS67 4.2 29.2 1.0
N B:LYS67 4.2 21.6 1.0
O3 B:PO4402 4.3 32.6 1.0
O2G B:ATP401 4.3 28.2 1.0
OE2 B:GLU85 4.3 19.9 1.0
CD B:GLU81 4.4 20.3 1.0
NH2 B:ARG57 4.6 36.5 1.0
O B:LYS65 4.7 19.1 1.0
C B:GLY66 4.7 23.1 1.0
O B:HOH606 4.7 22.1 1.0
O B:HOH571 4.7 23.0 1.0
O B:HOH613 4.8 21.8 1.0
O2B B:ATP401 4.9 28.9 1.0
CG B:LYS67 4.9 27.0 1.0

Magnesium binding site 5 out of 8 in 5xd5

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Magnesium binding site 5 out of 8 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:30.3
occ:1.00
 F A:F409 1.9 30.0 1.0
O1G A:ATP401 1.9 25.1 1.0
OE1 A:GLU85 2.0 30.0 1.0
O A:HOH564 2.1 29.2 1.0
O A:LYS65 2.1 26.5 1.0
OE1 A:GLU127 2.1 35.4 1.0
CD A:GLU85 3.0 27.9 1.0
CD A:GLU127 3.0 45.6 1.0
MG A:MG406 3.2 31.7 1.0
PG A:ATP401 3.2 31.2 1.0
C A:LYS65 3.3 25.8 1.0
OE2 A:GLU127 3.4 35.8 1.0
OE2 A:GLU85 3.4 30.8 1.0
O3G A:ATP401 3.6 29.8 1.0
MG A:MG408 3.7 31.1 1.0
CA A:GLY66 3.8 25.4 1.0
NH2 A:ARG55 4.0 35.9 1.0
N A:GLY66 4.0 23.1 1.0
O3B A:ATP401 4.1 38.7 1.0
OE1 A:GLU81 4.1 29.6 1.0
NZ A:LYS65 4.3 31.4 1.0
N A:LYS65 4.3 25.2 1.0
CG A:GLU85 4.4 30.6 1.0
O2G A:ATP401 4.4 31.8 1.0
CG A:GLU127 4.4 46.2 1.0
F A:F410 4.4 30.5 1.0
CA A:LYS65 4.4 25.4 1.0
O A:HOH557 4.4 47.7 1.0
CD A:LYS65 4.7 27.0 1.0
CG A:LYS65 4.7 25.5 1.0
F A:F411 4.7 32.9 1.0
O A:HOH506 4.7 29.3 1.0
CD A:GLU81 4.9 29.2 1.0
CD A:ARG55 4.9 34.0 1.0

Magnesium binding site 6 out of 8 in 5xd5

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Magnesium binding site 6 out of 8 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:31.7
occ:1.00
 F A:F410 2.0 30.5 1.0
F A:F409 2.0 30.0 1.0
OE1 A:GLU81 2.1 29.6 1.0
O A:HOH531 2.1 28.8 1.0
OE2 A:GLU127 2.2 35.8 1.0
OE1 A:GLU85 2.3 30.0 1.0
CD A:GLU81 3.1 29.2 1.0
CD A:GLU127 3.1 45.6 1.0
MG A:MG408 3.2 31.1 1.0
MG A:MG405 3.2 30.3 1.0
CD A:GLU85 3.3 27.9 1.0
OE2 A:GLU81 3.4 28.7 1.0
OE1 A:GLU127 3.5 35.4 1.0
MG A:MG407 3.5 30.5 1.0
CG A:GLU85 3.5 30.6 1.0
F A:F411 3.8 32.9 1.0
OE2 A:GLU84 4.1 34.7 1.0
O A:HOH515 4.2 29.2 1.0
O A:LYS65 4.2 26.5 1.0
CG A:GLU81 4.4 28.8 1.0
OE2 A:GLU85 4.4 30.8 1.0
CG A:GLU127 4.5 46.2 1.0
CA A:GLY66 4.6 25.4 1.0
O3G A:ATP401 4.6 29.8 1.0
O1G A:ATP401 4.6 25.1 1.0
CB A:GLU127 4.7 46.2 1.0
CB A:GLU81 4.7 30.3 1.0
O A:HOH564 4.9 29.2 1.0
C A:LYS65 4.9 25.8 1.0

Magnesium binding site 7 out of 8 in 5xd5

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Magnesium binding site 7 out of 8 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:30.5
occ:1.00
 F A:F410 1.9 30.5 1.0
O A:HOH549 2.0 35.2 1.0
O A:HOH515 2.0 29.2 1.0
F A:F411 2.0 32.9 1.0
OE2 A:GLU81 2.1 28.7 1.0
MG A:MG408 3.1 31.1 1.0
CD A:GLU81 3.1 29.2 1.0
OE1 A:GLU81 3.5 29.6 1.0
MG A:MG406 3.5 31.7 1.0
NH1 A:ARG80 3.8 32.3 1.0
F A:F409 3.9 30.0 1.0
OE2 A:GLU84 4.0 34.7 1.0
N A:LYS67 4.1 29.9 1.0
O A:HOH531 4.2 28.8 1.0
O A:LYS67 4.2 32.4 1.0
CG A:GLU81 4.4 28.8 1.0
NH2 A:ARG80 4.6 33.8 1.0
CZ A:ARG80 4.7 33.0 1.0
CA A:GLY66 4.7 25.4 1.0
C A:GLY66 4.8 28.6 1.0
O3G A:ATP401 4.8 29.8 1.0
CB A:LYS67 4.9 31.8 1.0
CA A:LYS67 4.9 31.5 1.0
C A:LYS67 5.0 28.6 1.0

Magnesium binding site 8 out of 8 in 5xd5

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Magnesium binding site 8 out of 8 in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:31.1
occ:1.00
 F A:F411 1.9 32.9 1.0
O3G A:ATP401 1.9 29.8 1.0
F A:F409 2.0 30.0 1.0
F A:F410 2.2 30.5 1.0
MG A:MG407 3.1 30.5 1.0
MG A:MG406 3.2 31.7 1.0
PG A:ATP401 3.2 31.2 1.0
O1G A:ATP401 3.6 25.1 1.0
NZ A:LYS67 3.6 37.7 1.0
MG A:MG405 3.7 30.3 1.0
OE2 A:GLU127 3.7 35.8 1.0
OE1 A:GLU127 3.9 35.4 1.0
CD A:GLU127 4.1 45.6 1.0
O3B A:ATP401 4.1 38.7 1.0
CA A:GLY66 4.1 25.4 1.0
OE2 A:GLU81 4.2 28.7 1.0
N A:LYS67 4.2 29.9 1.0
O2G A:ATP401 4.3 31.8 1.0
OE1 A:GLU81 4.3 29.6 1.0
CE A:LYS67 4.3 38.8 1.0
O A:HOH557 4.4 47.7 1.0
O A:HOH549 4.5 35.2 1.0
CD A:GLU81 4.5 29.2 1.0
OE1 A:GLU85 4.5 30.0 1.0
CG A:LYS67 4.7 36.3 1.0
O A:HOH515 4.8 29.2 1.0
C A:GLY66 4.8 28.6 1.0
O A:HOH531 4.9 28.8 1.0
O A:LYS65 4.9 26.5 1.0
O2B A:ATP401 4.9 41.7 1.0

Reference:

S.M.Arif, U.Varshney, M.Vijayan. Hydrolysis of Diadenosine Polyphosphates. Exploration of An Additional Role of Mycobacterium Smegmatis MUTT1 J. Struct. Biol. V. 199 165 2017.
ISSN: ESSN 1095-8657
PubMed: 28705712
DOI: 10.1016/J.JSB.2017.07.002
Page generated: Mon Sep 30 09:17:47 2024

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