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Fluorine 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:

Magnesium (Mg) 8 atoms
Chlorine (Cl) 7 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Mycobacterium Smegmatis MUTT1 in Complex with Atp, Magnesium Fluoride and Phosphate, PDB code: 5xd5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5xd5

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Fluorine binding site 1 out of 6 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 Fluorine with other atoms in the F 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:F411

b:19.2
occ:1.00
 MG B:MG407 1.9 19.8 1.0
MG B:MG408 1.9 21.9 1.0
MG B:MG410 1.9 23.8 1.0
F B:F412 2.5 21.9 1.0
OE2 B:GLU85 2.5 19.9 1.0
OE2 B:GLU127 2.8 21.4 1.0
O3G B:ATP401 2.8 23.3 1.0
OE1 B:GLU127 2.8 19.9 1.0
O1G B:ATP401 2.8 22.5 1.0
OE1 B:GLU81 3.0 19.7 1.0
O B:LYS65 3.0 19.1 1.0
F B:F413 3.1 22.1 1.0
CD B:GLU127 3.2 21.7 1.0
CA B:GLY66 3.3 21.9 1.0
PG B:ATP401 3.3 24.1 1.0
CD B:GLU81 3.5 20.3 1.0
O1 B:PO4402 3.6 39.9 1.0
CD B:GLU85 3.8 19.6 1.0
OE2 B:GLU81 3.8 19.5 1.0
MG B:MG409 3.8 23.9 1.0
C B:LYS65 3.9 20.2 1.0
O B:HOH588 3.9 18.8 1.0
O B:HOH613 4.0 21.8 1.0
N B:GLY66 4.0 21.1 1.0
O3B B:ATP401 4.4 27.2 1.0
C B:GLY66 4.4 23.1 1.0
O2G B:ATP401 4.5 28.2 1.0
N B:LYS67 4.5 21.6 1.0
OE1 B:GLU85 4.6 20.9 1.0
CG B:GLU85 4.7 19.5 1.0
CG B:GLU81 4.7 20.3 1.0
CG B:GLU127 4.7 22.1 1.0
P B:PO4402 5.0 35.2 1.0

Fluorine binding site 2 out of 6 in 5xd5

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Fluorine binding site 2 out of 6 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 Fluorine with other atoms in the F 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:F412

b:21.9
occ:1.00
 MG B:MG409 2.0 23.9 1.0
MG B:MG410 2.0 23.8 1.0
MG B:MG408 2.0 21.9 1.0
F B:F411 2.5 19.2 1.0
F B:F413 2.5 22.1 1.0
O1 B:PO4402 2.9 39.9 1.0
OE1 B:GLU127 3.0 19.9 1.0
O B:HOH531 3.0 23.7 1.0
O B:HOH571 3.0 23.0 1.0
OE2 B:GLU81 3.1 19.5 1.0
O B:HOH613 3.1 21.8 1.0
OE1 B:GLU81 3.1 19.7 1.0
O2 B:PO4402 3.4 39.4 1.0
CD B:GLU81 3.4 20.3 1.0
P B:PO4402 3.8 35.2 1.0
O3G B:ATP401 4.0 23.3 1.0
CD B:GLU127 4.0 21.7 1.0
OE2 B:GLU85 4.0 19.9 1.0
O B:HOH606 4.1 22.1 1.0
OE2 B:GLU84 4.1 25.8 1.0
MG B:MG407 4.3 19.8 1.0
OE2 B:GLU127 4.3 21.4 1.0
O3 B:PO4402 4.6 32.6 1.0
CA B:GLY66 4.7 21.9 1.0
O4 B:PO4402 4.8 40.5 1.0
CG B:GLU81 4.9 20.3 1.0
N B:LYS67 5.0 21.6 1.0

Fluorine binding site 3 out of 6 in 5xd5

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Fluorine binding site 3 out of 6 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 Fluorine with other atoms in the F 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:F413

b:22.1
occ:1.00
 MG B:MG410 1.9 23.8 1.0
MG B:MG409 2.0 23.9 1.0
F B:F412 2.5 21.9 1.0
N B:LYS67 2.8 21.6 1.0
O B:HOH531 2.8 23.7 1.0
O3G B:ATP401 2.9 23.3 1.0
O B:HOH606 3.0 22.1 1.0
OE2 B:GLU81 3.1 19.5 1.0
F B:F411 3.1 19.2 1.0
O1 B:PO4402 3.1 39.9 1.0
CE B:LYS67 3.5 29.2 1.0
CA B:GLY66 3.5 21.9 1.0
C B:GLY66 3.6 23.1 1.0
CB B:LYS67 3.6 24.5 1.0
NZ B:LYS67 3.7 28.3 1.0
CA B:LYS67 3.7 23.6 1.0
CG B:LYS67 3.8 27.0 1.0
CD B:GLU81 3.9 20.3 1.0
MG B:MG408 4.0 21.9 1.0
O B:HOH571 4.0 23.0 1.0
OE1 B:GLU81 4.2 19.7 1.0
PG B:ATP401 4.2 24.1 1.0
O B:LYS67 4.2 23.6 1.0
P B:PO4402 4.2 35.2 1.0
CD B:LYS67 4.3 29.8 1.0
O2 B:PO4402 4.3 39.4 1.0
O B:HOH761 4.4 36.7 1.0
C B:LYS67 4.5 24.1 1.0
O4 B:PO4402 4.5 40.5 1.0
O2G B:ATP401 4.8 28.2 1.0
O B:GLY66 4.8 21.5 1.0
MG B:MG407 4.8 19.8 1.0
O1G B:ATP401 4.8 22.5 1.0
N B:GLY66 4.9 21.1 1.0

Fluorine binding site 4 out of 6 in 5xd5

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Fluorine binding site 4 out of 6 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 Fluorine with other atoms in the F 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
A:F409

b:30.0
occ:1.00
 MG A:MG405 1.9 30.3 1.0
MG A:MG406 2.0 31.7 1.0
MG A:MG408 2.0 31.1 1.0
OE1 A:GLU85 2.6 30.0 1.0
F A:F410 2.6 30.5 1.0
O1G A:ATP401 2.7 25.1 1.0
OE1 A:GLU127 2.7 35.4 1.0
O3G A:ATP401 2.8 29.8 1.0
OE2 A:GLU127 2.8 35.8 1.0
F A:F411 3.0 32.9 1.0
CD A:GLU127 3.1 45.6 1.0
O A:LYS65 3.2 26.5 1.0
OE1 A:GLU81 3.2 29.6 1.0
PG A:ATP401 3.2 31.2 1.0
CA A:GLY66 3.4 25.4 1.0
CD A:GLU81 3.8 29.2 1.0
CD A:GLU85 3.8 27.9 1.0
MG A:MG407 3.9 30.5 1.0
O A:HOH564 3.9 29.2 1.0
C A:LYS65 4.0 25.8 1.0
OE2 A:GLU81 4.1 28.7 1.0
O A:HOH531 4.1 28.8 1.0
N A:GLY66 4.2 23.1 1.0
O3B A:ATP401 4.3 38.7 1.0
O2G A:ATP401 4.4 31.8 1.0
O A:HOH557 4.5 47.7 1.0
CG A:GLU127 4.6 46.2 1.0
C A:GLY66 4.6 28.6 1.0
OE2 A:GLU85 4.6 30.8 1.0
N A:LYS67 4.6 29.9 1.0
CG A:GLU85 4.7 30.6 1.0
CG A:GLU81 4.9 28.8 1.0

Fluorine binding site 5 out of 6 in 5xd5

Go back to Fluorine Binding Sites List in 5xd5
Fluorine binding site 5 out of 6 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 Fluorine with other atoms in the F 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:F410

b:30.5
occ:1.00
 MG A:MG407 1.9 30.5 1.0
MG A:MG406 2.0 31.7 1.0
MG A:MG408 2.2 31.1 1.0
F A:F411 2.6 32.9 1.0
F A:F409 2.6 30.0 1.0
O A:HOH515 2.9 29.2 1.0
O A:HOH531 3.0 28.8 1.0
OE2 A:GLU81 3.0 28.7 1.0
OE1 A:GLU81 3.1 29.6 1.0
OE2 A:GLU127 3.2 35.8 1.0
CD A:GLU81 3.4 29.2 1.0
O A:HOH549 3.9 35.2 1.0
OE2 A:GLU84 4.0 34.7 1.0
O3G A:ATP401 4.1 29.8 1.0
CD A:GLU127 4.1 45.6 1.0
OE1 A:GLU85 4.2 30.0 1.0
MG A:MG405 4.4 30.3 1.0
OE1 A:GLU127 4.5 35.4 1.0
CA A:GLY66 4.9 25.4 1.0
CG A:GLU81 4.9 28.8 1.0

Fluorine binding site 6 out of 6 in 5xd5

Go back to Fluorine Binding Sites List in 5xd5
Fluorine binding site 6 out of 6 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 Fluorine with other atoms in the F 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:F411

b:32.9
occ:1.00
 MG A:MG408 1.9 31.1 1.0
MG A:MG407 2.0 30.5 1.0
F A:F410 2.6 30.5 1.0
N A:LYS67 2.8 29.9 1.0
O A:HOH549 2.8 35.2 1.0
O3G A:ATP401 3.0 29.8 1.0
OE2 A:GLU81 3.0 28.7 1.0
F A:F409 3.0 30.0 1.0
CA A:GLY66 3.5 25.4 1.0
CB A:LYS67 3.6 31.8 1.0
C A:GLY66 3.6 28.6 1.0
CA A:LYS67 3.7 31.5 1.0
CD A:GLU81 3.7 29.2 1.0
CG A:LYS67 3.7 36.3 1.0
MG A:MG406 3.8 31.7 1.0
OE1 A:GLU81 4.0 29.6 1.0
NZ A:LYS67 4.0 37.7 1.0
O A:HOH515 4.1 29.2 1.0
O A:LYS67 4.1 32.4 1.0
CE A:LYS67 4.1 38.8 1.0
PG A:ATP401 4.2 31.2 1.0
C A:LYS67 4.4 28.6 1.0
CD A:LYS67 4.5 44.0 1.0
O2G A:ATP401 4.6 31.8 1.0
O1G A:ATP401 4.7 25.1 1.0
MG A:MG405 4.7 30.3 1.0
O A:GLY66 4.7 26.8 1.0
CG A:GLU81 4.8 28.8 1.0
N A:GLY66 4.8 23.1 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: Thu Aug 1 16:52:32 2024

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