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Magnesium in PDB 5oly: 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form

Enzymatic activity of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form

All present enzymatic activity of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form:
5.4.2.6;

Protein crystallography data

The structure of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form, PDB code: 5oly was solved by M.W.Bowler, J.Von Velsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.47 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.737, 36.714, 107.853, 90.00, 105.27, 90.00
R / Rfree (%) 20.4 / 25.5

Other elements in 5oly:

The structure of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form also contains other interesting chemical elements:

Fluorine (F) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form (pdb code 5oly). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form, PDB code: 5oly:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5oly

Go back to Magnesium Binding Sites List in 5oly
Magnesium binding site 1 out of 6 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:10.9
occ:1.00
 MG A:MGF301 0.0 10.9 1.0
F1 A:MGF301 1.7 13.8 1.0
F2 A:MGF301 1.9 7.7 1.0
O1 A:G6P303 2.0 7.6 1.0
OD1 A:ASP8 2.0 10.9 1.0
F3 A:MGF301 2.1 14.6 1.0
CG A:ASP8 3.0 10.7 1.0
C1 A:G6P303 3.3 16.1 1.0
OD2 A:ASP8 3.4 10.6 1.0
MG A:MG302 3.4 9.2 1.0
O2 A:G6P303 3.5 10.1 1.0
NZ A:LYS145 3.8 8.5 1.0
N A:ASP10 3.9 9.7 1.0
OD2 A:ASP10 3.9 9.3 1.0
OG A:SER114 3.9 14.3 1.0
C2 A:G6P303 4.0 7.0 1.0
N A:LEU9 4.0 9.8 1.0
N A:ALA115 4.1 13.2 1.0
CA A:SER114 4.2 11.8 1.0
O5 A:G6P303 4.2 10.3 1.0
CB A:ASP10 4.3 9.8 1.0
CB A:ASP8 4.4 9.9 1.0
CB A:SER114 4.4 5.2 1.0
CG A:ASP10 4.4 11.0 1.0
O A:ASP10 4.5 9.4 1.0
CA A:ASP10 4.6 15.0 1.0
C A:SER114 4.6 9.4 1.0
OE2 A:GLU169 4.7 12.2 1.0
C A:LEU9 4.7 9.4 1.0
CA A:LEU9 4.8 9.5 1.0
CA A:GLY46 4.8 10.8 1.0
CA A:ASP8 4.8 6.0 1.0
C A:ASP8 4.9 9.3 1.0
CB A:LEU9 4.9 7.2 1.0
CE A:LYS145 5.0 13.3 1.0

Magnesium binding site 2 out of 6 in 5oly

Go back to Magnesium Binding Sites List in 5oly
Magnesium binding site 2 out of 6 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:9.2
occ:1.00
 F3 A:MGF301 1.8 14.6 1.0
OD1 A:ASP170 2.0 11.0 1.0
OD2 A:ASP8 2.1 10.6 1.0
O A:ASP10 2.2 9.4 1.0
CG A:ASP170 3.1 11.4 1.0
CG A:ASP8 3.1 10.7 1.0
MG A:MGF301 3.4 10.9 1.0
C A:ASP10 3.4 10.1 1.0
OD1 A:ASP8 3.4 10.9 1.0
OD2 A:ASP170 3.4 9.1 1.0
O2 A:G6P303 3.8 10.1 1.0
OE1 A:GLU169 4.0 10.4 1.0
CA A:ASP10 4.1 15.0 1.0
CB A:ASP10 4.1 9.8 1.0
N A:ASP10 4.1 9.7 1.0
CB A:ASP170 4.4 8.5 1.0
CB A:ASP8 4.4 9.9 1.0
F2 A:MGF301 4.4 7.7 1.0
O1 A:G6P303 4.5 7.6 1.0
N A:GLY11 4.5 9.2 1.0
OE2 A:GLU169 4.5 12.2 1.0
N A:ASP170 4.6 11.7 1.0
F1 A:MGF301 4.6 13.8 1.0
CD A:GLU169 4.6 13.2 1.0
N A:GLY46 4.7 10.4 1.0
O A:HOH490 4.7 9.7 1.0
CA A:GLY11 4.8 10.5 1.0
CB A:SER171 4.8 4.1 1.0
CG2 A:VAL12 4.8 11.2 1.0
C A:LEU9 4.9 9.4 1.0
OG A:SER171 4.9 9.2 1.0
CA A:ASP170 4.9 7.2 1.0
C2 A:G6P303 4.9 7.0 1.0
CA A:GLY46 4.9 10.8 1.0
N A:SER171 5.0 8.1 1.0

Magnesium binding site 3 out of 6 in 5oly

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Magnesium binding site 3 out of 6 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:39.1
occ:1.00
 O A:HOH554 1.6 26.8 1.0
O A:GLY130 3.8 20.8 1.0
O A:PHE132 4.0 22.6 1.0
O A:HOH456 4.3 20.7 1.0
C A:GLY130 4.6 22.2 1.0
O A:HOH435 4.8 15.2 1.0
C A:PHE132 4.9 19.4 1.0
CA A:GLY130 4.9 23.7 1.0

Magnesium binding site 4 out of 6 in 5oly

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Magnesium binding site 4 out of 6 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:8.2
occ:1.00
 F3 G:MGF304 1.9 11.2 1.0
OD2 G:ASP8 2.0 8.7 1.0
OD1 G:ASP170 2.1 6.7 1.0
O G:ASP10 2.1 10.0 1.0
CG G:ASP170 3.0 9.1 1.0
CG G:ASP8 3.1 7.4 1.0
C G:ASP10 3.3 9.6 1.0
OD2 G:ASP170 3.3 8.3 1.0
OD1 G:ASP8 3.5 7.3 1.0
MG G:MGF304 3.5 7.9 1.0
O2 G:G6P303 3.8 10.0 1.0
OE1 G:GLU169 4.0 7.2 1.0
CA G:ASP10 4.1 6.4 1.0
CB G:ASP10 4.1 11.4 1.0
N G:ASP10 4.2 5.7 1.0
CB G:ASP8 4.3 9.9 1.0
N G:GLY11 4.3 6.8 1.0
CB G:ASP170 4.4 9.5 1.0
F2 G:MGF304 4.4 11.2 1.0
N G:GLY46 4.6 11.2 1.0
O G:HOH538 4.6 10.4 1.0
N G:ASP170 4.6 9.8 1.0
CA G:GLY11 4.6 10.9 1.0
OE2 G:GLU169 4.6 10.8 1.0
CD G:GLU169 4.6 10.3 1.0
CG2 G:VAL12 4.7 11.0 1.0
CB G:SER171 4.8 12.9 1.0
O1 G:G6P303 4.8 5.3 1.0
F1 G:MGF304 4.8 12.1 1.0
CA G:GLY46 4.8 10.6 1.0
OG G:SER171 4.9 12.3 1.0
C G:LEU9 4.9 5.6 1.0
CA G:ASP170 4.9 12.7 1.0
N G:SER171 4.9 14.8 1.0

Magnesium binding site 5 out of 6 in 5oly

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Magnesium binding site 5 out of 6 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:30.0
occ:1.00
 O G:HOH566 2.1 23.9 1.0
O G:HOH498 2.6 15.1 1.0
OE2 G:GLU67 4.1 32.2 1.0
OE1 G:GLU67 4.2 28.0 1.0
O G:HOH525 4.2 19.1 1.0
CD G:GLU67 4.4 26.8 1.0
CB G:SER65 4.8 22.9 1.0
O G:HOH611 5.0 23.4 1.0

Magnesium binding site 6 out of 6 in 5oly

Go back to Magnesium Binding Sites List in 5oly
Magnesium binding site 6 out of 6 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in A Closed Conformation, Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg304

b:7.9
occ:1.00
 MG G:MGF304 0.0 7.9 1.0
F1 G:MGF304 1.8 12.1 1.0
F2 G:MGF304 1.8 11.2 1.0
F3 G:MGF304 1.9 11.2 1.0
OD1 G:ASP8 2.0 7.3 1.0
O1 G:G6P303 2.2 5.3 1.0
CG G:ASP8 2.9 7.4 1.0
OD2 G:ASP8 3.3 8.7 1.0
C1 G:G6P303 3.4 8.0 1.0
O2 G:G6P303 3.5 10.0 1.0
MG G:MG301 3.5 8.2 1.0
OG G:SER114 3.8 10.0 1.0
OD2 G:ASP10 3.8 10.9 1.0
N G:ASP10 3.9 5.7 1.0
N G:ALA115 3.9 13.2 1.0
NZ G:LYS145 3.9 12.3 1.0
N G:LEU9 4.0 7.0 1.0
CA G:SER114 4.0 9.2 1.0
C2 G:G6P303 4.0 12.2 1.0
CB G:ASP10 4.1 11.4 1.0
O5 G:G6P303 4.3 15.1 1.0
CB G:ASP8 4.3 9.9 1.0
CB G:SER114 4.3 6.6 1.0
CG G:ASP10 4.3 6.7 1.0
O G:ASP10 4.4 10.0 1.0
C G:SER114 4.5 15.3 1.0
CA G:ASP10 4.5 6.4 1.0
CA G:GLY46 4.7 10.6 1.0
CA G:ASP8 4.7 7.2 1.0
C G:LEU9 4.7 5.6 1.0
OE2 G:GLU169 4.8 10.8 1.0
CA G:LEU9 4.8 6.4 1.0
C G:ASP8 4.9 5.3 1.0
C G:ASP10 4.9 9.6 1.0
CA G:ALA115 4.9 14.2 1.0
O G:ALA113 5.0 10.9 1.0
CB G:ALA115 5.0 24.5 1.0
N G:SER116 5.0 7.6 1.0

Reference:

A.Ampaw, M.Carroll, J.Von Velsen, D.Bhattasali, A.Cohen, M.W.Bowler, D.L.Jakeman. Observing Enzyme Ternary Transition State Analogue Complexes BY19F uc(Nmr) Spectroscopy. Chem Sci V. 8 8427 2017.
ISSN: ISSN 2041-6520
PubMed: 29619190
DOI: 10.1039/C7SC04204C
Page generated: Mon Sep 30 01:02:50 2024

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