Atomistry » Magnesium » PDB 5odz-5onh » 5oly
Atomistry »
  Magnesium »
    PDB 5odz-5onh »
      5oly »

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

Go back to Magnesium Binding Sites List in 5oly
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

Go back to Magnesium Binding Sites List in 5oly
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

Go back to Magnesium Binding Sites List in 5oly
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy