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Magnesium in PDB 2wf5: Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate

Enzymatic activity of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate

All present enzymatic activity of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate:
5.4.2.6;

Protein crystallography data

The structure of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate, PDB code: 2wf5 was solved by M.W.Bowler, N.J.Baxter, C.E.Webster, A.M.Hounslow, M.J.Cliff, N.H.Williams, F.Hollfelder, S.Gamblin, G.M.Blackburn, J.P.Waltho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.647, 54.659, 105.120, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.2

Other elements in 2wf5:

The structure of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate (pdb code 2wf5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate, PDB code: 2wf5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2wf5

Go back to Magnesium Binding Sites List in 2wf5
Magnesium binding site 1 out of 3 in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2801

b:14.9
occ:1.00
 O A:HOH2142 2.0 13.6 1.0
O A:HOH2058 2.1 18.2 1.0
O A:HOH2143 2.1 16.6 1.0
O A:HOH2060 2.2 23.3 1.0
CA A:GLY130 4.2 9.3 1.0
O A:HOH2059 4.2 29.9 1.0
O A:THR129 4.3 9.8 1.0
O A:HOH2144 4.3 15.0 1.0
O A:HOH2147 4.3 24.3 1.0
O A:PHE132 4.6 11.6 1.0
C A:THR129 4.7 9.2 1.0
CG2 A:THR129 4.7 13.1 1.0
N A:GLY130 4.7 8.9 1.0

Magnesium binding site 2 out of 3 in 2wf5

Go back to Magnesium Binding Sites List in 2wf5
Magnesium binding site 2 out of 3 in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2832

b:10.3
occ:1.00
 MG A:MGF2832 0.0 10.3 1.0
F3 A:MGF2832 1.8 12.5 1.0
F2 A:MGF2832 1.8 9.4 1.0
F1 A:MGF2832 1.9 8.5 1.0
OD1 A:ASP8 2.1 8.0 1.0
O1 A:BG61831 2.2 9.5 1.0
CG A:ASP8 3.1 6.9 1.0
C1 A:BG61831 3.2 9.1 1.0
OD2 A:ASP8 3.4 7.7 1.0
MG A:MG2833 3.5 8.1 1.0
O2 A:BG61831 3.6 9.5 1.0
O A:HOH2170 3.7 8.7 1.0
OG A:SER114 3.7 10.1 1.0
NZ A:LYS145 3.8 9.9 1.0
N A:ASP10 3.9 7.3 1.0
N A:ALA115 3.9 11.9 1.0
OD2 A:ASP10 3.9 9.0 1.0
C2 A:BG61831 4.0 8.9 1.0
CA A:SER114 4.0 10.7 1.0
N A:LEU9 4.0 6.5 1.0
CB A:SER114 4.2 10.6 1.0
CB A:ASP10 4.2 6.9 1.0
O5 A:BG61831 4.3 9.9 1.0
CG A:ASP10 4.4 8.2 1.0
CB A:ASP8 4.4 6.7 1.0
O A:ASP10 4.5 7.3 1.0
C A:SER114 4.5 11.5 1.0
CA A:ASP10 4.6 6.9 1.0
C A:LEU9 4.7 6.8 1.0
CA A:ASP8 4.8 6.6 1.0
CA A:LEU9 4.8 6.5 1.0
CA A:GLY46 4.8 10.2 1.0
O A:HOH2172 4.8 8.1 1.0
CB A:ALA115 4.9 13.5 1.0
C A:ASP8 4.9 6.6 1.0
CA A:ALA115 4.9 12.1 1.0
N A:SER116 5.0 10.5 1.0
OE2 A:GLU169 5.0 12.6 1.0

Magnesium binding site 3 out of 3 in 2wf5

Go back to Magnesium Binding Sites List in 2wf5
Magnesium binding site 3 out of 3 in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate and Trifluoromagnesate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2833

b:8.1
occ:1.00
 F1 A:MGF2832 1.9 8.5 1.0
OD2 A:ASP8 2.1 7.7 1.0
O A:HOH2170 2.1 8.7 1.0
OD1 A:ASP170 2.1 7.5 1.0
O A:HOH2172 2.1 8.1 1.0
O A:ASP10 2.2 7.3 1.0
CG A:ASP170 3.1 8.5 1.0
CG A:ASP8 3.1 6.9 1.0
C A:ASP10 3.3 7.0 1.0
OD2 A:ASP170 3.4 8.6 1.0
OD1 A:ASP8 3.4 8.0 1.0
MG A:MGF2832 3.5 10.3 1.0
O2 A:BG61831 3.9 9.5 1.0
CA A:ASP10 4.1 6.9 1.0
OE1 A:GLU169 4.1 10.8 1.0
CB A:ASP10 4.1 6.9 1.0
N A:ASP10 4.1 7.3 1.0
N A:GLY11 4.4 6.7 1.0
CB A:ASP8 4.4 6.7 1.0
CB A:ASP170 4.4 8.2 1.0
F2 A:MGF2832 4.5 9.4 1.0
O A:HOH2200 4.6 9.4 1.0
N A:ASP170 4.6 8.0 1.0
F3 A:MGF2832 4.6 12.5 1.0
CA A:GLY11 4.7 6.8 1.0
CB A:SER171 4.7 10.9 1.0
N A:GLY46 4.7 9.4 1.0
CD A:GLU169 4.8 10.0 1.0
OG A:SER171 4.8 10.8 1.0
O1 A:BG61831 4.8 9.5 1.0
OE2 A:GLU169 4.8 12.6 1.0
C A:LEU9 4.9 6.8 1.0
CG2 A:VAL12 4.9 9.1 1.0
CA A:ASP170 4.9 8.3 1.0
CA A:GLY46 5.0 10.2 1.0

Reference:

N.J.Baxter, M.W.Bowler, T.Alizadeh, M.J.Cliff, A.M.Hounslow, B.Wu, D.B.Berkowitz, N.H.Williams, G.M.Blackburn, J.P.Waltho. Atomic Details of Near-Transition State Conformers For Enzyme Phosphoryl Transfer Revealed By Mgf-3 Rather Than By Phosphoranes. Proc. Natl. Acad. Sci. V. 107 4555 2010U.S.A..
ISSN: ESSN 1091-6490
PubMed: 20164409
DOI: 10.1073/PNAS.0910333106
Page generated: Mon Dec 14 07:44:07 2020

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