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Sodium in PDB 2wf8: Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride

Enzymatic activity of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride

All present enzymatic activity of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride:
5.4.2.6;

Protein crystallography data

The structure of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride, PDB code: 2wf8 was solved by M.W.Bowler, N.J.Baxter, C.E.Webster, S.Pollard, T.Alizadeh, A.M.Hounslow, M.J.Cliff, W.Bermel, N.H.Williams, F.Hollfelder, 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 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.300, 54.300, 104.200, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.1

Other elements in 2wf8:

The structure of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride (pdb code 2wf8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride, PDB code: 2wf8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2wf8

Go back to Sodium Binding Sites List in 2wf8
Sodium binding site 1 out of 2 in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1225

b:15.7
occ:0.70
 O A:HOH2163 2.1 23.0 1.0
O A:HOH2152 2.1 18.4 1.0
O A:HOH2050 2.2 30.3 1.0
NE2 A:GLN98 4.0 16.2 0.5
O A:HOH2156 4.3 20.9 1.0
O A:HOH2154 4.3 31.7 1.0
OD2 A:ASP102 4.3 15.7 1.0
NE2 A:GLN98 4.4 10.5 0.5
OD1 A:ASP102 4.4 15.1 1.0
CD A:GLN98 4.5 14.2 0.5
O A:HOH2245 4.6 26.1 1.0
CD A:GLN98 4.6 9.8 0.5
CG A:GLN98 4.8 9.6 0.5
CG A:ASP102 4.8 13.1 1.0
CG A:GLN98 4.9 12.2 0.5

Sodium binding site 2 out of 2 in 2wf8

Go back to Sodium Binding Sites List in 2wf8
Sodium binding site 2 out of 2 in the Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Beta-Phosphoglucomutase Inhibited with Glucose-6- Phosphate, Glucose-1-Phosphate and Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1226

b:25.6
occ:1.00
 OE1 A:GLN98 2.2 15.7 0.5
O A:HOH2241 2.6 16.6 1.0
O A:HOH2148 2.8 15.6 1.0
O A:HOH2155 2.8 21.3 1.0
CD A:GLN98 2.9 14.2 0.5
O A:HOH2156 3.0 20.9 1.0
NE2 A:GLN98 3.4 16.2 0.5
CB A:GLN98 3.8 10.9 0.5
CG A:GLN98 3.8 12.2 0.5
CA A:GLY95 3.8 10.0 1.0
CB A:GLN98 3.9 9.9 0.5
CG2 A:THR208 4.0 14.8 1.0
CG A:GLN98 4.2 9.6 0.5
O A:GLY95 4.2 10.4 1.0
C A:GLY95 4.5 9.3 1.0
O A:HOH2161 4.6 15.4 1.0
O A:HOH2153 4.8 13.1 1.0
O A:HOH2150 4.8 24.9 1.0
O A:SER205 4.8 11.4 1.0
N A:GLY95 4.8 9.8 1.0
O A:HOH2154 5.0 31.7 1.0

Reference:

J.L.Griffin, M.W.Bowler, N.J.Baxter, K.N.Leigh, H.R.Dannatt, A.M.Hounslow, G.M.Blackburn, C.E.Webster, M.J.Cliff, J.P.Waltho. Near Attack Conformers Dominate Beta-Phosphoglucomutase Complexes Where Geometry and Charge Distribution Reflect Those of Substrate. Proc. Natl. Acad. Sci. V. 109 6910 2012U.S.A..
ISSN: ESSN 1091-6490
PubMed: 22505741
DOI: 10.1073/PNAS.1116855109
Page generated: Tue Dec 15 05:57:24 2020

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