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Sodium in PDB 6hdk: R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Aluminium Tetrafluoride and Beta-G6P to 1.2 A.

Enzymatic activity of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Aluminium Tetrafluoride and Beta-G6P to 1.2 A.

All present enzymatic activity of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Aluminium Tetrafluoride and Beta-G6P to 1.2 A.:
5.4.2.6;

Protein crystallography data

The structure of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Aluminium Tetrafluoride and Beta-G6P to 1.2 A., PDB code: 6hdk was solved by A.J.Robertson, C.Bisson, J.P.Waltho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.17 / 1.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.230, 54.290, 104.240, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 16.7

Other elements in 6hdk:

The structure of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Aluminium Tetrafluoride and Beta-G6P to 1.2 A. also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Magnesium (Mg) 1 atom
Aluminium (Al) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Aluminium Tetrafluoride and Beta-G6P to 1.2 A. (pdb code 6hdk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Aluminium Tetrafluoride and Beta-G6P to 1.2 A., PDB code: 6hdk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6hdk

Go back to Sodium Binding Sites List in 6hdk
Sodium binding site 1 out of 2 in the R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Aluminium Tetrafluoride and Beta-G6P to 1.2 A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Aluminium Tetrafluoride and Beta-G6P to 1.2 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:18.4
occ:1.00
 O A:GLU124 2.2 11.8 1.0
OD1 A:ASN127 2.3 15.9 1.0
O A:HOH571 2.3 24.0 1.0
O A:HOH543 2.4 42.6 1.0
O A:HOH479 2.4 19.8 1.0
O A:HOH560 2.5 26.4 1.0
C A:GLU124 3.4 10.6 1.0
CG A:ASN127 3.5 14.6 1.0
O A:HOH527 4.0 48.4 1.0
O A:ARG125 4.1 11.7 1.0
C A:ARG125 4.2 10.2 1.0
CA A:ARG125 4.2 10.6 1.0
N A:ARG125 4.2 10.2 1.0
ND2 A:ASN127 4.2 21.2 1.0
N A:ASN127 4.2 10.6 1.0
O A:HOH563 4.3 29.1 1.0
CA A:GLU124 4.3 12.0 1.0
CA A:ASN127 4.4 10.6 1.0
CB A:ASN127 4.6 12.4 1.0
O A:HOH608 4.6 29.7 1.0
O A:HOH568 4.8 35.5 1.0
CB A:GLU124 4.8 15.0 1.0
OE2 A:GLU124 4.8 39.1 1.0
NH1 A:ARG125 4.8 17.6 1.0
O A:HOH565 4.8 30.5 1.0
N A:MET126 4.9 9.4 1.0
O A:HOH586 5.0 39.1 1.0

Sodium binding site 2 out of 2 in 6hdk

Go back to Sodium Binding Sites List in 6hdk
Sodium binding site 2 out of 2 in the R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Aluminium Tetrafluoride and Beta-G6P to 1.2 A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of R49A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis Complexed with Aluminium Tetrafluoride and Beta-G6P to 1.2 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:27.8
occ:1.00
 O A:HOH574 2.3 37.2 1.0
O A:PHE132 2.4 15.3 1.0
O A:HOH541 2.5 38.0 1.0
O A:THR129 2.5 13.0 1.0
O A:HOH569 2.7 18.8 0.5
C A:THR129 3.5 11.9 1.0
C A:PHE132 3.5 12.3 1.0
O A:HOH569 3.6 24.7 0.5
CA A:GLY130 3.9 13.3 1.0
N A:PHE132 4.0 11.3 1.0
C A:GLY130 4.0 14.2 1.0
N A:GLY130 4.1 13.2 1.0
CG2 A:THR129 4.1 15.9 1.0
O A:GLY130 4.2 19.8 1.0
CA A:PHE132 4.2 11.3 1.0
CB A:PHE132 4.4 10.8 1.0
O A:HOH481 4.5 40.8 1.0
O A:HOH498 4.6 38.3 1.0
N A:TYR131 4.6 11.8 1.0
CA A:THR129 4.6 11.8 1.0
O A:HOH607 4.6 37.8 1.0
N A:ASP133 4.7 12.0 1.0
C A:TYR131 4.9 12.9 1.0
CB A:THR129 4.9 13.9 1.0
CA A:ASP133 5.0 13.6 1.0

Reference:

A.J.Robertson, C.Bisson, J.P.Waltho. Transition State of Phospho-Enzyme Hydrolysis in Beta-Phosphoglucomutase. To Be Published.
Page generated: Tue Dec 15 12:20:10 2020

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