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Sodium in PDB 6hdf: D170N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in An Open Conformer to 1.4 A.

Enzymatic activity of D170N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in An Open Conformer to 1.4 A.

All present enzymatic activity of D170N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in An Open Conformer to 1.4 A.:
5.4.2.6;

Protein crystallography data

The structure of D170N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in An Open Conformer to 1.4 A., PDB code: 6hdf was solved by H.P.Wood, 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) 52.98 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.770, 119.310, 53.170, 90.00, 94.80, 90.00
R / Rfree (%) 17.2 / 22.4

Sodium Binding Sites:

The binding sites of Sodium atom in the D170N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in An Open Conformer to 1.4 A. (pdb code 6hdf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the D170N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in An Open Conformer to 1.4 A., PDB code: 6hdf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6hdf

Go back to Sodium Binding Sites List in 6hdf
Sodium binding site 1 out of 2 in the D170N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in An Open Conformer to 1.4 A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of D170N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in An Open Conformer to 1.4 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:19.9
occ:1.00
OD1 A:ASN170 2.1 18.8 1.0
O A:HOH517 2.2 27.3 1.0
O A:ASP10 2.3 14.8 1.0
OD2 A:ASP8 2.4 18.0 1.0
OE1 A:GLU169 2.7 20.0 1.0
CG A:ASN170 3.3 17.3 1.0
O A:HOH424 3.5 22.3 1.0
CG A:ASP8 3.5 13.9 1.0
C A:ASP10 3.5 13.0 1.0
CD A:GLU169 3.7 17.2 1.0
CB A:ASP8 3.9 13.6 1.0
O A:HOH426 3.9 21.2 1.0
OE2 A:GLU169 4.0 14.9 1.0
ND2 A:ASN170 4.1 20.7 1.0
N A:ASN170 4.2 13.3 1.0
N A:GLY11 4.4 14.1 1.0
CA A:GLY11 4.4 13.8 1.0
CB A:ASN170 4.4 14.2 1.0
CA A:ASP10 4.5 12.2 1.0
OD1 A:ASP8 4.5 14.8 1.0
N A:SER171 4.6 15.1 1.0
CB A:ASP10 4.6 13.7 1.0
N A:ASP10 4.7 12.6 1.0
CG2 A:VAL12 4.7 15.0 1.0
CB A:SER171 4.7 17.8 1.0
OG A:SER171 4.7 18.4 1.0
CA A:ASN170 4.7 14.4 1.0
C A:GLY11 4.9 13.4 1.0
C A:ASN170 4.9 15.0 1.0
OD2 A:ASP10 5.0 21.7 1.0
CG A:GLU169 5.0 12.8 1.0

Sodium binding site 2 out of 2 in 6hdf

Go back to Sodium Binding Sites List in 6hdf
Sodium binding site 2 out of 2 in the D170N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in An Open Conformer to 1.4 A.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of D170N Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in An Open Conformer to 1.4 A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:20.9
occ:1.00
OD1 B:ASN170 2.2 19.0 1.0
O B:ASP10 2.3 16.8 1.0
OD2 B:ASP8 2.3 18.8 1.0
O B:HOH520 2.3 31.4 1.0
OE1 B:GLU169 2.7 21.7 1.0
CG B:ASP8 3.3 14.1 1.0
CG B:ASN170 3.4 19.8 1.0
C B:ASP10 3.5 17.6 1.0
O B:HOH436 3.5 24.3 1.0
CD B:GLU169 3.6 18.2 1.0
CB B:ASP8 3.8 15.4 1.0
O B:HOH403 3.8 24.3 1.0
OE2 B:GLU169 3.9 19.5 1.0
ND2 B:ASN170 4.2 21.8 1.0
N B:ASN170 4.2 17.6 1.0
N B:GLY11 4.4 16.0 1.0
OD1 B:ASP8 4.4 18.8 1.0
CA B:ASP10 4.4 14.1 1.0
CA B:GLY11 4.5 16.3 1.0
O B:HOH503 4.5 24.7 1.0
CB B:ASN170 4.5 18.9 1.0
CB B:ASP10 4.6 15.7 1.0
N B:SER171 4.6 18.6 1.0
N B:ASP10 4.6 13.1 1.0
CG2 B:VAL12 4.7 14.6 1.0
CA B:ASN170 4.7 17.8 1.0
OG B:SER171 4.8 20.9 1.0
CB B:SER171 4.8 20.4 1.0
C B:GLY11 4.9 15.2 1.0
CG B:GLU169 4.9 16.6 1.0
C B:ASN170 4.9 20.9 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 12:20:09 2020

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