Atomistry » Sodium » PDB 4gg1-4gxi » 4gib
Atomistry »
  Sodium »
    PDB 4gg1-4gxi »
      4gib »

Sodium in PDB 4gib: 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile

Enzymatic activity of 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile

All present enzymatic activity of 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile:
5.4.2.6;

Protein crystallography data

The structure of 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile, PDB code: 4gib was solved by G.Minasov, A.Halavaty, L.Shuvalova, I.Dubrovska, J.Winsor, S.Grimshaw, L.Papazisi, W.F.Anderson, Center For Structural Genomics Of Infectiousdiseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.92 / 2.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.807, 51.364, 79.442, 90.00, 112.04, 90.00
R / Rfree (%) 19.3 / 25.9

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile (pdb code 4gib). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile, PDB code: 4gib:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4gib

Go back to Sodium Binding Sites List in 4gib
Sodium binding site 1 out of 4 in the 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:24.1
occ:1.00
 O A:HOH470 2.3 29.1 1.0
O A:HOH402 2.4 19.0 1.0
O A:MET184 2.5 21.4 1.0
OD1 A:ASN199 2.5 23.7 1.0
OD1 A:ASN180 2.6 24.2 1.0
OH A:TYR220 3.1 37.5 1.0
CG A:ASN199 3.4 24.8 1.0
CG A:ASN180 3.5 27.8 1.0
ND2 A:ASN199 3.6 26.6 1.0
C A:MET184 3.6 22.5 1.0
CZ A:TYR220 3.8 36.6 1.0
CA A:ASN180 3.9 25.8 1.0
CE1 A:TYR220 3.9 39.6 1.0
CB A:ASN180 3.9 25.2 1.0
N A:SER186 4.1 22.4 1.0
CA A:PHE185 4.2 23.2 1.0
N A:PHE185 4.3 22.3 1.0
OG A:SER186 4.4 22.6 1.0
N A:MET184 4.5 23.5 1.0
ND2 A:ASN180 4.5 22.7 1.0
C A:PHE185 4.6 22.7 1.0
CA A:MET184 4.7 22.6 1.0
CB A:SER186 4.7 22.2 1.0
O A:HOH463 4.7 31.2 1.0
N A:ASN180 4.7 24.2 1.0
O A:ASN180 4.8 28.0 1.0
CB A:ASN199 4.8 25.0 1.0
C A:ASN180 4.8 26.2 1.0
CE2 A:TYR220 4.9 38.3 1.0

Sodium binding site 2 out of 4 in 4gib

Go back to Sodium Binding Sites List in 4gib
Sodium binding site 2 out of 4 in the 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:23.5
occ:0.50
 O A:HOH427 2.2 41.4 1.0
OD2 A:ASP8 2.2 33.9 1.0
OE1 A:GLU170 2.2 35.1 1.0
OD1 A:ASP171 2.3 27.2 1.0
O A:ASP10 2.5 25.1 1.0
CD A:GLU170 3.2 32.1 1.0
CG A:ASP8 3.3 33.3 1.0
CG A:ASP171 3.4 28.2 1.0
OE2 A:GLU170 3.6 27.7 1.0
C A:ASP10 3.6 25.8 1.0
O1 A:PO4303 3.8 54.8 1.0
CB A:ASP8 3.9 28.6 1.0
N A:ASP171 3.9 24.2 1.0
OD2 A:ASP171 4.0 33.4 1.0
CB A:ASP10 4.3 26.3 1.0
OD1 A:ASP8 4.3 33.7 1.0
CB A:ASP171 4.4 25.6 1.0
CA A:ASP10 4.4 26.9 1.0
CE A:LYS44 4.5 45.2 1.0
CG A:GLU170 4.5 28.2 1.0
NZ A:LYS44 4.5 45.4 1.0
CA A:ASP171 4.5 25.2 1.0
N A:ALA172 4.5 26.4 1.0
CG2 A:VAL12 4.6 22.4 1.0
N A:ASP10 4.6 27.0 1.0
N A:GLY11 4.6 26.7 1.0
NZ A:LYS146 4.7 34.9 1.0
CA A:GLY11 4.8 26.7 1.0
CG A:ASP10 4.8 32.5 1.0
C A:ASP171 4.8 25.4 1.0
OD2 A:ASP10 4.9 37.3 1.0
CB A:ALA172 4.9 27.3 1.0
CA A:GLU170 4.9 23.7 1.0
C A:GLU170 4.9 24.0 1.0

Sodium binding site 3 out of 4 in 4gib

Go back to Sodium Binding Sites List in 4gib
Sodium binding site 3 out of 4 in the 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:28.1
occ:0.50
 O B:HOH432 2.3 27.8 1.0
O B:HOH450 2.4 42.3 1.0
O B:MET184 2.4 28.4 1.0
OD1 B:ASN199 2.6 30.1 1.0
OD1 B:ASN180 2.7 27.4 1.0
OH B:TYR220 3.1 59.4 1.0
CG B:ASN199 3.6 34.0 1.0
C B:MET184 3.6 25.8 1.0
CG B:ASN180 3.6 28.7 1.0
ND2 B:ASN199 3.8 37.6 1.0
CZ B:TYR220 3.9 58.7 1.0
CA B:ASN180 3.9 29.8 1.0
CB B:ASN180 4.0 30.9 1.0
O B:HOH449 4.1 30.5 1.0
CA B:PHE185 4.2 24.7 1.0
CE1 B:TYR220 4.2 56.9 1.0
N B:PHE185 4.3 25.5 1.0
N B:SER186 4.3 25.6 1.0
OG B:SER186 4.3 28.7 1.0
N B:MET184 4.4 30.1 1.0
O B:ASN180 4.6 31.9 1.0
CA B:MET184 4.6 26.6 1.0
ND2 B:ASN180 4.7 26.8 1.0
C B:PHE185 4.7 24.6 1.0
C B:ASN180 4.8 31.7 1.0
C B:ASN183 4.8 33.6 1.0
N B:ASN180 4.8 28.8 1.0
CE2 B:TYR220 4.9 57.8 1.0
CB B:ASN199 5.0 33.6 1.0

Sodium binding site 4 out of 4 in 4gib

Go back to Sodium Binding Sites List in 4gib
Sodium binding site 4 out of 4 in the 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:21.5
occ:0.50
 OE2 B:GLU170 2.1 37.0 1.0
OD1 B:ASP171 2.2 37.1 1.0
O B:ASP10 2.3 22.9 1.0
OD2 B:ASP8 2.4 28.9 1.0
CG B:ASP171 3.3 36.3 1.0
CD B:GLU170 3.3 35.9 1.0
C B:ASP10 3.5 24.6 1.0
O1 B:PO4304 3.5 55.6 1.0
CG B:ASP8 3.5 27.2 1.0
OD2 B:ASP171 3.9 41.0 1.0
N B:ASP171 4.0 29.3 1.0
CB B:ASP8 4.0 25.2 1.0
OE1 B:GLU170 4.1 38.5 1.0
CB B:ASP10 4.1 25.4 1.0
CE B:LYS44 4.1 48.9 1.0
OD2 B:ASP10 4.1 34.5 1.0
CA B:ASP10 4.2 25.6 1.0
CB B:ASP171 4.4 31.0 1.0
CG B:GLU170 4.4 33.5 1.0
CB B:ALA172 4.4 32.6 1.0
N B:GLY11 4.5 25.3 1.0
CG B:ASP10 4.5 29.3 1.0
N B:ASP10 4.5 25.9 1.0
N B:ALA172 4.6 31.4 1.0
CA B:ASP171 4.6 30.8 1.0
OD1 B:ASP8 4.6 25.1 1.0
CG2 B:VAL12 4.7 25.3 1.0
C B:ASP171 4.7 31.8 1.0
CA B:GLY11 4.7 25.0 1.0
NZ B:LYS44 4.8 47.1 1.0
P B:PO4304 4.9 59.4 1.0
C B:GLU170 4.9 28.1 1.0
CA B:GLU170 4.9 28.1 1.0

Reference:

G.Minasov, A.Halavaty, L.Shuvalova, I.Dubrovska, J.Winsor, S.Grimshaw, L.Papazisi, W.F.Anderson. 2.27 Angstrom Crystal Structure of Beta-Phosphoglucomutase (Pgmb) From Clostridium Difficile. To Be Published.
Page generated: Mon Oct 7 15:35:27 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy