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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

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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

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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

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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

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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: Sun Aug 17 19:29:07 2025

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