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Sodium in PDB 7ugh: Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid

Enzymatic activity of Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid

All present enzymatic activity of Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid:
4.2.1.11;

Protein crystallography data

The structure of Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid, PDB code: 7ugh was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.26 / 1.95
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.86, 96.86, 216.64, 90, 90, 90
R / Rfree (%) 15.3 / 19.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid (pdb code 7ugh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid, PDB code: 7ugh:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7ugh

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Sodium binding site 1 out of 4 in the Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:31.5
occ:1.00
 OE2 A:GLU379 2.2 30.8 1.0
OD2 A:ASP406 2.3 30.9 1.0
OD2 A:ASP333 2.4 33.2 1.0
O2 A:2PG601 2.4 44.3 0.7
O A:HOH828 2.5 31.0 1.0
O1 A:2PG601 2.5 36.0 0.7
C1 A:2PG601 2.8 38.9 0.7
CG A:ASP333 3.3 35.3 1.0
CG A:ASP406 3.3 33.3 1.0
O A:HOH710 3.3 38.1 1.0
CD A:GLU379 3.4 32.0 1.0
OD1 A:ASP333 3.5 33.5 1.0
NZ A:LYS482 3.6 37.0 1.0
CB A:ASP406 3.8 31.6 1.0
CD2 A:LEU429 4.1 29.9 1.0
OE1 A:GLU379 4.2 33.1 1.0
CG A:GLU379 4.2 31.0 1.0
OD2 A:ASP380 4.3 34.3 1.0
NZ A:LYS431 4.3 35.5 1.0
C2 A:2PG601 4.3 38.0 0.7
OD1 A:ASP406 4.4 32.5 1.0
O A:HOH753 4.4 46.8 1.0
CB A:ASP333 4.6 31.7 1.0
O A:HOH893 4.6 50.7 1.0
O3 A:2PG601 4.7 46.3 0.7
O1P A:2PG601 4.9 41.7 0.7
OE2 A:GLU253 4.9 52.9 1.0

Sodium binding site 2 out of 4 in 7ugh

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Sodium binding site 2 out of 4 in the Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na608

b:52.9
occ:1.00
 O A:GLY242 2.3 37.6 1.0
O A:HOH816 2.4 47.1 1.0
O A:ALA245 2.4 46.7 1.0
O A:HOH780 2.5 42.2 1.0
O A:GLY247 3.2 41.3 1.0
O A:HOH763 3.3 41.0 1.0
C A:GLY242 3.4 42.3 1.0
C A:ALA245 3.5 47.6 1.0
OE1 A:GLN351 3.7 48.4 1.0
CA A:GLY242 4.2 40.6 1.0
N A:ALA245 4.2 47.0 1.0
N A:LYS243 4.3 47.2 1.0
C A:GLY247 4.4 39.0 1.0
N A:GLY246 4.4 46.5 1.0
N A:GLY242 4.4 36.8 1.0
O A:LEU249 4.4 37.4 1.0
CA A:ALA245 4.4 47.0 1.0
C A:GLY246 4.4 46.0 1.0
CA A:LYS243 4.5 50.3 1.0
CA A:GLY246 4.5 43.8 1.0
N A:GLY247 4.5 44.6 1.0
C A:LYS243 4.6 49.2 1.0
OE1 A:GLN250 4.8 40.8 1.0
O A:GLY246 4.9 48.0 1.0
CD A:GLN351 4.9 53.8 1.0
O A:LYS243 5.0 53.8 1.0
N A:HIS244 5.0 51.5 1.0

Sodium binding site 3 out of 4 in 7ugh

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Sodium binding site 3 out of 4 in the Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na607

b:32.0
occ:1.00
 OE2 B:GLU379 2.2 32.1 1.0
OD2 B:ASP406 2.2 29.7 1.0
O B:HOH758 2.4 30.7 1.0
O1 B:2PG602 2.4 42.5 0.8
OD2 B:ASP333 2.4 34.5 1.0
O2 B:2PG602 2.6 37.5 0.8
C1 B:2PG602 2.8 39.4 0.8
CG B:ASP406 3.3 32.0 1.0
CG B:ASP333 3.3 36.2 1.0
CD B:GLU379 3.3 33.4 1.0
OD1 B:ASP333 3.5 30.3 1.0
O B:HOH733 3.5 37.2 1.0
NZ B:LYS482 3.6 35.0 1.0
CB B:ASP406 3.7 28.8 1.0
O B:HOH922 3.9 42.1 1.0
CD2 B:LEU429 4.1 28.9 1.0
OE1 B:GLU379 4.2 30.4 1.0
NZ B:LYS431 4.2 34.3 1.0
CG B:GLU379 4.2 29.3 1.0
OD2 B:ASP380 4.3 33.8 1.0
C2 B:2PG602 4.3 36.1 0.8
OD1 B:ASP406 4.3 30.3 1.0
CB B:ASP333 4.6 33.0 1.0
OE2 B:GLU253 4.7 57.4 1.0
O3 B:2PG602 4.7 41.1 0.8
O B:HOH926 4.8 50.7 1.0
O1P B:2PG602 4.9 38.4 0.8

Sodium binding site 4 out of 4 in 7ugh

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Sodium binding site 4 out of 4 in the Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Enolase Family Protein From Naegleria Fowleri with Bound 2-Phosphoglyceric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na608

b:53.9
occ:1.00
 O B:HOH774 2.3 44.8 1.0
O B:ALA245 2.4 46.4 1.0
O B:HOH844 2.4 48.6 1.0
O B:GLY242 2.4 43.9 1.0
O B:HOH837 2.8 45.4 1.0
O B:GLY247 3.2 43.6 1.0
C B:GLY242 3.5 46.4 1.0
C B:ALA245 3.5 48.0 1.0
OE1 B:GLN351 4.0 50.7 1.0
CA B:GLY242 4.2 41.7 1.0
N B:ALA245 4.3 48.7 1.0
O B:LEU249 4.3 39.3 1.0
N B:GLY246 4.3 46.0 1.0
C B:GLY247 4.3 46.4 1.0
C B:GLY246 4.3 48.0 1.0
N B:GLY247 4.4 47.5 1.0
CA B:GLY246 4.4 47.2 1.0
N B:GLY242 4.4 37.6 1.0
CA B:ALA245 4.4 47.6 1.0
N B:LYS243 4.4 47.4 1.0
CA B:LYS243 4.7 51.0 1.0
C B:LYS243 4.8 50.1 1.0
O B:GLY246 4.8 46.1 1.0
OE1 B:GLN250 4.8 44.6 1.0
CB B:ALA245 5.0 45.1 1.0
CA B:GLY247 5.0 44.9 1.0

Reference:

M.J.Bolejack, N.D.Debouver, J.C.Morris, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Nadp-Linked Putative Oxidoreductase From Klebsiella Pneumoniae To Be Published.
Page generated: Fri Apr 7 16:39:19 2023

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