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Sodium in PDB 3gc2: 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid

Enzymatic activity of 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid

All present enzymatic activity of 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid:
4.2.1.113;

Protein crystallography data

The structure of 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid, PDB code: 3gc2 was solved by G.Minasov, Z.Wawrzak, T.Skarina, O.Onopriyenko, S.N.Peterson, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.07 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 149.968, 149.968, 39.120, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.5

Other elements in 3gc2:

The structure of 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid (pdb code 3gc2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid, PDB code: 3gc2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3gc2

Go back to Sodium Binding Sites List in 3gc2
Sodium binding site 1 out of 2 in the 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na321

b:34.8
occ:1.00
 OD2 A:ASP213 2.2 25.3 1.0
OE1 A:GLU190 2.3 24.9 1.0
O A:HOH388 2.3 36.3 1.0
O A:HOH410 2.4 31.7 1.0
OD1 A:ASP161 2.4 31.1 1.0
OD2 A:ASP161 2.7 36.8 1.0
CG A:ASP161 2.8 26.1 1.0
OD1 A:ASN163 2.9 31.8 1.0
O A:HOH587 3.2 31.8 1.0
CG A:ASP213 3.3 21.5 1.0
CD A:GLU190 3.5 26.6 1.0
CB A:ASP213 3.8 15.6 1.0
CG A:ASN163 3.8 28.2 1.0
CB A:GLU190 4.0 19.5 1.0
NZ A:LYS235 4.0 23.1 1.0
O A:HOH600 4.1 20.9 1.0
O A:HOH362 4.1 23.9 1.0
CB A:ASP161 4.1 22.3 1.0
ND2 A:ASN163 4.2 33.1 1.0
OE2 A:GLU190 4.3 26.1 1.0
O3 A:SIN400 4.3 45.8 0.7
CG A:GLU190 4.3 21.0 1.0
OD1 A:ASP213 4.4 22.4 1.0
N A:ASN163 4.8 20.2 1.0
NZ A:LYS133 4.8 40.8 1.0
CA A:ASP161 4.8 21.4 1.0
CA A:ASN163 4.9 20.2 1.0
CB A:ASN163 5.0 21.7 1.0

Sodium binding site 2 out of 2 in 3gc2

Go back to Sodium Binding Sites List in 3gc2
Sodium binding site 2 out of 2 in the 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na322

b:53.6
occ:1.00
 O A:HOH642 2.2 30.5 1.0
O A:HOH590 2.3 39.8 1.0
O3 A:SIN401 2.4 41.6 0.6
O A:HOH614 2.4 20.5 1.0
O A:GLU40 2.5 19.2 1.0
O A:GLU93 2.5 20.0 1.0
O3 A:SIN401 2.9 41.7 0.4
C A:GLU93 3.4 19.3 1.0
C4 A:SIN401 3.5 42.5 0.6
C A:GLU40 3.6 20.5 1.0
N A:GLU40 3.9 22.1 1.0
CA A:LEU94 4.0 20.1 0.6
N A:LEU94 4.0 19.6 0.6
N A:LEU94 4.0 19.9 0.4
CA A:LEU94 4.1 20.6 0.4
C4 A:SIN401 4.1 42.5 0.4
O A:HOH493 4.1 37.3 1.0
O4 A:SIN401 4.2 37.6 0.6
O A:LEU94 4.3 20.6 0.6
CA A:GLU93 4.4 18.1 1.0
CA A:GLU40 4.4 21.5 1.0
C A:LEU94 4.4 21.2 0.6
O A:LEU94 4.4 20.8 0.4
C A:LEU94 4.4 21.3 0.4
C3 A:SIN401 4.5 46.8 0.6
CB A:GLU93 4.5 17.8 1.0
N A:GLY41 4.7 19.4 1.0
O4 A:SIN401 4.8 37.8 0.4
CA A:GLY41 4.9 19.6 1.0
C A:ARG39 4.9 23.2 1.0
C3 A:SIN401 5.0 42.4 0.4
CB A:GLU40 5.0 21.8 1.0
CA A:ARG39 5.0 25.1 1.0

Reference:

G.Minasov, Z.Wawrzak, T.Skarina, O.Onopriyenko, S.N.Peterson, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.85 Angstrom Crystal Structure of O-Succinylbenzoate Synthase From Salmonella Typhimurium in Complex with Succinic Acid To Be Published.
Page generated: Mon Oct 7 09:57:38 2024

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