Atomistry » Sodium » PDB 3fvs-3gdg » 3gc2
Atomistry »
  Sodium »
    PDB 3fvs-3gdg »
      3gc2 »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy