Sodium in PDB 8v8y: Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Orthorhombic P Form)

Enzymatic activity of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Orthorhombic P Form)

All present enzymatic activity of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Orthorhombic P Form):
6.3.2.9;

Protein crystallography data

The structure of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Orthorhombic P Form), PDB code: 8v8y 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) 40.58 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.106, 68.693, 100.473, 90, 90, 90
R / Rfree (%) 15.7 / 18.6

Other elements in 8v8y:

The structure of Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Orthorhombic P Form) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Orthorhombic P Form) (pdb code 8v8y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Orthorhombic P Form), PDB code: 8v8y:

Sodium binding site 1 out of 1 in 8v8y

Go back to Sodium Binding Sites List in 8v8y
Sodium binding site 1 out of 1 in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Orthorhombic P Form)


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 Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Orthorhombic P Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:22.3
occ:1.00
 O A:HOH710 2.2 27.9 1.0
O A:SER5 2.4 33.1 1.0
O A:HOH740 2.5 33.9 1.0
OE1 A:GLU107 2.5 27.4 1.0
O A:HOH754 2.5 29.2 1.0
CD A:GLU107 3.5 28.6 1.0
C A:SER5 3.6 42.7 1.0
OE2 A:GLU107 3.7 32.3 1.0
O A:ARG106 4.0 25.0 1.0
CA A:MET6 4.2 40.5 1.0
NE2 A:GLN109 4.2 33.1 1.0
O A:HOH613 4.3 39.0 1.0
N A:MET6 4.4 43.6 1.0
N A:ALA7 4.4 33.5 1.0
CA A:GLU107 4.6 21.6 1.0
O A:HOH792 4.6 32.4 1.0
CA A:SER5 4.7 46.5 1.0
C A:MET6 4.7 41.4 1.0
CG A:GLU107 4.8 24.1 1.0
C A:ARG106 4.9 21.1 1.0
O A:ALA7 4.9 36.4 1.0
CB A:SER5 4.9 38.6 1.0
CB A:GLU107 5.0 19.8 1.0

Reference:

S.Seibold, S.Lovell, K.P.Battaile. Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Orthorhombic P Form) To Be Published.
Page generated: Wed Oct 9 13:58:57 2024

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