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Magnesium 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:

Sodium (Na) 1 atom
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Apo Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli (Orthorhombic P Form), PDB code: 8v8y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8v8y

Go back to Magnesium Binding Sites List in 8v8y
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg505

b:31.2
occ:1.00
 O A:HOH901 2.3 29.2 1.0
OD1 A:ASP378 4.3 39.8 1.0
CG A:ARG377 4.6 38.9 1.0
CD A:ARG377 4.6 31.4 1.0
OD2 A:ASP378 4.8 41.5 1.0

Magnesium binding site 2 out of 2 in 8v8y

Go back to Magnesium Binding Sites List in 8v8y
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg506

b:33.6
occ:1.00
 O A:HOH774 2.1 34.7 1.0
O A:HOH911 2.3 44.0 1.0
OD2 A:ASP28 4.0 34.7 1.0
O A:HOH814 4.2 26.0 1.0
O A:HOH789 4.3 29.9 1.0
OD1 A:ASP28 4.4 28.6 1.0
CG A:ASP28 4.6 28.3 1.0
CB A:ALA32 4.9 24.0 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: Fri Aug 15 17:31:17 2025

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