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Chlorine 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
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 8v8y

Go back to Chlorine Binding Sites List in 8v8y
Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl502

b:32.8
occ:1.00
 O A:HOH848 2.8 41.0 1.0
O A:HOH815 3.2 28.8 1.0
N A:SER122 3.3 15.8 1.0
NE A:ARG308 3.4 25.8 1.0
N A:THR123 3.5 15.0 1.0
C A:GLY120 3.6 16.6 1.0
CA A:GLY120 3.6 16.5 1.0
CB A:SER122 3.6 19.4 1.0
OG1 A:THR123 3.8 17.9 1.0
N A:LYS121 3.8 15.9 1.0
N A:GLY120 3.9 18.7 1.0
CA A:SER122 3.9 19.4 1.0
CG A:ARG308 3.9 23.3 1.0
O A:GLY120 4.0 15.5 1.0
OG A:SER122 4.1 26.3 1.0
C A:SER122 4.1 16.0 1.0
CD A:ARG308 4.2 34.7 1.0
O A:HOH700 4.3 33.7 1.0
CB A:THR123 4.3 15.3 1.0
C A:LYS121 4.3 14.2 1.0
NH2 A:ARG308 4.3 23.3 1.0
CZ A:ARG308 4.3 23.1 1.0
O A:HOH821 4.5 29.3 1.0
CA A:THR123 4.5 14.3 1.0
CA A:LYS121 4.7 17.1 1.0
CG A:LYS325 4.8 26.9 1.0
CE A:LYS325 4.8 37.6 1.0
CD1 A:LEU305 5.0 20.5 1.0

Chlorine binding site 2 out of 3 in 8v8y

Go back to Chlorine Binding Sites List in 8v8y
Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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:Cl503

b:54.7
occ:1.00
 O A:ALA288 4.0 21.2 1.0
O A:GLU158 4.8 17.8 1.0

Chlorine binding site 3 out of 3 in 8v8y

Go back to Chlorine Binding Sites List in 8v8y
Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl504

b:29.4
occ:1.00
 O A:HOH838 2.8 27.1 1.0
OG A:SER421 3.1 23.4 1.0
N A:SER421 3.1 21.1 1.0
CB A:SER421 3.8 21.4 1.0
CA A:ALA420 3.8 21.8 1.0
CG2 A:THR327 3.9 24.6 1.0
CB A:ALA420 3.9 24.7 1.0
C A:ALA420 4.0 21.3 1.0
N A:PHE428 4.0 20.4 1.0
CA A:SER421 4.0 20.2 1.0
CB A:PHE428 4.1 20.7 1.0
CD2 A:LEU422 4.3 26.1 1.0
CG A:LEU422 4.3 27.5 1.0
CA A:PHE428 4.4 21.8 1.0
N A:LEU422 4.5 21.9 1.0
CB A:THR327 4.6 26.8 1.0
C A:ASN427 4.6 20.8 1.0
C A:SER421 4.7 19.9 1.0
CD2 A:PHE428 4.8 25.2 1.0
CA A:ASN427 4.8 22.8 1.0
CG A:PHE428 4.9 21.8 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: Thu Dec 28 03:37:14 2023

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