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Chlorine in PDB 9dqw: Crystal Structure of Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp

Enzymatic activity of Crystal Structure of Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp

All present enzymatic activity of Crystal Structure of Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp:
6.3.2.9;

Protein crystallography data

The structure of Crystal Structure of Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp, PDB code: 9dqw 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) 47.09 / 1.45
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 65.441, 65.441, 135.609, 90, 90, 90
R / Rfree (%) 15 / 16.5

Other elements in 9dqw:

The structure of Crystal Structure of Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp (pdb code 9dqw). 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 Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp, PDB code: 9dqw:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 9dqw

Go back to Chlorine Binding Sites List in 9dqw
Chlorine binding site 1 out of 3 in the Crystal Structure of Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp


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 Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:19.7
occ:1.00
 OG A:SER415 3.2 18.4 1.0
O A:HOH909 3.2 20.6 1.0
O A:HOH706 3.2 23.6 1.0
N A:SER415 3.2 16.2 1.0
O A:HOH627 3.3 21.6 1.0
CB A:SER415 3.8 15.5 1.0
CB A:ALA414 3.9 16.5 1.0
CA A:ALA414 3.9 14.9 1.0
CB A:PHE422 4.0 17.2 1.0
N A:PHE422 4.0 16.5 1.0
CA A:SER415 4.0 17.0 1.0
C A:ALA414 4.1 16.2 1.0
CD2 A:LEU416 4.3 22.6 1.0
CG A:LEU416 4.4 22.0 1.0
CD2 A:PHE422 4.4 20.8 1.0
CA A:PHE422 4.4 15.9 1.0
O18 A:UMA502 4.4 19.3 1.0
CG2 A:THR321 4.5 16.5 1.0
N A:LEU416 4.6 18.4 1.0
O A:HOH984 4.7 29.3 1.0
C A:SER415 4.7 15.5 1.0
O A:HOH831 4.7 22.0 1.0
CG A:PHE422 4.7 16.5 1.0
C A:ASN421 4.8 17.0 1.0
CA A:ASN421 5.0 17.7 1.0

Chlorine binding site 2 out of 3 in 9dqw

Go back to Chlorine Binding Sites List in 9dqw
Chlorine binding site 2 out of 3 in the Crystal Structure of Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp


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 Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:36.6
occ:1.00
 ND2 A:ASN240 2.6 48.1 1.0
NZ A:LYS254 2.9 22.6 1.0
NH1 A:ARG249 3.0 40.2 1.0
CB A:ASN240 3.3 29.0 1.0
CG A:ASN240 3.4 41.5 1.0
CE A:LYS254 3.4 23.0 1.0
CD A:ARG249 3.6 42.9 1.0
CG A:LYS254 3.9 18.7 1.0
CZ A:ARG249 4.0 44.5 1.0
CG A:ARG249 4.2 30.0 1.0
NE A:ARG249 4.2 38.1 1.0
CD A:LYS254 4.3 20.4 1.0
CB A:TRP247 4.4 16.9 1.0
O A:HOH607 4.5 36.6 1.0
CG A:TRP247 4.5 17.0 1.0
CD1 A:TRP247 4.5 16.8 1.0
OD1 A:ASN240 4.6 47.3 1.0
CA A:ASN240 4.7 25.9 1.0

Chlorine binding site 3 out of 3 in 9dqw

Go back to Chlorine Binding Sites List in 9dqw
Chlorine binding site 3 out of 3 in the Crystal Structure of Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp


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 Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:32.9
occ:1.00
 N A:TYR3 3.0 27.9 1.0
NE A:ARG27 3.1 32.0 0.5
NH2 A:ARG27 3.3 29.6 0.5
NE2 A:GLN4 3.3 30.1 1.0
CZ A:ARG27 3.6 25.4 0.5
CA A:TYR3 3.9 24.3 1.0
CA A:ASP2 3.9 35.3 1.0
N A:GLN4 3.9 28.5 1.0
C A:ASP2 3.9 33.8 1.0
CB A:TYR3 4.0 24.7 1.0
CG A:GLN4 4.0 33.8 1.0
CD2 A:TYR3 4.0 23.3 1.0
O A:ALA1 4.1 47.1 1.0
C A:TYR3 4.2 28.1 1.0
CD A:GLN4 4.2 33.9 1.0
CD A:ARG27 4.2 30.4 0.5
CB A:ARG27 4.2 36.4 0.5
CB A:ARG27 4.2 36.4 0.5
OD1 A:ASP2 4.3 36.1 1.0
CG A:TYR3 4.4 21.2 1.0
CG A:ARG27 4.5 31.9 0.5
CG A:ASP2 4.6 44.9 1.0
CG A:ARG27 4.6 33.2 0.5
O A:ARG27 4.6 35.2 1.0
CD A:ARG27 4.7 30.9 0.5
CA A:GLN4 4.8 30.4 1.0
N A:ASP2 4.8 36.2 1.0
CB A:ASP2 4.8 37.5 1.0
CG2 A:VAL29 4.9 30.1 1.0
C A:ALA1 4.9 46.6 1.0
NH1 A:ARG27 4.9 30.3 0.5
CB A:GLN4 4.9 31.8 1.0

Reference:

S.Seibold, L.Liu, S.Lovell, K.P.Battaile. Crystal Structure of Udp-N-Acetylmuramoylalanine--D-Glutamate Ligase (Murd) From E. Coli in Complex with Uma and Amp-Pnp To Be Published.
Page generated: Thu Oct 31 18:10:22 2024

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