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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy