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Chlorine in PDB 7u56: Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp

Enzymatic activity of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp

All present enzymatic activity of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp:
6.3.2.4;

Protein crystallography data

The structure of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp, PDB code: 7u56 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) 39.13 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.35, 115.42, 68.48, 90, 90, 90
R / Rfree (%) 16.2 / 19.9

Other elements in 7u56:

The structure of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp (pdb code 7u56). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp, PDB code: 7u56:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7u56

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Chlorine binding site 1 out of 4 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp


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 D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:23.7
occ:1.00
 O A:HOH685 2.8 30.1 1.0
NH1 A:ARG311 3.1 23.2 1.0
N A:TYR339 3.2 15.4 1.0
N A:GLY332 3.3 25.9 1.0
O A:GLY332 3.5 29.6 1.0
CB A:TYR339 3.6 15.6 1.0
N A:MET338 3.7 18.1 1.0
CB A:PRO331 3.7 22.5 1.0
CB A:MET338 3.8 16.9 1.0
CD A:ARG311 3.8 16.2 1.0
CA A:GLY332 3.8 27.7 1.0
CA A:TYR339 4.0 15.2 1.0
CA A:MET338 4.0 16.7 1.0
C A:MET338 4.1 18.5 1.0
C A:PRO331 4.1 21.2 1.0
C A:GLY332 4.1 23.2 1.0
CB A:SER337 4.1 23.3 1.0
CA A:PRO331 4.1 22.3 1.0
O A:HOH673 4.2 35.8 1.0
CZ A:ARG311 4.2 23.8 1.0
O A:HOH524 4.3 22.9 1.0
C A:SER337 4.4 19.4 1.0
NE A:ARG311 4.5 17.0 1.0
O A:HOH657 4.5 31.7 1.0
CA A:SER337 4.7 23.5 1.0
CG A:MET338 4.9 16.0 1.0
CG A:ARG311 4.9 12.8 1.0
OG A:SER337 4.9 21.3 1.0
CD A:PRO340 4.9 20.8 1.0
CG A:TYR339 4.9 15.0 1.0

Chlorine binding site 2 out of 4 in 7u56

Go back to Chlorine Binding Sites List in 7u56
Chlorine binding site 2 out of 4 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp


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 D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:26.4
occ:1.00
 N A:ASN247 3.1 14.4 1.0
O2 A:EDO405 3.1 35.4 1.0
O A:HOH699 3.1 25.8 1.0
N A:HIS249 3.2 16.7 1.0
O A:HIS249 3.5 22.6 1.0
N A:ASP248 3.6 18.3 1.0
C A:HIS249 3.7 21.6 1.0
CA A:HIS249 3.7 19.0 1.0
C A:ASN247 3.8 17.8 1.0
CB A:HIS249 3.8 20.7 1.0
O A:HOH516 3.8 37.7 1.0
CA A:ASN247 3.9 17.4 1.0
CA A:GLY246 3.9 15.3 1.0
C2 A:EDO405 3.9 36.0 1.0
C A:GLY246 4.0 14.6 1.0
CD2 A:LEU360 4.1 21.3 1.0
CB A:ASN247 4.2 15.2 1.0
C A:ASP248 4.2 21.7 1.0
CA A:ASP248 4.4 21.7 1.0
N A:PRO250 4.5 20.0 1.0
NH2 A:ARG356 4.5 34.0 1.0
O A:ASN247 4.6 18.7 1.0
CG A:HIS249 4.6 27.0 1.0
CD2 A:HIS249 4.6 27.3 1.0
O A:HOH565 4.9 26.9 1.0
CB A:ASP248 5.0 19.5 1.0

Chlorine binding site 3 out of 4 in 7u56

Go back to Chlorine Binding Sites List in 7u56
Chlorine binding site 3 out of 4 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp


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 D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:21.2
occ:1.00
 O B:HOH785 2.9 34.5 1.0
NH1 B:ARG311 3.1 22.3 1.0
N B:GLY332 3.2 23.0 1.0
N B:TYR339 3.2 11.7 1.0
CB B:PRO331 3.6 19.6 1.0
CB B:TYR339 3.6 12.7 1.0
N B:MET338 3.7 17.0 1.0
O B:HOH792 3.8 38.5 1.0
CD B:ARG311 3.8 14.4 1.0
CB B:MET338 3.9 16.1 1.0
O B:GLY332 3.9 21.5 1.0
CA B:GLY332 4.0 21.9 1.0
CA B:PRO331 4.0 18.0 1.0
CA B:TYR339 4.0 13.8 1.0
C B:PRO331 4.0 18.4 1.0
CA B:MET338 4.1 16.1 1.0
C B:MET338 4.1 14.2 1.0
CZ B:ARG311 4.2 22.6 1.0
CB B:SER337 4.3 21.6 1.0
C B:GLY332 4.4 20.7 1.0
NE B:ARG311 4.4 16.9 1.0
C B:SER337 4.4 20.6 1.0
O B:HOH551 4.5 24.7 1.0
CA B:SER337 4.7 25.5 1.0
CG B:ARG311 4.9 12.4 1.0
CG B:TYR339 4.9 13.6 1.0
CD B:PRO340 5.0 17.2 1.0
CG B:PRO331 5.0 18.4 1.0
CG B:MET338 5.0 18.5 1.0
OG B:SER337 5.0 22.9 1.0
CB B:ARG311 5.0 11.9 1.0

Chlorine binding site 4 out of 4 in 7u56

Go back to Chlorine Binding Sites List in 7u56
Chlorine binding site 4 out of 4 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl408

b:21.7
occ:1.00
 O1 B:EDO405 3.0 30.5 1.0
N B:ASN247 3.0 12.5 1.0
N B:HIS249 3.2 14.2 1.0
O B:HOH748 3.3 23.6 1.0
O B:HOH529 3.4 29.9 1.0
O B:HIS249 3.6 15.1 1.0
N B:ASP248 3.6 12.5 1.0
C B:HIS249 3.7 16.5 1.0
CA B:HIS249 3.7 19.1 1.0
O B:HOH507 3.7 32.3 1.0
CA B:ASN247 3.8 13.5 1.0
C B:ASN247 3.8 16.6 1.0
CA B:GLY246 3.9 11.4 1.0
CB B:HIS249 3.9 19.2 1.0
C B:GLY246 3.9 13.0 1.0
C1 B:EDO405 4.0 26.1 1.0
CB B:ASN247 4.1 12.6 1.0
CD2 B:LEU360 4.1 15.2 1.0
C B:ASP248 4.2 16.5 1.0
NH2 B:ARG356 4.4 26.7 1.0
N B:PRO250 4.4 16.4 1.0
CA B:ASP248 4.5 17.4 1.0
O B:ASN247 4.6 15.8 1.0
ND1 B:HIS249 4.6 28.7 1.0
CG B:HIS249 4.8 27.8 1.0
O B:HOH577 4.9 27.5 1.0
O B:HOH555 5.0 21.4 1.0
CA B:PRO250 5.0 14.3 1.0
CG B:ASN247 5.0 13.7 1.0

Reference:

J.Abendroth, M.J.Bolejack, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of D-Alanine--D-Alanine Ligase From Klebsiella Pneumoniae Subsp. Pneumoniae in Complex with Amp To Be Published.
Page generated: Sun Jul 13 07:43:28 2025

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