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Chlorine in PDB 1xxx: Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis

Enzymatic activity of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis:
4.2.1.52;

Protein crystallography data

The structure of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis, PDB code: 1xxx was solved by G.Kefala, S.Panjikar, R.Janowski, M.S.Weiss, Tb Structural Genomicsconsortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.28
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.790, 87.370, 139.850, 90.00, 107.78, 90.00
R / Rfree (%) 14.8 / 21.5

Other elements in 1xxx:

The structure of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis (pdb code 1xxx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis, PDB code: 1xxx:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 1xxx

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Chlorine binding site 1 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2009

b:26.7
occ:1.00
 O A:HOH3122 2.9 16.9 1.0
OG A:SER179 3.0 31.2 1.0
NZ A:LYS174 3.1 29.5 1.0
O A:HOH3134 3.1 32.9 1.0
CE A:LYS174 3.4 32.8 1.0
CB A:SER179 3.5 27.4 1.0
CD1 A:ILE183 3.7 25.8 1.0
CD A:PRO155 3.8 26.4 1.0
CB A:PRO155 3.8 26.1 1.0
CD1 A:ILE158 3.9 27.6 1.0
CA A:PRO155 4.0 27.9 1.0
N A:PRO155 4.0 28.1 1.0
CG A:PRO155 4.0 28.6 1.0
CB A:ASP176 4.5 29.0 1.0
O A:ILE153 4.5 29.5 1.0
O A:HOH3013 4.6 21.2 1.0
OD2 A:ASP176 4.6 37.5 1.0
O A:HOH3073 4.6 18.7 1.0
N A:GLY180 4.7 26.4 1.0
C A:SER179 4.7 27.4 1.0
O A:HOH3027 4.7 16.4 1.0
CA A:SER179 4.7 27.4 1.0
CG A:ASP176 4.8 33.4 1.0
C A:GLU154 4.8 28.4 1.0
OD1 A:ASP144 4.9 29.0 1.0
CD A:LYS174 4.9 33.3 1.0
OH A:TYR191 5.0 27.5 1.0

Chlorine binding site 2 out of 8 in 1xxx

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Chlorine binding site 2 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2010

b:36.4
occ:1.00
 O B:HOH3193 2.9 43.5 1.0
OG B:SER179 3.0 33.4 1.0
NZ B:LYS174 3.0 31.9 1.0
O B:HOH3168 3.1 24.5 1.0
CE B:LYS174 3.4 33.9 1.0
CD1 B:ILE183 3.6 27.8 1.0
CB B:SER179 3.6 29.1 1.0
CD B:PRO155 3.7 27.5 1.0
CB B:PRO155 3.8 27.5 1.0
CD1 B:ILE158 3.9 27.1 1.0
CG B:PRO155 3.9 27.6 1.0
CA B:PRO155 4.0 27.5 1.0
N B:PRO155 4.0 27.6 1.0
O B:ILE153 4.4 30.2 1.0
O B:HOH3015 4.4 20.4 1.0
O B:HOH3025 4.5 20.4 1.0
O B:HOH3167 4.6 29.6 1.0
CB B:ASP176 4.6 30.5 1.0
N B:GLY180 4.7 28.3 1.0
C B:SER179 4.8 28.6 1.0
OD1 B:ASP144 4.8 29.1 1.0
OD2 B:ASP176 4.8 36.5 1.0
C B:GLU154 4.8 28.6 1.0
CA B:SER179 4.8 28.8 1.0
CD B:LYS174 4.9 32.1 1.0
CG B:ASP176 5.0 33.1 1.0
CG1 B:ILE183 5.0 26.4 1.0

Chlorine binding site 3 out of 8 in 1xxx

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Chlorine binding site 3 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2011

b:31.0
occ:1.00
 OG C:SER179 2.9 32.7 1.0
O C:HOH3024 3.0 18.4 1.0
NZ C:LYS174 3.0 29.0 1.0
O C:HOH3168 3.1 38.0 1.0
CE C:LYS174 3.4 37.1 1.0
CB C:SER179 3.5 27.8 1.0
CD1 C:ILE183 3.7 28.4 1.0
CB C:PRO155 3.8 27.8 1.0
CD C:PRO155 3.9 26.8 1.0
CD1 C:ILE158 3.9 25.0 1.0
CG C:PRO155 4.0 28.6 1.0
CA C:PRO155 4.0 27.9 1.0
N C:PRO155 4.1 27.9 1.0
O C:HOH3050 4.5 24.2 1.0
O C:ILE153 4.5 29.4 1.0
CB C:ASP176 4.6 32.0 1.0
O C:HOH3015 4.7 26.5 1.0
C C:SER179 4.7 27.7 1.0
N C:GLY180 4.7 27.9 1.0
OD2 C:ASP176 4.7 39.3 1.0
CA C:SER179 4.7 28.6 1.0
O C:HOH3033 4.7 17.1 1.0
OD1 C:ASP144 4.8 28.7 1.0
CD C:LYS174 4.9 33.2 1.0
C C:GLU154 4.9 28.5 1.0
CG C:ASP176 4.9 33.5 1.0

Chlorine binding site 4 out of 8 in 1xxx

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Chlorine binding site 4 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


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 Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2012

b:31.6
occ:1.00
 OG D:SER179 2.9 31.9 1.0
O D:HOH3079 3.0 22.7 1.0
NZ D:LYS174 3.2 29.3 1.0
O D:HOH3146 3.2 27.7 1.0
CB D:SER179 3.5 30.1 1.0
CE D:LYS174 3.5 32.1 1.0
CD1 D:ILE183 3.7 26.6 1.0
CD D:PRO155 3.8 26.2 1.0
CB D:PRO155 3.9 26.1 1.0
CA D:PRO155 4.0 27.5 1.0
CG D:PRO155 4.0 26.4 1.0
CD1 D:ILE158 4.0 26.9 1.0
N D:PRO155 4.1 27.0 1.0
O D:ILE153 4.5 28.8 1.0
O D:HOH3022 4.5 16.1 1.0
CB D:ASP176 4.6 29.6 1.0
O D:HOH3029 4.6 17.4 1.0
N D:GLY180 4.7 28.4 1.0
C D:SER179 4.7 27.1 1.0
OD2 D:ASP176 4.7 36.7 1.0
O D:HOH3017 4.7 22.4 1.0
CA D:SER179 4.7 28.6 1.0
CG D:ASP176 4.8 31.3 1.0
C D:GLU154 4.9 27.8 1.0
CG1 D:ILE183 4.9 27.0 1.0
OD1 D:ASP144 4.9 28.9 1.0
CD D:LYS174 5.0 31.8 1.0

Chlorine binding site 5 out of 8 in 1xxx

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Chlorine binding site 5 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl2013

b:42.3
occ:1.00
 NZ E:LYS174 3.0 28.2 1.0
OG E:SER179 3.0 33.0 1.0
CE E:LYS174 3.3 35.8 1.0
CB E:SER179 3.6 28.0 1.0
CD1 E:ILE183 3.7 25.4 1.0
CD E:PRO155 3.7 26.3 1.0
CB E:PRO155 3.8 27.6 1.0
CD1 E:ILE158 3.9 27.8 1.0
CA E:PRO155 4.0 26.9 1.0
CG E:PRO155 4.0 27.2 1.0
N E:PRO155 4.0 26.8 1.0
O E:ILE153 4.4 27.4 1.0
O E:HOH3105 4.4 35.3 1.0
O E:HOH3026 4.4 26.4 1.0
O E:HOH3017 4.5 32.2 1.0
CB E:ASP176 4.6 30.9 1.0
OD2 E:ASP176 4.7 33.9 1.0
N E:GLY180 4.8 26.6 1.0
C E:GLU154 4.8 26.9 1.0
CD E:LYS174 4.8 31.7 1.0
C E:SER179 4.8 27.1 1.0
OD1 E:ASP144 4.8 28.0 1.0
CA E:SER179 4.8 28.1 1.0
CG E:ASP176 4.9 31.3 1.0
CG1 E:ILE183 5.0 26.3 1.0

Chlorine binding site 6 out of 8 in 1xxx

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Chlorine binding site 6 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl2014

b:37.3
occ:1.00
 OG F:SER179 2.9 30.4 1.0
O F:HOH3032 3.0 33.5 1.0
O F:HOH3048 3.1 26.7 1.0
NZ F:LYS174 3.1 28.9 1.0
CE F:LYS174 3.4 34.0 1.0
CB F:SER179 3.6 27.1 1.0
CD1 F:ILE183 3.6 26.6 1.0
CD F:PRO155 3.7 26.7 1.0
CB F:PRO155 3.8 26.5 1.0
CD1 F:ILE158 3.8 26.3 1.0
CA F:PRO155 3.9 27.6 1.0
N F:PRO155 4.0 27.3 1.0
CG F:PRO155 4.0 27.2 1.0
O F:ILE153 4.4 29.8 1.0
O F:HOH3097 4.5 38.9 1.0
O F:HOH3024 4.5 19.1 1.0
O F:HOH3019 4.5 34.2 1.0
OD2 F:ASP176 4.7 34.4 1.0
CB F:ASP176 4.7 29.2 1.0
C F:SER179 4.7 27.8 1.0
C F:GLU154 4.7 27.7 1.0
CA F:SER179 4.8 28.1 1.0
N F:GLY180 4.8 26.8 1.0
OD1 F:ASP144 4.9 25.9 1.0
CG1 F:ILE183 4.9 27.4 1.0
CG F:ASP176 4.9 33.4 1.0
CD F:LYS174 4.9 33.2 1.0
OH F:TYR191 5.0 29.1 1.0

Chlorine binding site 7 out of 8 in 1xxx

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Chlorine binding site 7 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl2015

b:39.1
occ:1.00
 OG G:SER179 2.9 34.7 1.0
NZ G:LYS174 3.1 32.3 1.0
O G:HOH3154 3.1 27.7 1.0
CE G:LYS174 3.5 36.0 1.0
CD1 G:ILE183 3.5 27.4 1.0
CB G:SER179 3.6 30.1 1.0
CD G:PRO155 3.7 25.8 1.0
CB G:PRO155 3.8 27.6 1.0
CA G:PRO155 3.9 26.9 1.0
CD1 G:ILE158 3.9 25.4 1.0
CG G:PRO155 3.9 28.2 1.0
N G:PRO155 3.9 27.5 1.0
O G:ILE153 4.4 28.7 1.0
O G:HOH3018 4.4 28.8 1.0
O G:HOH3029 4.6 18.2 1.0
O G:HOH3168 4.6 29.5 1.0
N G:GLY180 4.7 28.9 1.0
C G:SER179 4.7 29.0 1.0
CB G:ASP176 4.7 31.6 1.0
CA G:SER179 4.8 29.9 1.0
C G:GLU154 4.8 28.3 1.0
CG1 G:ILE183 4.8 27.7 1.0
OD2 G:ASP176 4.9 35.3 1.0
OD1 G:ASP144 4.9 31.0 1.0
OH G:TYR191 4.9 27.8 1.0

Chlorine binding site 8 out of 8 in 1xxx

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Chlorine binding site 8 out of 8 in the Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Dihydrodipicolinate Synthase (Dapa, RV2753C) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl2016

b:42.6
occ:1.00
 OG H:SER179 3.0 32.4 1.0
NZ H:LYS174 3.1 28.9 1.0
O H:HOH3127 3.2 39.2 1.0
CE H:LYS174 3.4 36.6 1.0
CB H:SER179 3.5 28.5 1.0
CD1 H:ILE183 3.6 26.0 1.0
CD H:PRO155 3.8 26.6 1.0
CB H:PRO155 3.8 27.1 1.0
CD1 H:ILE158 3.9 25.7 1.0
CA H:PRO155 3.9 28.0 1.0
N H:PRO155 4.0 27.6 1.0
CG H:PRO155 4.0 28.0 1.0
O H:ILE153 4.4 29.1 1.0
O H:HOH3038 4.4 23.4 1.0
O H:HOH3048 4.5 26.1 1.0
OD2 H:ASP176 4.7 40.3 1.0
N H:GLY180 4.7 27.5 1.0
C H:SER179 4.7 27.7 1.0
CB H:ASP176 4.7 30.5 1.0
O H:HOH3021 4.7 33.4 1.0
CA H:SER179 4.8 28.8 1.0
OD1 H:ASP144 4.8 30.6 1.0
C H:GLU154 4.8 27.7 1.0
CD H:LYS174 4.9 35.7 1.0
CG H:ASP176 5.0 35.5 1.0
CG1 H:ILE183 5.0 25.1 1.0

Reference:

G.Kefala, G.L.Evans, M.D.Griffin, S.R.Devenish, F.G.Pearce, M.A.Perugini, J.A.Gerrard, M.S.Weiss, R.C.Dobson. Crystal Structure and Kinetic Study of Dihydrodipicolinate Synthase From Mycobacterium Tuberculosis. Biochem.J. V. 411 351 2008.
ISSN: ISSN 0264-6021
PubMed: 18062777
DOI: 10.1042/BJ20071360
Page generated: Sat Jul 20 04:04:56 2024

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