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Chlorine in PDB 3khp: Crystal Structure of A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution

Protein crystallography data

The structure of Crystal Structure of A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution, PDB code: 3khp was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), 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) 40.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.290, 135.170, 162.400, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution (pdb code 3khp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution, PDB code: 3khp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3khp

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Chlorine binding site 1 out of 7 in the Crystal Structure of A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution


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 A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:18.3
occ:1.00
 O A:HOH389 3.0 25.9 1.0
NE A:ARG187 3.2 15.7 1.0
NH2 A:ARG187 3.3 17.7 1.0
O A:HOH550 3.3 37.9 1.0
O A:LEU183 3.3 15.4 1.0
C A:LEU183 3.6 15.0 1.0
N A:GLY185 3.6 16.1 1.0
NE C:ARG22 3.6 19.8 1.0
CA A:GLY185 3.7 15.8 1.0
CZ A:ARG187 3.7 16.5 1.0
CA A:LEU183 3.7 14.1 1.0
CD C:ARG22 3.8 19.4 1.0
CG C:ARG22 3.8 18.9 1.0
O A:ARG182 3.8 13.8 1.0
CB C:ARG22 4.3 17.6 1.0
CD A:ARG187 4.3 16.3 1.0
C A:SER184 4.3 16.1 1.0
N A:SER184 4.4 15.5 1.0
CB A:LEU183 4.5 14.4 1.0
C A:GLY185 4.5 15.7 1.0
CD2 A:LEU183 4.6 10.9 1.0
CZ C:ARG22 4.7 20.5 1.0
C A:ARG182 4.7 14.0 1.0
N A:LEU183 4.7 13.5 1.0
CA A:SER184 4.7 15.9 1.0
O A:GLY185 4.8 16.2 1.0
NH1 A:ARG187 5.0 18.3 1.0
CG A:ARG187 5.0 15.3 1.0
O C:HOH373 5.0 31.3 1.0

Chlorine binding site 2 out of 7 in 3khp

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Chlorine binding site 2 out of 7 in the Crystal Structure of A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution


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 A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:33.4
occ:1.00
 N A:GLY34 2.9 15.7 1.0
N A:GLY36 3.1 18.7 1.0
CA A:GLY34 3.2 15.7 1.0
C A:GLY34 3.4 16.2 1.0
CA A:GLY36 3.5 18.8 1.0
OD2 A:ASP37 3.7 26.7 1.0
N A:THR35 3.8 16.9 1.0
O A:GLY34 3.8 15.7 1.0
O A:HOH402 3.9 34.5 1.0
N A:ASP37 3.9 20.5 1.0
C A:GLY36 4.0 19.8 1.0
C A:ALA33 4.1 15.5 1.0
CG A:ASP37 4.2 24.7 1.0
C A:THR35 4.3 17.8 1.0
CA A:ALA33 4.5 14.6 1.0
O A:HOH308 4.5 16.8 1.0
O A:GLY32 4.6 14.8 1.0
CA A:THR35 4.6 17.3 1.0
OD1 A:ASP37 4.7 28.2 1.0
O A:HOH344 4.8 19.1 1.0
CB A:ASP37 4.9 21.4 1.0
NH1 A:ARG219 5.0 19.8 1.0

Chlorine binding site 3 out of 7 in 3khp

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Chlorine binding site 3 out of 7 in the Crystal Structure of A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution


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 A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:20.2
occ:1.00
 NH2 B:ARG187 3.0 15.5 1.0
O B:HOH425 3.2 25.3 1.0
O B:LEU183 3.2 15.6 1.0
NE B:ARG187 3.3 12.2 1.0
C B:LEU183 3.5 14.5 1.0
CA B:LEU183 3.6 14.2 1.0
N B:GLY185 3.6 15.1 1.0
CZ B:ARG187 3.6 14.6 1.0
CA B:GLY185 3.7 15.1 1.0
NE D:ARG22 3.7 20.1 1.0
O B:ARG182 3.8 12.7 1.0
CG D:ARG22 3.8 18.1 1.0
CD D:ARG22 3.8 19.1 1.0
CB D:ARG22 4.1 16.3 1.0
N B:SER184 4.3 15.1 1.0
C B:SER184 4.4 15.1 1.0
CB B:LEU183 4.5 13.9 1.0
CD B:ARG187 4.5 14.7 1.0
CD2 B:LEU183 4.5 12.4 1.0
C B:GLY185 4.6 15.4 1.0
N B:LEU183 4.6 14.1 1.0
C B:ARG182 4.6 13.7 1.0
CA B:SER184 4.7 14.6 1.0
O B:HOH551 4.7 28.4 1.0
O D:HOH531 4.8 34.0 1.0
O B:GLY185 4.8 14.9 1.0
CZ D:ARG22 4.8 20.5 1.0
O B:HOH470 4.8 25.0 1.0
NH1 B:ARG187 4.9 15.7 1.0

Chlorine binding site 4 out of 7 in 3khp

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Chlorine binding site 4 out of 7 in the Crystal Structure of A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution


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 A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:25.5
occ:1.00
 N B:GLY34 3.2 14.9 1.0
N B:GLY36 3.3 18.6 1.0
CA B:GLY34 3.5 15.2 1.0
O B:HOH469 3.5 36.5 1.0
C B:GLY34 3.6 15.6 1.0
CA B:GLY36 3.6 18.9 1.0
N B:THR35 3.9 16.1 1.0
OD1 B:ASP37 3.9 23.2 1.0
O B:GLY34 4.0 14.1 1.0
N B:ASP37 4.0 20.2 1.0
C B:GLY36 4.1 19.8 1.0
C B:ALA33 4.2 13.8 1.0
C B:THR35 4.5 18.1 1.0
O B:HOH319 4.5 23.1 1.0
CG B:ASP37 4.6 24.4 1.0
CA B:ALA33 4.6 13.3 1.0
O B:GLY32 4.7 12.4 1.0
O B:HOH414 4.7 31.6 1.0
CA B:THR35 4.8 17.1 1.0

Chlorine binding site 5 out of 7 in 3khp

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Chlorine binding site 5 out of 7 in the Crystal Structure of A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution


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 A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:24.5
occ:1.00
 O A:HOH440 3.0 18.7 1.0
NH2 C:ARG187 3.1 16.3 1.0
NE C:ARG187 3.3 15.3 1.0
O C:LEU183 3.5 15.8 1.0
NE A:ARG22 3.6 19.7 1.0
CZ C:ARG187 3.6 16.9 1.0
CD A:ARG22 3.7 17.2 1.0
N C:GLY185 3.7 16.6 1.0
CG A:ARG22 3.7 16.6 1.0
C C:LEU183 3.8 16.1 1.0
O C:ARG182 3.8 17.9 1.0
CA C:GLY185 3.8 17.2 1.0
CA C:LEU183 3.8 15.7 1.0
CB A:ARG22 4.2 15.5 1.0
C C:SER184 4.5 16.5 1.0
N C:SER184 4.5 15.9 1.0
CD C:ARG187 4.5 16.4 1.0
C C:GLY185 4.5 17.2 1.0
CZ A:ARG22 4.6 23.2 1.0
CD2 C:LEU183 4.6 11.2 1.0
O C:GLY185 4.7 18.4 1.0
CB C:LEU183 4.7 14.7 1.0
C C:ARG182 4.7 16.5 1.0
N C:LEU183 4.8 16.1 1.0
O C:HOH439 4.9 28.4 1.0
CA C:SER184 4.9 16.4 1.0
NH1 C:ARG187 4.9 16.1 1.0

Chlorine binding site 6 out of 7 in 3khp

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Chlorine binding site 6 out of 7 in the Crystal Structure of A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution


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 A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:21.5
occ:1.00
 NH2 D:ARG187 3.0 16.4 1.0
NE D:ARG187 3.2 16.4 1.0
O D:LEU183 3.4 16.0 1.0
O B:HOH486 3.4 34.9 1.0
NE B:ARG22 3.5 20.7 1.0
CD B:ARG22 3.5 18.5 1.0
CZ D:ARG187 3.5 15.2 1.0
C D:LEU183 3.6 15.1 1.0
N D:GLY185 3.6 16.0 1.0
CG B:ARG22 3.7 17.0 1.0
CA D:LEU183 3.7 14.4 1.0
CA D:GLY185 3.8 16.1 1.0
O D:ARG182 3.9 15.7 1.0
O D:HOH325 3.9 30.4 1.0
CB B:ARG22 4.2 15.8 1.0
N D:SER184 4.4 14.6 1.0
C D:SER184 4.4 15.7 1.0
CD D:ARG187 4.5 17.4 1.0
CB D:LEU183 4.5 13.7 1.0
CD2 D:LEU183 4.6 10.3 1.0
CZ B:ARG22 4.6 21.9 1.0
C D:GLY185 4.6 16.5 1.0
C D:ARG182 4.7 14.3 1.0
N D:LEU183 4.7 14.3 1.0
CA D:SER184 4.8 15.0 1.0
O D:GLY185 4.8 17.1 1.0
NH1 D:ARG187 4.9 17.6 1.0

Chlorine binding site 7 out of 7 in 3khp

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Chlorine binding site 7 out of 7 in the Crystal Structure of A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution


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 A Possible Dehydrogenase From Mycobacterium Tuberculosis at 2.3A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl303

b:44.4
occ:1.00
 O D:HOH293 3.4 18.1 1.0
N D:GLY210 3.4 14.2 1.0
CE1 D:HIS191 3.5 16.7 1.0
CB D:LEU78 3.7 36.4 1.0
O D:HOH559 3.8 13.4 1.0
NE2 D:HIS191 3.8 12.3 1.0
O D:HOH534 4.1 23.9 1.0
CA D:GLY210 4.2 14.4 1.0
CA D:HIS209 4.3 13.3 1.0
C D:HIS209 4.4 14.3 1.0
N D:LEU78 4.5 39.6 1.0
CA D:LEU78 4.7 36.7 1.0
CG D:LEU78 4.7 35.4 1.0
N D:LEU79 4.7 36.2 1.0
O D:LEU208 4.7 13.8 1.0
CD1 D:LEU78 4.7 34.3 1.0
ND1 D:HIS191 4.8 16.9 1.0

Reference:

L.Baugh, I.Phan, D.W.Begley, M.C.Clifton, B.Armour, D.M.Dranow, B.M.Taylor, M.M.Muruthi, J.Abendroth, J.W.Fairman, D.Fox, S.H.Dieterich, B.L.Staker, A.S.Gardberg, R.Choi, S.N.Hewitt, A.J.Napuli, J.Myers, L.K.Barrett, Y.Zhang, M.Ferrell, E.Mundt, K.Thompkins, N.Tran, S.Lyons-Abbott, A.Abramov, A.Sekar, D.Serbzhinskiy, D.Lorimer, G.W.Buchko, R.Stacy, L.J.Stewart, T.E.Edwards, W.C.Van Voorhis, P.J.Myler. Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003
Page generated: Sat Jul 20 22:41:12 2024

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