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Chlorine in PDB 4wyg: Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit

Enzymatic activity of Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit

All present enzymatic activity of Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit:
2.6.1.62;

Protein crystallography data

The structure of Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit, PDB code: 4wyg was solved by R.Dai, B.C.Finzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.40 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.124, 66.433, 205.318, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 18

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit (pdb code 4wyg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit, PDB code: 4wyg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4wyg

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Chlorine binding site 1 out of 6 in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit


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 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:22.5
occ:0.20
 CL1 A:3W1503 0.0 22.5 0.2
CAL A:3W1503 1.7 14.4 0.2
CAG A:3W1503 2.0 14.8 0.2
NAK A:3W1503 2.1 14.9 0.2
CAH A:3W1503 2.6 14.6 0.2
O A:HOH737 2.6 13.8 1.0
CAG A:3W1503 2.7 16.0 0.2
O2S A:EPE502 2.8 16.4 1.0
CAH A:3W1503 3.1 14.9 0.5
NE1 A:TRP64 3.2 13.3 1.0
CAL A:3W1503 3.3 15.1 0.2
CG A:ARG400 3.3 13.3 1.0
NAO A:3W1503 3.4 15.1 0.2
O1S A:EPE502 3.7 15.9 1.0
NAO A:3W1503 3.7 15.2 0.2
NAK A:3W1503 3.8 12.2 0.2
CZ2 A:TRP64 3.8 15.2 1.0
CE2 A:TRP64 3.8 15.5 1.0
O A:HOH740 3.8 14.8 1.0
S A:EPE502 3.9 14.5 1.0
CAL A:3W1503 3.9 15.9 0.5
CAH A:3W1503 4.0 12.8 0.2
NAO A:3W1503 4.0 15.0 0.5
CAJ A:3W1503 4.2 12.4 0.5
CB A:ARG400 4.2 11.2 1.0
CL1 A:3W1503 4.3 26.8 0.5
O A:ARG400 4.3 11.5 1.0
O A:PRO401 4.4 12.2 1.0
CE B:MET91 4.4 13.1 1.0
CD1 A:TRP64 4.4 10.6 1.0
CD A:ARG400 4.4 17.3 1.0
NE A:ARG400 4.4 12.9 1.0
CAJ A:3W1503 4.5 12.7 0.2
CL1 A:3W1503 4.5 25.4 0.2
CB A:PHE402 4.6 11.7 1.0
O3S A:EPE502 4.8 16.2 1.0
CAN A:3W1503 4.9 12.2 0.5
CD2 A:PHE402 4.9 15.1 1.0
C A:ARG400 4.9 11.3 1.0
NAK A:3W1503 5.0 18.9 0.5
CAG A:3W1503 5.0 14.0 0.5
CAJ A:3W1503 5.0 13.8 0.2

Chlorine binding site 2 out of 6 in 4wyg

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Chlorine binding site 2 out of 6 in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit


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 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:26.8
occ:0.54
 CL1 A:3W1503 0.0 26.8 0.5
CL1 A:3W1503 0.2 25.4 0.2
CAL A:3W1503 1.5 15.1 0.2
CAL A:3W1503 1.7 15.9 0.5
CAG A:3W1503 2.1 16.0 0.2
CAG A:3W1503 2.5 14.8 0.2
CAH A:3W1503 2.6 12.8 0.2
NAK A:3W1503 2.7 12.2 0.2
CAG A:3W1503 2.7 14.0 0.5
CAH A:3W1503 2.7 14.9 0.5
CAL A:3W1503 3.3 14.4 0.2
NAK A:3W1503 3.6 14.9 0.2
NAO A:3W1503 3.6 15.1 0.2
C10 A:EPE502 3.7 13.4 1.0
O A:HOH740 3.7 14.8 1.0
NAO A:3W1503 3.8 15.0 0.5
NAK A:3W1503 3.8 18.9 0.5
NAO A:3W1503 3.9 15.2 0.2
O A:HOH703 3.9 24.4 1.0
O1S A:EPE502 3.9 15.9 1.0
O2S A:EPE502 4.0 16.4 1.0
CD2 A:TYR25 4.0 10.0 1.0
S A:EPE502 4.1 14.5 1.0
CB A:PHE402 4.2 11.7 1.0
CAH A:3W1503 4.2 14.6 0.2
CB A:TYR25 4.2 11.1 1.0
CL1 A:3W1503 4.3 22.5 0.2
CG A:TYR25 4.4 10.9 1.0
O A:HOH732 4.5 22.2 1.0
C9 A:EPE502 4.7 16.9 1.0
CE2 A:TYR25 4.9 8.5 1.0
O A:HOH849 5.0 26.1 1.0
N1 A:EPE502 5.0 18.9 1.0

Chlorine binding site 3 out of 6 in 4wyg

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Chlorine binding site 3 out of 6 in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit


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 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:25.4
occ:0.25
 CL1 A:3W1503 0.0 25.4 0.2
CL1 A:3W1503 0.2 26.8 0.5
CAL A:3W1503 1.7 15.1 0.2
CAL A:3W1503 1.9 15.9 0.5
CAG A:3W1503 2.3 16.0 0.2
CAH A:3W1503 2.7 12.8 0.2
CAG A:3W1503 2.7 14.8 0.2
CAG A:3W1503 2.8 14.0 0.5
NAK A:3W1503 2.8 12.2 0.2
CAH A:3W1503 2.9 14.9 0.5
CAL A:3W1503 3.6 14.4 0.2
C10 A:EPE502 3.7 13.4 1.0
O A:HOH740 3.8 14.8 1.0
O A:HOH703 3.8 24.4 1.0
NAO A:3W1503 3.8 15.1 0.2
NAK A:3W1503 3.8 14.9 0.2
NAK A:3W1503 3.9 18.9 0.5
NAO A:3W1503 4.0 15.0 0.5
NAO A:3W1503 4.0 15.2 0.2
O1S A:EPE502 4.1 15.9 1.0
CD2 A:TYR25 4.1 10.0 1.0
O2S A:EPE502 4.2 16.4 1.0
CB A:TYR25 4.2 11.1 1.0
CB A:PHE402 4.2 11.7 1.0
S A:EPE502 4.2 14.5 1.0
O A:HOH732 4.3 22.2 1.0
CG A:TYR25 4.4 10.9 1.0
CAH A:3W1503 4.4 14.6 0.2
CL1 A:3W1503 4.5 22.5 0.2
C9 A:EPE502 4.7 16.9 1.0
O A:HOH849 4.8 26.1 1.0
N1 A:EPE502 4.9 18.9 1.0
CE2 A:TYR25 4.9 8.5 1.0

Chlorine binding site 4 out of 6 in 4wyg

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Chlorine binding site 4 out of 6 in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit


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 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:24.2
occ:0.58
 CL1 B:3W1503 0.0 24.2 0.6
CAL B:3W1503 1.7 15.7 0.6
CAG B:3W1503 2.1 18.8 0.4
CAG B:3W1503 2.7 22.3 0.6
NAK B:3W1503 2.7 13.6 0.4
CAH B:3W1503 2.8 19.7 0.6
CAL B:3W1503 3.3 14.7 0.4
C10 B:EPE502 3.6 14.9 0.4
C10 B:EPE502 3.7 14.9 0.6
O B:HOH724 3.8 20.4 1.0
O B:HOH672 3.8 19.8 1.0
NAK B:3W1503 3.8 21.6 0.6
NAO B:3W1503 3.8 17.3 0.6
NAO B:3W1503 3.9 20.1 0.4
O3S B:EPE502 3.9 20.2 0.4
O3S B:EPE502 3.9 20.3 0.6
O1S B:EPE502 3.9 17.9 0.4
O1S B:EPE502 4.0 18.0 0.6
S B:EPE502 4.1 17.5 0.4
CB B:PHE402 4.1 16.6 1.0
S B:EPE502 4.1 17.5 0.6
CD2 B:TYR25 4.1 12.2 1.0
CL1 B:3W1503 4.2 36.2 0.4
CAH B:3W1503 4.2 14.8 0.4
O B:HOH779 4.3 31.8 1.0
CB B:TYR25 4.3 12.4 1.0
CG B:TYR25 4.4 10.9 1.0
C9 B:EPE502 4.5 16.7 0.4
C9 B:EPE502 4.6 15.7 0.6
O B:HOH692 4.7 22.4 1.0
N1 B:EPE502 4.8 20.9 0.4
CG B:PHE402 4.8 18.4 1.0
N1 B:EPE502 4.9 20.6 0.6
CE2 B:TYR25 4.9 12.2 1.0
CE B:MET174 5.0 21.1 0.5

Chlorine binding site 5 out of 6 in 4wyg

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Chlorine binding site 5 out of 6 in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit


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 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:36.2
occ:0.42
 CL1 B:3W1503 0.0 36.2 0.4
CAL B:3W1503 1.7 14.7 0.4
O1S B:EPE502 2.3 17.9 0.4
O1S B:EPE502 2.4 18.0 0.6
CAH B:3W1503 2.7 14.8 0.4
CAG B:3W1503 2.7 18.8 0.4
O B:HOH712 3.0 17.6 1.0
CAH B:3W1503 3.1 19.7 0.6
CG B:ARG400 3.3 13.8 1.0
O3S B:EPE502 3.3 20.3 0.6
O3S B:EPE502 3.3 20.2 0.4
S B:EPE502 3.4 17.5 0.4
NE1 B:TRP64 3.4 13.7 1.0
S B:EPE502 3.4 17.5 0.6
CZ2 B:TRP64 3.7 17.8 1.0
NAO B:3W1503 3.8 20.1 0.4
NAK B:3W1503 3.8 13.6 0.4
O B:HOH724 3.8 20.4 1.0
CAL B:3W1503 3.9 15.7 0.6
CE2 B:TRP64 3.9 16.7 1.0
NAO B:3W1503 4.0 17.3 0.6
NE B:ARG400 4.2 16.7 1.0
CL1 B:3W1503 4.2 24.2 0.6
O2S B:EPE502 4.3 17.5 0.4
CB B:ARG400 4.3 15.2 1.0
CD B:ARG400 4.3 16.9 1.0
O2S B:EPE502 4.4 17.4 0.6
CE A:MET91 4.4 14.1 1.0
CAJ B:3W1503 4.4 13.0 0.6
O B:ARG400 4.5 17.5 1.0
O B:PRO401 4.5 17.8 1.0
CD1 B:TRP64 4.6 14.8 1.0
CB B:PHE402 4.7 16.6 1.0
C10 B:EPE502 4.7 14.9 0.4
C10 B:EPE502 4.8 14.9 0.6
O A:GLY93 4.9 20.1 1.0
CAG B:3W1503 5.0 22.3 0.6
NAK B:3W1503 5.0 21.6 0.6
CH2 B:TRP64 5.0 16.6 1.0

Chlorine binding site 6 out of 6 in 4wyg

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Chlorine binding site 6 out of 6 in the Crystal Structure of 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit


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 7,8-Diaminopelargonic Acid Synthase (Bioa) From Mycobacterium Tuberculosis Complexed with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl506

b:91.2
occ:1.00
 CL1 B:3W1506 0.0 91.2 1.0
CAL B:3W1506 1.7 55.3 1.0
CAH B:3W1506 2.7 58.4 1.0
CAG B:3W1506 2.7 44.0 1.0
O B:HOH729 3.7 27.6 1.0
O B:HOH846 3.7 40.3 1.0
NAO B:3W1506 3.8 49.2 1.0
NAK B:3W1506 3.8 43.8 1.0
OD1 B:ASP233 4.0 25.5 1.0
OD1 B:ASP194 4.7 30.2 1.0

Reference:

R.Dai, T.W.Geders, F.Liu, S.W.Park, D.Schnappinger, C.C.Aldrich, B.C.Finzel. Fragment-Based Exploration of Binding Site Flexibility in Mycobacterium Tuberculosis Bioa. J.Med.Chem. V. 58 5208 2015.
ISSN: ISSN 0022-2623
PubMed: 26068403
DOI: 10.1021/ACS.JMEDCHEM.5B00092
Page generated: Fri Jul 26 03:10:15 2024

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