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Chlorine in PDB 9dqi: D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase)

Enzymatic activity of D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase)

All present enzymatic activity of D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase):
2.2.1.9;

Protein crystallography data

The structure of D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase), PDB code: 9dqi was solved by J.M.Johnston, N.A.T.Ho, F.M.Given, E.M.M.Bulloch, T.M.Allison, W.Jiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.13 / 2.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.565, 139.978, 183.859, 90, 90, 90
R / Rfree (%) 19.5 / 23.1

Other elements in 9dqi:

The structure of D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase) (pdb code 9dqi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase), PDB code: 9dqi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 9dqi

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Chlorine binding site 1 out of 5 in the D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:68.0
occ:1.00
 OG1 A:THR442 2.8 74.8 1.0
N A:GLY439 3.2 56.7 1.0
CB A:THR442 3.5 61.8 1.0
CD A:PRO379 3.6 61.5 1.0
CG A:PRO379 3.7 59.4 1.0
CA A:GLY375 3.7 49.0 1.0
CB A:SER377 3.8 79.4 1.0
CG2 A:THR442 3.9 68.7 1.0
C A:GLY375 4.0 61.7 1.0
CA A:GLY439 4.0 47.4 1.0
O A:HOH746 4.0 65.8 1.0
CA A:ILE438 4.0 52.2 1.0
C A:ILE438 4.1 56.9 1.0
N A:SER377 4.2 71.4 1.0
O A:GLY375 4.2 63.6 1.0
CB A:ILE438 4.3 53.0 1.0
OG A:SER377 4.5 85.6 1.0
N A:ALA376 4.5 69.3 1.0
CA A:SER377 4.6 74.5 1.0
N A:GLY375 4.6 53.5 1.0
CB A:PRO379 4.8 58.3 1.0
O A:GLY439 4.9 62.0 1.0
C A:GLY439 4.9 60.2 1.0
N A:ASN378 4.9 75.1 1.0
CA A:THR442 4.9 56.6 1.0

Chlorine binding site 2 out of 5 in 9dqi

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Chlorine binding site 2 out of 5 in the D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:73.7
occ:1.00
 N A:LEU185 2.9 56.3 1.0
CA A:PRO184 3.7 53.3 1.0
N A:VAL186 3.7 51.2 1.0
CG D:GLU479 3.7 61.2 1.0
C A:PRO184 3.8 46.6 1.0
CA A:LEU185 3.8 52.2 1.0
CB A:LEU185 3.9 42.3 1.0
CB D:GLU479 3.9 53.8 1.0
CD D:GLU479 4.0 77.6 1.0
CG2 A:VAL186 4.1 50.6 1.0
OE1 D:GLU479 4.1 79.9 1.0
CB A:PRO184 4.2 51.1 1.0
C A:LEU185 4.2 59.5 1.0
CG1 A:VAL186 4.3 53.0 1.0
CG A:LEU185 4.5 54.9 1.0
CB A:VAL186 4.6 52.4 1.0
OE2 D:GLU479 4.6 87.2 1.0
CB A:GLU183 4.7 51.6 1.0
CA A:VAL186 4.8 52.9 1.0
O A:PRO184 5.0 61.1 1.0
CD1 A:LEU185 5.0 45.5 1.0
N A:PRO184 5.0 56.7 1.0

Chlorine binding site 3 out of 5 in 9dqi

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Chlorine binding site 3 out of 5 in the D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl605

b:71.7
occ:1.00
 NH1 D:ARG381 2.8 53.5 1.0
NH1 D:ARG399 3.2 52.3 1.0
NH2 D:ARG381 3.3 62.7 1.0
N D:SER377 3.4 47.0 1.0
CZ D:ARG381 3.5 57.2 1.0
CB D:ALA376 3.8 37.8 1.0
NH2 D:ARG399 3.8 56.1 1.0
CZ D:ARG399 4.0 60.7 1.0
CB D:ALA402 4.0 51.2 1.0
CA D:SER377 4.1 56.7 1.0
CA D:ALA376 4.2 47.2 1.0
C D:ALA376 4.3 55.1 1.0
O D:SER377 4.5 54.4 1.0
O D:ALA402 4.6 50.6 1.0
CG1 D:VAL380 4.7 41.6 1.0
C D:SER377 4.8 54.1 1.0
NE D:ARG381 4.8 61.8 1.0
CA D:ALA402 4.9 46.5 1.0
CD2 D:LEU280 5.0 54.6 1.0

Chlorine binding site 4 out of 5 in 9dqi

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Chlorine binding site 4 out of 5 in the D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:54.0
occ:1.00
 N B:ARG268 3.2 49.1 1.0
NH1 B:ARG331 3.3 62.4 1.0
CZ3 B:TRP328 3.6 59.9 1.0
CD B:ARG331 3.6 56.1 1.0
CD2 B:LEU267 3.9 56.2 1.0
O B:ARG268 4.0 54.3 1.0
CA B:ARG268 4.0 56.4 1.0
CA B:LEU267 4.0 60.5 1.0
CB B:ARG268 4.0 59.8 1.0
C B:LEU267 4.1 54.4 1.0
C B:ARG268 4.2 58.3 1.0
CZ B:ARG331 4.2 58.5 1.0
NE B:ARG331 4.3 57.8 1.0
CB B:LEU267 4.4 58.6 1.0
CH2 B:TRP328 4.4 69.1 1.0
CE3 B:TRP328 4.5 54.3 1.0
CG B:ARG268 4.6 65.0 1.0
CG B:LEU267 4.8 63.5 1.0
CG B:ARG331 4.8 47.8 1.0
O B:LEU266 4.9 61.3 1.0

Chlorine binding site 5 out of 5 in 9dqi

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Chlorine binding site 5 out of 5 in the D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of D306N Mutant of M.Tuberculosis Mend (Sephchc Synthase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl603

b:70.1
occ:1.00
 OG1 B:THR442 2.7 73.7 1.0
N B:GLY439 3.3 57.9 1.0
CB B:THR442 3.4 61.9 1.0
OG B:SER377 3.5 81.3 1.0
CG B:PRO379 3.8 66.6 1.0
CD B:PRO379 3.8 64.5 1.0
CG2 B:THR442 3.9 75.0 1.0
CA B:GLY375 3.9 62.0 1.0
CA B:ILE438 4.0 57.4 1.0
CA B:GLY439 4.1 66.3 1.0
CB B:ILE438 4.1 56.6 1.0
C B:ILE438 4.1 60.4 1.0
C B:GLY375 4.5 65.2 1.0
CB B:SER377 4.5 85.8 1.0
CG2 B:ILE438 4.6 59.6 1.0
N B:SER377 4.8 71.1 1.0
CA B:THR442 4.8 69.0 1.0
N B:GLY375 4.8 49.3 1.0
O B:GLY439 4.8 59.9 1.0
C B:GLY439 4.9 70.0 1.0
O B:GLY375 4.9 68.2 1.0
N B:ALA376 5.0 66.4 1.0

Reference:

N.A.T.Ho, F.M.Given, T.Stanborough, M.Klein, T.M.Allison, E.M.M.Bulloch, W.Jiao, J.M.Johnston. Apparent Reversal of Allosteric Response in Mycobacterium Tuberculosis Mend Reveals Links to Half-of-Sites Reactivity. Chembiochem 00943 2025.
ISSN: ESSN 1439-7633
PubMed: 39945237
DOI: 10.1002/CBIC.202400943
Page generated: Sun Jul 13 16:23:44 2025

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