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Chlorine in PDB 9hgq: Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic

Enzymatic activity of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic

All present enzymatic activity of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic:
4.1.3.30;

Protein crystallography data

The structure of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic, PDB code: 9hgq was solved by W.Stuart, M.Isupov, N.J.Harmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.49 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.31, 73.31, 184.141, 90, 90, 120
R / Rfree (%) 18.9 / 24.3

Other elements in 9hgq:

The structure of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic (pdb code 9hgq). 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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic, PDB code: 9hgq:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 9hgq

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Chlorine binding site 1 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:48.4
occ:1.00
 N A:ASP54 3.7 32.2 1.0
ND2 A:ASN48 3.8 29.5 1.0
CB A:ASP54 4.0 29.9 1.0
CD1 B:LEU271 4.1 34.0 1.0
OD1 A:ASN48 4.1 35.5 1.0
CE1 B:TYR268 4.1 58.5 1.0
CA A:PRO53 4.3 35.5 1.0
CG A:ASN48 4.4 35.2 1.0
CA A:ASP54 4.4 37.1 1.0
C A:PRO53 4.5 31.8 1.0
CZ B:TYR268 4.6 68.4 1.0
CD1 B:TYR273 4.6 68.8 1.0
CB A:PRO53 4.7 34.5 1.0
OH B:TYR268 4.7 69.2 1.0
CD1 B:TYR268 4.7 53.8 1.0
CE1 B:TYR273 4.7 73.0 1.0
O A:HOH516 5.0 50.6 1.0

Chlorine binding site 2 out of 8 in 9hgq

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Chlorine binding site 2 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl311

b:63.4
occ:1.00
 CD1 A:TYR273 3.3 98.5 1.0
CE1 A:TYR268 3.4 84.0 1.0
CE1 A:TYR273 3.4 87.3 1.0
N B:ASP54 3.4 33.4 1.0
ND2 B:ASN48 3.5 34.7 1.0
CB B:ASP54 3.7 33.0 1.0
CD1 A:TYR268 4.0 81.4 1.0
OD1 B:ASN48 4.0 40.9 1.0
CA B:PRO53 4.1 36.8 1.0
CD1 A:LEU271 4.1 37.1 1.0
CZ A:TYR268 4.1 71.3 1.0
CG A:TYR273 4.2 88.7 1.0
CA B:ASP54 4.2 38.2 1.0
OH A:TYR268 4.2 61.8 1.0
CG B:ASN48 4.2 38.4 1.0
C B:PRO53 4.2 37.6 1.0
CZ A:TYR273 4.4 96.1 1.0
CB B:PRO53 4.5 36.5 1.0
O B:HOH405 4.7 41.2 1.0
CB A:TYR273 4.8 65.7 1.0
CD2 A:TYR273 5.0 90.8 1.0

Chlorine binding site 3 out of 8 in 9hgq

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Chlorine binding site 3 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl312

b:87.2
occ:1.00
 O A:VAL197 3.5 42.4 1.0
O A:ALA196 3.8 38.7 1.0
CD A:LYS198 4.1 75.9 1.0
CG A:LYS198 4.1 63.4 1.0
C A:VAL197 4.1 45.5 1.0
CG1 A:VAL172 4.1 42.9 1.0
CE A:LYS198 4.2 79.2 1.0
CB A:LYS198 4.3 43.5 1.0
CA A:VAL197 4.5 50.4 1.0
CB A:VAL172 4.5 39.3 1.0
SG A:CYS169 4.8 47.6 1.0
O A:CYS169 4.8 40.9 1.0
C A:ALA196 4.9 49.3 1.0
CB A:CYS169 4.9 46.0 1.0
N A:LYS198 5.0 47.9 1.0

Chlorine binding site 4 out of 8 in 9hgq

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Chlorine binding site 4 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl313

b:85.3
occ:1.00
 NE2 A:HIS75 3.2 71.8 1.0
CD2 A:HIS75 3.4 64.5 1.0
O A:ALA72 3.8 42.2 1.0
CE1 A:HIS75 3.9 81.8 1.0
C A:ALA73 4.1 36.8 1.0
O A:ALA73 4.1 38.0 1.0
N A:THR74 4.1 34.9 1.0
CG A:HIS75 4.2 72.4 1.0
O A:HOH535 4.3 54.8 1.0
CA A:THR74 4.3 37.1 1.0
C A:THR74 4.4 38.2 1.0
ND1 A:HIS75 4.5 81.8 1.0
O A:HOH453 4.5 52.2 1.0
C A:ALA72 4.6 40.7 1.0
N A:HIS75 4.6 42.1 1.0
CA A:ALA73 4.8 31.9 1.0
O A:THR71 4.9 38.4 1.0
O A:THR74 4.9 44.8 1.0
N A:ALA73 5.0 33.9 1.0
O A:HOH433 5.0 39.1 1.0

Chlorine binding site 5 out of 8 in 9hgq

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Chlorine binding site 5 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl314

b:72.4
occ:1.00
 O A:HOH444 3.5 31.3 1.0
O A:ARG101 3.7 37.7 1.0
NE A:ARG68 4.0 54.9 1.0
C A:ARG101 4.2 38.4 1.0
CA A:ALA102 4.3 29.5 1.0
CG A:ARG68 4.5 41.4 1.0
N A:ALA102 4.5 34.1 1.0
CD A:ARG68 4.6 34.5 1.0
CB A:ARG101 4.7 26.4 1.0
NH2 A:ARG68 4.8 54.0 1.0
CB A:ALA102 4.8 28.7 1.0
CZ A:ARG68 4.8 60.0 1.0

Chlorine binding site 6 out of 8 in 9hgq

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Chlorine binding site 6 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl311

b:79.7
occ:1.00
 O B:HOH533 3.4 58.0 1.0
CE2 B:TYR276 4.0 37.6 1.0
CZ B:TYR276 4.0 33.2 1.0
CD2 B:TYR276 4.2 41.1 1.0
O B:ALA275 4.2 52.9 1.0
CE1 B:TYR276 4.2 33.3 1.0
CG B:TYR276 4.4 44.5 1.0
CD1 B:TYR276 4.4 42.0 1.0
C B:ALA275 4.5 51.7 1.0
CB B:ALA275 4.5 43.8 1.0
OH B:TYR276 4.6 36.7 1.0
N B:TYR276 4.7 49.1 1.0
CA B:TYR276 4.7 43.2 1.0
O B:HOH487 4.7 47.7 1.0
CB B:LYS279 4.8 44.9 1.0

Chlorine binding site 7 out of 8 in 9hgq

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Chlorine binding site 7 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl312

b:75.8
occ:1.00
 NE2 B:HIS75 3.4 69.8 1.0
CD2 B:HIS75 3.5 59.6 1.0
O B:ALA72 3.8 36.3 1.0
N B:THR74 4.0 36.8 1.0
C B:ALA73 4.1 37.7 1.0
CE1 B:HIS75 4.2 66.3 1.0
O B:HOH432 4.2 42.0 1.0
O B:ALA73 4.3 37.0 1.0
CA B:THR74 4.3 38.8 1.0
O B:HOH534 4.3 49.0 1.0
CG B:HIS75 4.3 69.3 1.0
C B:THR74 4.4 39.3 1.0
C B:ALA72 4.5 36.8 1.0
N B:HIS75 4.5 42.1 1.0
O B:THR71 4.7 37.3 1.0
ND1 B:HIS75 4.7 73.6 1.0
CA B:ALA73 4.7 46.9 1.0
O B:HOH448 4.8 38.5 1.0
O B:THR74 4.8 39.2 1.0
O B:HOH507 4.8 55.3 1.0
N B:ALA73 4.9 32.5 1.0
O B:HOH477 5.0 52.8 1.0

Chlorine binding site 8 out of 8 in 9hgq

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Chlorine binding site 8 out of 8 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Substrate 2-Mic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl313

b:87.0
occ:1.00
 O B:ALA176 3.8 55.6 1.0
O B:GLY175 4.3 48.4 1.0
O B:VAL172 4.4 62.8 1.0
C B:GLY175 4.5 61.5 1.0
CA B:GLY175 4.5 50.5 1.0
C B:ALA176 4.6 49.5 1.0
O B:HOH455 4.7 49.8 1.0
O B:HOH454 4.8 56.0 1.0
OD1 B:ASP177 4.9 46.6 1.0
CA B:ASP177 4.9 38.5 1.0

Reference:

W.S.Stuart, C.H.Jenkins, P.M.Ireland, M.N.Isupov, I.H.Norville, N.J.Harmer. Structure and Catalytic Mechanism of Methylisocitrate Lyase, A Potential Drug Target Against Coxiella Burnetii. J.Biol.Chem. V. 301 08517 2025.
ISSN: ESSN 1083-351X
PubMed: 40250561
DOI: 10.1016/J.JBC.2025.108517
Page generated: Sat Aug 23 00:42:03 2025

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