Chlorine in PDB 9hra: Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid

All present enzymatic activity of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid:
4.1.3.30;

The structure of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid, PDB code: 9hra 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)	52.59 / 2.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.199, 101.203, 115.683, 90, 91.15, 90
R / Rfree (%)	20.8 / 25.7

The structure of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid (pdb code 9hra). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 23 binding sites of Chlorine where determined in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid, PDB code: 9hra:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 23 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


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 Products Succinic and Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl307 b:50.1 occ:1.00 CE2 A:TYR273 3.4 117.9 1.0 N F:ASP54 3.6 47.9 1.0 ND2 F:ASN48 3.7 34.0 1.0 O F:HOH441 3.8 36.5 1.0 CE1 A:TYR268 3.9 78.7 1.0 CB F:ASP54 3.9 42.6 1.0 OD1 F:ASN48 3.9 35.6 1.0 CD2 A:TYR273 4.0 131.6 1.0 CD1 A:LEU271 4.2 60.4 1.0 CG F:ASN48 4.2 33.8 1.0 CA F:PRO53 4.3 42.9 1.0 CA F:ASP54 4.4 43.1 1.0 CD1 A:TYR268 4.4 74.4 1.0 C F:PRO53 4.5 50.9 1.0 CZ A:TYR273 4.5 117.3 1.0 OH A:TYR273 4.8 95.3 1.0 CB F:PRO53 4.8 33.5 1.0 CZ A:TYR268 4.9 86.7 1.0

Chlorine binding site 2 out of 23 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


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 Products Succinic and Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl308 b:52.9 occ:1.00 CD A:LYS198 4.1 74.5 1.0 O A:VAL197 4.1 47.7 1.0 CG1 A:VAL172 4.2 33.4 1.0 O A:ALA196 4.3 54.2 1.0 O A:CYS169 4.3 47.5 1.0 CB A:VAL172 4.4 39.0 1.0 SG A:CYS169 4.6 48.5 1.0 CB A:CYS169 4.6 63.4 1.0 C A:VAL197 4.6 50.2 1.0 CA A:CYS169 4.7 42.3 1.0 CG A:LYS198 4.7 67.5 1.0 CA A:VAL197 4.8 50.7 1.0 C A:CYS169 4.9 38.6 1.0 CB A:LYS198 5.0 52.0 1.0 CE A:LYS198 5.0 77.8 1.0

Chlorine binding site 3 out of 23 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


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 Products Succinic and Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl308 b:51.0 occ:1.00 O B:HOH474 3.0 29.3 1.0 N B:ASP54 3.6 27.6 1.0 CE2 D:TYR273 3.7 73.9 1.0 CB B:ASP54 3.7 35.1 1.0 ND2 B:ASN48 4.0 48.5 1.0 CE1 D:TYR268 4.0 66.2 1.0 OD1 B:ASN48 4.2 49.1 1.0 CA B:ASP54 4.3 27.3 1.0 CD2 D:TYR273 4.3 95.0 1.0 CA B:PRO53 4.5 40.0 1.0 C B:PRO53 4.5 31.7 1.0 CG B:ASN48 4.6 51.6 1.0 CD1 D:LEU271 4.7 46.6 1.0 CD1 D:TYR268 4.7 64.8 1.0 CZ D:TYR273 4.7 83.8 1.0 CB B:PRO53 4.9 36.6 1.0 OH D:TYR273 4.9 83.5 1.0 CZ D:TYR268 5.0 62.9 1.0

Chlorine binding site 4 out of 23 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


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 Products Succinic and Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl309 b:65.8 occ:1.00 O B:HOH447 3.8 42.0 1.0 O B:CYS169 4.0 48.6 1.0 CG1 B:VAL172 4.2 28.8 1.0 CB B:CYS169 4.3 46.3 1.0 CB B:VAL172 4.4 33.0 1.0 CA B:CYS169 4.4 54.7 1.0 SG B:CYS169 4.5 55.8 1.0 C B:CYS169 4.6 58.8 1.0 O B:ALA196 4.6 50.2 1.0

Chlorine binding site 5 out of 23 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


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 Products Succinic and Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl310 b:64.8 occ:1.00 O B:GLY51 3.7 45.7 1.0 CD2 B:LEU52 3.7 51.0 1.0 O B:LEU50 3.8 39.6 1.0 O D:ALA72 4.1 61.1 1.0 CA D:ALA73 4.1 43.5 1.0 C B:GLY51 4.1 44.0 1.0 CB D:ALA73 4.2 43.4 1.0 CG B:LEU52 4.3 53.2 1.0 C D:ALA72 4.6 47.8 1.0 CA B:GLY51 4.6 42.5 1.0 O D:HOH408 4.7 19.7 1.0 N D:ALA73 4.7 35.3 1.0 N B:LEU52 4.8 46.0 1.0 C B:LEU50 4.8 35.9 1.0

Chlorine binding site 6 out of 23 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


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 Products Succinic and Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl305 b:58.7 occ:1.00 O D:HOH439 3.4 49.9 1.0 N D:ASP54 3.4 51.2 1.0 ND2 D:ASN48 3.4 44.8 1.0 CE2 B:TYR273 3.6 106.0 1.0 OD1 D:ASN48 3.9 47.9 1.0 CE1 B:TYR268 3.9 100.3 1.0 CB D:ASP54 3.9 52.0 1.0 CA D:PRO53 4.0 50.5 1.0 CD1 B:LEU271 4.1 49.6 1.0 CD2 B:TYR273 4.1 108.4 1.0 CG D:ASN48 4.1 44.9 1.0 C D:PRO53 4.2 51.2 1.0 CA D:ASP54 4.3 48.7 1.0 CB D:PRO53 4.4 45.6 1.0 CD1 B:TYR268 4.4 98.0 1.0 CZ B:TYR273 4.7 133.8 1.0 O D:HOH429 4.8 56.6 1.0 CZ B:TYR268 4.9 87.0 1.0 OH B:TYR273 5.0 138.5 1.0

Chlorine binding site 7 out of 23 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


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 Products Succinic and Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl306 b:75.8 occ:1.00 O D:ALA196 3.7 81.1 1.0 SG D:CYS169 3.7 64.1 1.0 CB D:CYS169 3.9 65.6 1.0 OE2 D:GLU173 4.3 98.3 1.0 CA D:CYS169 4.5 57.2 1.0 CD D:LYS198 4.7 94.1 1.0 O D:CYS169 4.7 79.5 1.0 C D:ALA196 4.8 88.5 1.0 CG D:LYS198 4.9 90.1 1.0 CA D:VAL197 4.9 74.4 1.0 C D:CYS169 5.0 72.4 1.0

Chlorine binding site 8 out of 23 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


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 Products Succinic and Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl307 b:59.7 occ:1.00 CD2 D:LEU52 3.5 22.6 1.0 O B:ALA72 3.9 53.4 1.0 O D:LEU50 4.0 36.9 1.0 CG D:LEU52 4.2 34.2 1.0 O D:HOH412 4.2 39.4 1.0 O D:GLY51 4.3 47.5 1.0 CA B:ALA73 4.4 32.1 1.0 C B:ALA72 4.5 37.3 1.0 CB B:ALA73 4.6 28.3 1.0 C D:GLY51 4.6 45.6 1.0 N B:ALA73 4.8 34.6 1.0

Chlorine binding site 9 out of 23 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl309 b:53.0 occ:1.00 CE2 F:TYR273 3.1 81.4 1.0 N A:ASP54 3.6 41.7 1.0 CD2 F:TYR273 3.7 81.1 1.0 CE1 F:TYR268 3.8 71.7 1.0 ND2 A:ASN48 4.0 38.8 1.0 CB A:ASP54 4.1 31.5 1.0 CZ F:TYR273 4.1 101.7 1.0 CA A:PRO53 4.2 36.7 1.0 CD1 F:LEU271 4.2 45.0 1.0 CD1 F:TYR268 4.3 69.0 1.0 OH F:TYR273 4.3 92.6 1.0 OD1 A:ASN48 4.3 34.5 1.0 CA A:ASP54 4.4 37.7 1.0 C A:PRO53 4.4 46.4 1.0 CB A:PRO53 4.5 36.0 1.0 CG A:ASN48 4.6 43.0 1.0 CZ F:TYR268 4.7 82.3 1.0 OH F:TYR268 4.9 77.2 1.0 CG F:TYR273 5.0 88.2 1.0

Chlorine binding site 10 out of 23 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Products Succinic and Pyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl310 b:81.6 occ:1.00 CG1 F:VAL172 4.0 45.0 1.0 O F:CYS169 4.2 44.5 1.0 CB F:VAL172 4.3 65.8 1.0 O F:VAL197 4.3 42.2 1.0 CG F:GLU173 4.6 93.3 1.0 CB F:CYS169 4.6 46.0 1.0 OE2 F:GLU173 4.6 134.6 1.0 CA F:CYS169 4.6 54.2 1.0 O F:ALA196 4.7 64.4 1.0 SG F:CYS169 4.7 51.3 1.0 C F:CYS169 4.8 60.5 1.0 C F:VAL197 4.9 42.2 1.0

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