Chlorine in PDB 8gr9: Crystal Structure of Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A

The structure of Crystal Structure of Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A, PDB code: 8gr9 was solved by K.Nishio, K.Nakatsukasa, T.Kamura, T.Mizushima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.13 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.079, 129.659, 68.127, 90, 116.57, 90
R / Rfree (%)	17.8 / 19.8

The structure of Crystal Structure of Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Chlorine atom in the Crystal Structure of Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A (pdb code 8gr9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A, PDB code: 8gr9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A


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 Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:25.4 occ:0.64 CL A:CL506 0.0 25.4 0.6 CL A:CL506 2.2 16.2 0.4 O A:HOH904 2.9 42.6 1.0 N B:VAL262 3.3 12.1 1.0 NE A:ARG440 3.5 34.9 1.0 ND1 B:HIS293 3.6 17.6 1.0 CG2 B:VAL262 3.7 16.1 1.0 NH2 A:ARG440 3.8 36.3 1.0 CA B:ASN261 3.8 12.1 1.0 CB B:ASN261 3.9 13.3 1.0 CE1 B:HIS293 3.9 15.3 1.0 O B:HOH888 4.0 32.1 1.0 CG B:HIS293 4.0 15.2 1.0 CB B:VAL262 4.0 14.0 1.0 CZ A:ARG440 4.1 41.0 1.0 C B:ASN261 4.1 11.9 1.0 CA B:VAL262 4.3 12.6 1.0 CG2 A:ILE438 4.4 20.5 1.0 NE2 B:HIS293 4.4 14.1 1.0 CD A:ARG440 4.5 30.3 1.0 CB B:HIS293 4.5 14.3 1.0 CD2 B:HIS293 4.5 14.0 1.0 CG A:ARG440 4.5 22.7 1.0 CB A:ARG440 4.9 16.4 1.0 CA B:HIS293 4.9 14.8 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A


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 Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:16.2 occ:0.37 CL A:CL506 0.0 16.2 0.4 CL A:CL506 2.2 25.4 0.6 O B:LEU292 3.2 19.4 1.0 NH2 A:ARG440 3.2 36.3 1.0 CA B:HIS293 3.7 14.8 1.0 CB B:HIS293 3.7 14.3 1.0 C B:LEU292 3.9 15.9 1.0 O B:HOH888 3.9 32.1 1.0 CG2 A:ILE438 3.9 20.5 1.0 ND1 B:HIS293 3.9 17.6 1.0 CD1 A:ILE438 3.9 23.1 1.0 CG B:HIS293 4.0 15.2 1.0 O A:HOH904 4.1 42.6 1.0 N B:HIS293 4.1 15.1 1.0 CZ A:ARG440 4.2 41.0 1.0 NE A:ARG440 4.2 34.9 1.0 CG2 B:VAL262 4.4 16.1 1.0 O B:HOH736 4.6 35.8 1.0 CG1 A:ILE438 4.7 20.6 1.0 CB B:LEU292 4.8 16.9 1.0 CE1 B:HIS293 4.8 15.3 1.0 CB A:ILE438 4.8 17.9 1.0 CB B:VAL262 4.9 14.0 1.0 C B:HIS293 5.0 15.8 1.0 CA B:LEU292 5.0 13.9 1.0 CD2 B:HIS293 5.0 14.0 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A


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 Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:37.0 occ:0.86 O A:HOH954 2.8 43.2 1.0 N A:LYS52 2.9 19.4 1.0 O A:HOH868 3.2 41.0 1.0 CB A:LYS52 3.6 18.6 1.0 CA A:THR51 3.7 16.7 1.0 C A:THR51 3.8 18.6 1.0 CA A:LYS52 3.8 18.0 1.0 CG2 A:THR51 4.1 21.5 1.0 O A:LYS52 4.3 21.2 1.0 O A:LYS50 4.3 20.7 1.0 CB A:THR51 4.4 19.8 1.0 C A:LYS52 4.6 19.7 1.0 O A:HOH928 4.7 49.7 1.0 OG1 A:THR51 4.7 22.4 1.0 N A:THR51 4.8 17.9 1.0 CG2 B:ILE456 4.9 19.2 1.0 C A:LYS50 5.0 17.7 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A


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 Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:30.1 occ:0.70 CL B:CL503 0.0 30.1 0.7 CL B:CL503 2.1 27.6 0.3 O B:HOH987 2.8 43.1 1.0 NH1 B:ARG420 3.4 15.7 1.0 ND2 B:ASN261 3.8 17.7 1.0 CG B:ASN261 3.9 13.8 1.0 CB B:ASN261 3.9 13.3 1.0 O B:HOH971 3.9 41.6 1.0 CE1 B:HIS293 4.1 15.3 1.0 O A:HOH904 4.1 42.6 1.0 O B:HOH846 4.1 25.9 1.0 CB B:HIS257 4.1 13.5 1.0 NH2 B:ARG420 4.2 16.9 1.0 CZ B:ARG420 4.3 13.1 1.0 O B:HOH888 4.3 32.1 1.0 OD1 B:ASN261 4.5 15.4 1.0 O B:HIS257 4.5 14.3 1.0 O B:HOH710 4.5 27.2 1.0 CG B:HIS257 4.6 14.2 1.0 ND1 B:HIS257 4.7 17.2 1.0 CZ B:PHE416 4.8 16.0 1.0 ND1 B:HIS293 4.8 17.6 1.0 O B:HOH646 5.0 17.3 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A


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 Peroxisomal Citrate Synthase (CIT2) From Saccharomyces Cerevisiae in Complex with Oxaloacetate and Coenzyme-A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:27.6 occ:0.30 CL B:CL503 0.0 27.6 0.3 CL B:CL503 2.1 30.1 0.7 O B:HOH971 2.9 41.6 1.0 O A:HOH904 3.3 42.6 1.0 ND1 B:HIS257 3.5 17.2 1.0 O B:HOH803 3.6 28.1 1.0 O B:HIS257 3.7 14.3 1.0 O B:HOH818 3.7 23.5 1.0 CB B:ASN261 3.7 13.3 1.0 ND2 B:ASN261 3.8 17.7 1.0 CG B:HIS257 4.0 14.2 1.0 CG B:ASN261 4.1 13.8 1.0 CB B:HIS257 4.2 13.5 1.0 O B:HOH987 4.2 43.1 1.0 CE1 B:HIS257 4.2 19.1 1.0 O B:HOH710 4.6 27.2 1.0 O B:HOH1013 4.6 40.2 1.0 C B:HIS257 4.7 11.2 1.0 O B:HOH888 4.8 32.1 1.0 CD2 B:HIS257 4.9 16.5 1.0 CA B:ASN261 5.0 12.1 1.0

K.Nishio, T.Kawarasaki, Y.Sugiura, S.Matsumoto, A.Konoshima, Y.Takano, M.Hayashi, F.Okumura, T.Kamura, T.Mizushima, K.Nakatsukasa. Defective Import of Mitochondrial Metabolic Enzyme Elicits Ectopic Metabolic Stress. Sci Adv V. 9 F1956 2023.
ISSN: ESSN 2375-2548
PubMed: 37058555
DOI: 10.1126/SCIADV.ADF1956