Potassium 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:

Chlorine

(Cl)

5 atoms

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium 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 Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 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 Potassium with other atoms in the K 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:K504 b:34.7 occ:0.51 K A:K504 0.0 34.7 0.5 K A:K504 2.4 44.6 0.5 OE1 A:GLU302 2.7 33.6 1.0 O A:HOH806 2.9 23.7 1.0 OE2 A:GLU299 3.2 29.7 1.0 O A:HOH734 3.3 28.6 1.0 OE1 A:GLU299 3.3 25.1 1.0 CD A:GLU299 3.5 24.3 1.0 O A:HOH615 3.6 27.7 1.0 CB A:GLU302 3.8 24.3 1.0 CD A:GLU302 3.8 32.5 1.0 O A:HOH814 3.9 29.8 1.0 O A:HOH897 4.1 39.1 1.0 O A:HOH911 4.1 28.2 1.0 O A:HOH611 4.2 28.6 1.0 O B:ALA179 4.2 27.9 1.0 O A:HOH927 4.4 38.9 1.0 CG A:GLU302 4.4 25.1 1.0 CA B:ALA179 4.4 22.5 1.0 CA A:GLU299 4.5 17.6 1.0 CG A:GLU299 4.7 21.3 1.0 O A:GLU299 4.8 19.0 1.0 CB B:ALA179 4.8 22.1 1.0 C B:ALA179 4.8 28.1 1.0 OE2 A:GLU302 4.8 33.4 1.0 CB A:GLU299 4.9 17.8 1.0

Potassium binding site 2 out of 4 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 Potassium with other atoms in the K 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:K504 b:44.6 occ:0.49 K A:K504 0.0 44.6 0.5 K A:K504 2.4 34.7 0.5 O B:ALA179 2.8 27.9 1.0 O A:HOH927 3.1 38.9 1.0 OE1 A:GLU302 3.5 33.6 1.0 C B:ALA179 3.7 28.1 1.0 O A:HOH897 3.9 39.1 1.0 CA B:ALA179 3.9 22.5 1.0 CB B:ALA179 4.0 22.1 1.0 O A:HOH814 4.1 29.8 1.0 CD A:GLU302 4.2 32.5 1.0 CB A:GLU302 4.3 24.3 1.0 O A:HOH911 4.3 28.2 1.0 O A:HOH734 4.4 28.6 1.0 O A:HOH806 4.5 23.7 1.0 O A:HOH615 4.6 27.7 1.0 CG A:GLU302 4.7 25.1 1.0 O B:HOH1027 4.8 49.0 1.0 OE2 A:GLU302 4.9 33.4 1.0 N B:GLN180 4.9 27.9 1.0

Potassium binding site 3 out of 4 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 Potassium with other atoms in the K 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:K505 b:23.8 occ:0.71 O A:GLY260 2.7 14.9 1.0 O B:GLU439 2.7 14.4 1.0 ND1 A:HIS265 2.8 13.9 1.0 CD1 B:LEU269 3.2 16.5 1.0 CB A:HIS265 3.3 12.2 1.0 CG A:HIS265 3.5 13.3 1.0 C B:GLU439 3.6 13.5 1.0 CA A:VAL262 3.6 11.8 1.0 O A:ASN261 3.6 13.1 1.0 CD B:PRO441 3.6 13.1 1.0 C A:ASN261 3.7 12.9 1.0 C A:GLY260 3.7 13.7 1.0 N A:VAL262 3.7 12.3 1.0 CA B:ARG440 3.8 12.8 1.0 CE1 A:HIS265 3.9 13.7 1.0 CG2 A:VAL262 4.0 13.4 1.0 N B:ARG440 4.0 13.0 1.0 CG B:LEU269 4.3 16.1 1.0 CD2 B:LEU269 4.4 16.0 1.0 CA A:ASN261 4.4 12.0 1.0 CG B:GLU439 4.4 16.0 1.0 CB A:VAL262 4.4 12.6 1.0 N A:ASN261 4.5 12.9 1.0 CA A:GLY260 4.6 14.0 1.0 C A:VAL262 4.6 11.4 1.0 N B:PRO441 4.6 13.3 1.0 CB B:ARG440 4.6 12.9 1.0 O A:VAL262 4.7 12.8 1.0 CB B:GLU439 4.7 15.0 1.0 CG B:ARG440 4.7 15.2 1.0 CG B:PRO441 4.7 17.9 1.0 CD2 A:HIS265 4.7 14.4 1.0 CA B:GLU439 4.7 14.2 1.0 C B:ARG440 4.8 13.9 1.0 CA A:HIS265 4.8 11.8 1.0 NE2 A:HIS265 4.9 15.1 1.0

Potassium binding site 4 out of 4 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 Potassium with other atoms in the K 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:K502 b:24.3 occ:0.71 O B:GLY260 2.7 15.3 1.0 O A:GLU439 2.7 16.5 1.0 ND1 B:HIS265 2.8 13.0 1.0 CD1 A:LEU269 3.1 20.5 1.0 CB B:HIS265 3.3 12.2 1.0 CG B:HIS265 3.5 13.0 1.0 O B:ASN261 3.6 13.6 1.0 C A:GLU439 3.6 16.3 1.0 C B:ASN261 3.6 11.9 1.0 CA B:VAL262 3.7 12.6 1.0 CD A:PRO441 3.7 16.4 1.0 CA A:ARG440 3.8 14.5 1.0 C B:GLY260 3.8 13.0 1.0 N B:VAL262 3.8 12.1 1.0 CE1 B:HIS265 3.9 14.9 1.0 N A:ARG440 4.0 15.0 1.0 CG2 B:VAL262 4.1 16.1 1.0 CG A:LEU269 4.2 23.2 1.0 CA B:ASN261 4.4 12.1 1.0 CD2 A:LEU269 4.4 18.8 1.0 N B:ASN261 4.5 13.4 1.0 CB B:VAL262 4.5 14.0 1.0 CG A:GLU439 4.5 18.3 1.0 CB A:ARG440 4.6 16.4 1.0 N A:PRO441 4.6 14.9 1.0 C B:VAL262 4.6 11.7 1.0 O B:VAL262 4.7 12.4 1.0 C A:ARG440 4.7 16.6 1.0 CA B:GLY260 4.7 13.5 1.0 CD2 B:HIS265 4.8 14.2 1.0 CG A:PRO441 4.8 18.3 1.0 CB A:GLU439 4.8 16.9 1.0 CA B:HIS265 4.8 10.5 1.0 CA A:GLU439 4.8 15.6 1.0 CG A:ARG440 4.9 22.7 1.0 NE2 B:HIS265 5.0 16.1 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