Potassium in PDB 9eaf: Carboxyspermidine Decarboxylase From Clostridium Leptum

The structure of Carboxyspermidine Decarboxylase From Clostridium Leptum, PDB code: 9eaf was solved by S.J.Jones, D.J.Bell, J.S.Mcfarlane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.85 / 1.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.57, 80.85, 140.535, 90, 90, 90
R / Rfree (%)	15 / 18.9

The binding sites of Potassium atom in the Carboxyspermidine Decarboxylase From Clostridium Leptum (pdb code 9eaf). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Carboxyspermidine Decarboxylase From Clostridium Leptum, PDB code: 9eaf:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Carboxyspermidine Decarboxylase From Clostridium Leptum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Carboxyspermidine Decarboxylase From Clostridium Leptum within 5.0Å range: probe atom residue distance (Å) B Occ A:K401 b:11.1 occ:1.00 O A:MET198 2.6 10.5 1.0 O A:SER196 2.7 9.9 1.0 O A:GLY231 2.8 10.4 1.0 O A:TYR230 2.8 11.5 1.0 O A:HOH751 2.8 17.3 1.0 HG12 A:VAL232 3.3 11.9 1.0 HG13 A:VAL232 3.5 11.9 1.0 C A:GLY231 3.5 10.0 1.0 HA3 A:GLY231 3.7 12.5 1.0 O A:HOH743 3.8 36.0 1.0 C A:MET198 3.8 9.1 1.0 C A:SER196 3.8 9.8 1.0 CG1 A:VAL232 3.8 9.9 1.0 O A:HOH546 4.0 12.3 1.0 C A:TYR230 4.0 10.8 1.0 HA A:LYS199 4.0 11.6 1.0 CA A:GLY231 4.1 10.4 1.0 HA A:SER196 4.1 11.1 1.0 HA A:VAL232 4.1 11.8 1.0 N A:VAL232 4.3 10.5 1.0 H A:MET198 4.3 12.1 1.0 N A:MET198 4.4 10.1 1.0 HG11 A:VAL232 4.5 11.9 1.0 N A:GLY231 4.5 10.7 1.0 CA A:SER196 4.6 9.3 1.0 C A:GLN197 4.6 10.3 1.0 HA A:GLN197 4.6 12.0 1.0 O A:HOH770 4.6 22.7 1.0 CA A:VAL232 4.6 9.8 1.0 HG A:SER196 4.7 10.9 1.0 N A:LYS199 4.7 9.4 1.0 O A:LEU195 4.7 10.9 1.0 CA A:MET198 4.7 10.0 1.0 HB3 A:TYR230 4.7 13.3 1.0 CA A:LYS199 4.7 9.6 1.0 N A:GLN197 4.8 9.9 1.0 CB A:VAL232 4.9 10.5 1.0 CA A:GLN197 4.9 10.0 1.0 HA2 A:GLY231 5.0 12.5 1.0

Potassium binding site 2 out of 2 in the Carboxyspermidine Decarboxylase From Clostridium Leptum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Carboxyspermidine Decarboxylase From Clostridium Leptum within 5.0Å range: probe atom residue distance (Å) B Occ B:K401 b:11.4 occ:1.00 O B:MET198 2.6 11.1 1.0 O B:SER196 2.6 10.7 1.0 O B:GLY231 2.8 11.2 1.0 O B:TYR230 2.8 11.6 1.0 O B:HOH763 2.8 18.0 1.0 O B:HOH756 3.3 39.2 1.0 HG12 B:VAL232 3.3 11.2 1.0 HG13 B:VAL232 3.4 11.2 1.0 C B:GLY231 3.5 9.8 1.0 HA3 B:GLY231 3.7 12.1 1.0 C B:SER196 3.8 10.0 1.0 C B:MET198 3.8 10.2 1.0 CG1 B:VAL232 3.8 9.3 1.0 C B:TYR230 4.0 10.9 1.0 O B:HOH565 4.0 11.3 1.0 HA B:LYS199 4.0 12.0 1.0 HA B:SER196 4.0 11.5 1.0 CA B:GLY231 4.1 10.0 1.0 HA B:VAL232 4.1 11.0 1.0 H B:MET198 4.3 12.5 1.0 N B:VAL232 4.3 9.1 1.0 N B:MET198 4.3 10.4 1.0 HG11 B:VAL232 4.5 11.2 1.0 CA B:SER196 4.5 9.6 1.0 N B:GLY231 4.5 10.6 1.0 C B:GLN197 4.6 10.4 1.0 HA B:GLN197 4.6 13.3 1.0 CA B:VAL232 4.6 9.1 1.0 O B:LEU195 4.6 10.9 1.0 HG B:SER196 4.6 12.1 1.0 HB3 B:TYR230 4.7 13.1 1.0 CA B:MET198 4.7 10.1 1.0 N B:GLN197 4.7 9.8 1.0 N B:LYS199 4.7 9.7 1.0 CA B:LYS199 4.8 10.0 1.0 CA B:GLN197 4.9 11.1 1.0 CB B:VAL232 4.9 9.6 1.0 HA2 B:GLY231 5.0 12.1 1.0

S.J.Jones, D.J.Bell, J.S.Mcfarlane. Structure of Clostridium Leptum Carboxyspermidine Decarboxylase and Comparison to Homologs Prevalent Within the Human Gut Microbiome. Acta Crystallogr.,Sect.F 2025.
ISSN: ESSN 2053-230X
PubMed: 39887002
DOI: 10.1107/S2053230X25000482