Iron in PDB 9nh3: Helicobacter Pylori Strain SS1 Kata

All present enzymatic activity of Helicobacter Pylori Strain SS1 Kata:
1.11.1.6;

The structure of Helicobacter Pylori Strain SS1 Kata, PDB code: 9nh3 was solved by A.Baylink, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.30 / 1.87
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.512, 96.198, 154.754, 90, 90, 90
R / Rfree (%)	14.2 / 19.1

The structure of Helicobacter Pylori Strain SS1 Kata also contains other interesting chemical elements:

Sodium	(Na)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Iron atom in the Helicobacter Pylori Strain SS1 Kata (pdb code 9nh3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Helicobacter Pylori Strain SS1 Kata, PDB code: 9nh3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Helicobacter Pylori Strain SS1 Kata


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Helicobacter Pylori Strain SS1 Kata within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:11.3 occ:1.00 FE A:HEM601 0.0 11.3 1.0 OH A:TYR339 1.9 9.2 1.0 NB A:HEM601 2.0 9.0 1.0 NA A:HEM601 2.0 9.6 1.0 ND A:HEM601 2.1 7.8 1.0 NC A:HEM601 2.1 10.2 1.0 O A:HOH777 2.4 8.2 0.3 CZ A:TYR339 3.0 9.2 1.0 C4A A:HEM601 3.0 8.5 1.0 C4B A:HEM601 3.0 9.6 1.0 C1B A:HEM601 3.0 11.5 1.0 C1D A:HEM601 3.0 8.6 1.0 C4C A:HEM601 3.0 11.8 1.0 C1C A:HEM601 3.1 10.8 1.0 C1A A:HEM601 3.1 11.0 1.0 C4D A:HEM601 3.1 13.1 1.0 CHB A:HEM601 3.3 8.3 1.0 HE A:ARG335 3.4 10.2 1.0 CHD A:HEM601 3.4 11.0 1.0 CHC A:HEM601 3.4 13.1 1.0 CHA A:HEM601 3.5 10.6 1.0 HH21 A:ARG335 3.5 15.0 1.0 HE2 A:TYR339 3.7 11.3 1.0 CE2 A:TYR339 3.8 9.5 1.0 HE1 A:TYR339 3.8 12.6 1.0 CE1 A:TYR339 3.8 10.5 1.0 HZ A:PHE142 3.9 12.1 1.0 HG21 A:VAL55 4.0 10.2 1.0 NE A:ARG335 4.1 8.5 1.0 O A:HOH777 4.2 10.3 0.7 NH2 A:ARG335 4.2 12.6 1.0 C3B A:HEM601 4.2 12.7 1.0 C3A A:HEM601 4.2 8.7 1.0 C2B A:HEM601 4.2 9.4 1.0 C2D A:HEM601 4.3 8.8 1.0 C2A A:HEM601 4.3 8.2 1.0 C3C A:HEM601 4.3 13.2 1.0 C3D A:HEM601 4.3 11.1 1.0 C2C A:HEM601 4.3 16.1 1.0 CZ A:PHE142 4.3 10.1 1.0 HHB A:HEM601 4.3 9.9 1.0 HHD A:HEM601 4.4 13.2 1.0 HHC A:HEM601 4.4 15.7 1.0 HHA A:HEM601 4.5 12.7 1.0 HG23 A:VAL55 4.5 10.2 1.0 HD2 A:HIS56 4.5 13.7 1.0 CZ A:ARG335 4.5 11.3 1.0 HG2 A:ARG335 4.6 11.8 1.0 CG2 A:VAL55 4.6 8.5 1.0 NE2 A:HIS56 4.7 11.9 1.0 HH22 A:ARG335 4.8 15.0 1.0 HE1 A:PHE142 4.8 11.6 1.0 CD2 A:HIS56 4.8 11.4 1.0 CE1 A:PHE142 4.8 9.7 1.0 CE2 A:PHE142 4.9 10.4 1.0 HE2 A:PHE142 4.9 12.5 1.0 HG11 A:VAL127 4.9 13.8 1.0 HG22 A:VAL55 5.0 10.2 1.0

Iron binding site 2 out of 2 in the Helicobacter Pylori Strain SS1 Kata


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Helicobacter Pylori Strain SS1 Kata within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:13.4 occ:1.00 FE B:HEM601 0.0 13.4 1.0 OH B:TYR339 1.9 12.3 1.0 NB B:HEM601 2.0 14.3 1.0 ND B:HEM601 2.1 10.0 1.0 NA B:HEM601 2.1 8.0 1.0 NC B:HEM601 2.1 10.1 1.0 O B:HOH953 2.8 10.2 0.3 C4B B:HEM601 3.0 11.5 1.0 CZ B:TYR339 3.0 13.0 1.0 C1B B:HEM601 3.0 11.1 1.0 C4A B:HEM601 3.0 9.6 1.0 C4C B:HEM601 3.1 10.3 1.0 C1C B:HEM601 3.1 12.1 1.0 C1D B:HEM601 3.1 10.1 1.0 C4D B:HEM601 3.1 9.5 1.0 C1A B:HEM601 3.1 9.5 1.0 HE B:ARG335 3.4 11.5 1.0 CHB B:HEM601 3.4 9.8 1.0 CHC B:HEM601 3.4 14.5 1.0 CHD B:HEM601 3.4 11.0 1.0 HH21 B:ARG335 3.4 14.3 1.0 CHA B:HEM601 3.5 11.4 1.0 HE2 B:TYR339 3.7 10.8 1.0 CE2 B:TYR339 3.7 9.0 1.0 HE1 B:TYR339 3.8 13.3 1.0 CE1 B:TYR339 3.8 11.1 1.0 HZ B:PHE142 3.9 14.9 1.0 HG21 B:VAL55 4.0 10.5 1.0 NE B:ARG335 4.1 9.6 1.0 O B:HOH953 4.1 10.6 0.7 NH2 B:ARG335 4.1 11.9 1.0 C3B B:HEM601 4.2 13.6 1.0 C2B B:HEM601 4.2 10.6 1.0 C3A B:HEM601 4.3 11.0 1.0 C3C B:HEM601 4.3 10.4 1.0 C2C B:HEM601 4.3 14.9 1.0 C3D B:HEM601 4.3 12.6 1.0 C2D B:HEM601 4.3 9.1 1.0 C2A B:HEM601 4.3 10.6 1.0 CZ B:PHE142 4.3 12.4 1.0 HHC B:HEM601 4.4 17.4 1.0 HHB B:HEM601 4.4 11.8 1.0 HD2 B:HIS56 4.4 12.4 1.0 HHD B:HEM601 4.4 13.2 1.0 HE2 B:HIS56 4.4 14.5 1.0 HHA B:HEM601 4.4 13.7 1.0 HG23 B:VAL55 4.5 10.5 1.0 CZ B:ARG335 4.5 12.8 1.0 HG2 B:ARG335 4.6 14.5 1.0 CG2 B:VAL55 4.7 8.8 1.0 HH22 B:ARG335 4.7 14.3 1.0 CD2 B:HIS56 4.8 10.3 1.0 NE2 B:HIS56 4.8 12.1 1.0 HG11 B:VAL127 4.8 15.7 1.0 CE2 B:PHE142 4.9 10.5 1.0 CE1 B:PHE142 4.9 11.7 1.0 HE1 B:PHE142 4.9 14.1 1.0 HE2 B:PHE142 4.9 12.5 1.0 HG12 B:VAL127 5.0 15.7 1.0 CD2 B:TYR339 5.0 9.8 1.0

A.Baylink, A.Baylink. N/A N/A.
ISSN: ISSN 2692-8205
PubMed: 40501634
DOI: 10.1101/2025.06.02.657526