Chlorine in PDB 9hdm: Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine

The structure of Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine, PDB code: 9hdm was solved by F.Friedrich, F.Genz, O.Einsle, M.Mueller, N.D.Fessner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.96 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.983, 108.293, 115.732, 90, 90, 90
R / Rfree (%)	17.5 / 20.1

The structure of Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine (pdb code 9hdm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine, PDB code: 9hdm:

Chlorine binding site 1 out of 1 in the Crystal Structure of Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine


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 Pyrimidine Nucleoside 2'-Hydroxylase (PDN2'H) From Neurospora Crassa in Complex with Thymidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:23.4 occ:1.00 OH B:TYR102 3.0 21.8 1.0 O B:HOH776 3.0 45.7 1.0 NH1 B:ARG196 3.3 21.1 1.0 O B:HOH787 3.3 48.2 1.0 C6 B:THM403 3.7 19.4 1.0 C5M B:THM403 3.8 22.9 1.0 CD B:ARG196 3.9 19.4 1.0 CE2 B:TYR102 3.9 16.9 1.0 CZ B:TYR102 3.9 20.9 1.0 C3' B:THM403 3.9 20.5 1.0 C2' B:THM403 3.9 19.7 1.0 C5 B:THM403 4.2 21.0 1.0 O3' B:THM403 4.3 24.1 1.0 CZ B:ARG196 4.3 19.6 1.0 O B:HOH603 4.4 26.2 1.0 CE2 B:PHE339 4.5 17.9 1.0 NE B:ARG196 4.6 18.8 1.0 CZ B:PHE339 4.6 19.8 1.0 O B:HOH599 4.6 30.6 1.0 N1 B:THM403 4.7 17.9 1.0 C1' B:THM403 4.9 19.6 1.0 CD2 B:LEU79 5.0 23.5 1.0

F.Genz, F.Friedrich, C.Lonarz, O.Einsle, M.Jung, M.Muller, N.D.Fessner. Identification and Characterization of Pyrimidine Nucleoside 2'-Hydroxylase Acs Catalysis 2025.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.4C07764