Nickel in PDB 5c3r: Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU)

The structure of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU), PDB code: 5c3r was solved by W.Li, T.Zhang, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.817, 155.775, 75.992, 90.00, 91.65, 90.00
R / Rfree (%)	18.1 / 22.5

The binding sites of Nickel atom in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU) (pdb code 5c3r). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU), PDB code: 5c3r:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:18.3 occ:1.00 O5 A:AKG402 2.1 19.9 1.0 O1 A:AKG402 2.2 18.9 1.0 OD1 A:ASP216 2.2 14.1 1.0 O A:HOH505 2.3 18.0 1.0 NE2 A:HIS214 2.3 12.6 1.0 NE2 A:HIS271 2.3 11.0 1.0 C2 A:AKG402 2.8 20.0 1.0 C1 A:AKG402 2.9 19.5 1.0 CG A:ASP216 3.1 14.1 1.0 CD2 A:HIS271 3.2 11.1 1.0 CD2 A:HIS214 3.2 12.6 1.0 OD2 A:ASP216 3.3 14.2 1.0 CE1 A:HIS214 3.3 12.7 1.0 CE1 A:HIS271 3.3 11.1 1.0 O3 A:HMU403 3.9 27.6 1.0 O A:HOH628 4.0 25.9 1.0 O2 A:AKG402 4.1 19.4 1.0 C3 A:AKG402 4.3 19.9 1.0 CG A:HIS271 4.3 11.2 1.0 CG A:HIS214 4.4 12.9 1.0 ND1 A:HIS271 4.4 11.2 1.0 ND1 A:HIS214 4.4 12.9 1.0 CM5 A:HMU403 4.4 27.8 1.0 CB A:ASP216 4.5 13.8 1.0 CE1 A:PHE292 4.5 11.6 1.0 C4 A:AKG402 4.8 20.0 1.0 N A:ASP216 4.8 13.4 1.0 CA A:ASP216 4.9 13.6 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:23.8 occ:1.00 O2 B:AKG402 2.1 28.4 1.0 NE2 B:HIS214 2.2 18.2 1.0 O5 B:AKG402 2.2 30.3 1.0 O B:HOH545 2.3 27.9 1.0 NE2 B:HIS271 2.3 15.7 1.0 OD1 B:ASP216 2.3 19.8 1.0 C1 B:AKG402 2.9 29.3 1.0 C2 B:AKG402 2.9 29.8 1.0 CE1 B:HIS214 3.1 18.2 1.0 CD2 B:HIS271 3.2 15.8 1.0 CG B:ASP216 3.2 19.5 1.0 CD2 B:HIS214 3.3 18.4 1.0 CE1 B:HIS271 3.3 15.7 1.0 OD2 B:ASP216 3.4 19.7 1.0 O1 B:AKG402 4.1 29.0 1.0 O3 B:HMU403 4.1 38.1 1.0 O B:HOH611 4.1 31.8 1.0 ND1 B:HIS214 4.2 18.4 1.0 CM5 B:HMU403 4.3 38.6 1.0 CG B:HIS271 4.3 16.0 1.0 CG B:HIS214 4.3 18.4 1.0 ND1 B:HIS271 4.4 15.7 1.0 C3 B:AKG402 4.4 29.4 1.0 CB B:ASP216 4.6 19.5 1.0 CE1 B:PHE292 4.7 17.4 1.0 O B:HOH580 4.7 58.5 1.0 C4 B:AKG402 4.8 28.9 1.0 N B:ASP216 4.9 18.8 1.0 CA B:ASP216 5.0 19.4 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni401 b:20.5 occ:1.00 O2 C:AKG402 2.1 22.2 1.0 O5 C:AKG402 2.2 22.5 1.0 O C:HOH503 2.3 21.5 1.0 OD1 C:ASP216 2.3 15.8 1.0 NE2 C:HIS271 2.3 11.2 1.0 NE2 C:HIS214 2.3 16.0 1.0 C2 C:AKG402 2.8 22.9 1.0 C1 C:AKG402 2.8 23.1 1.0 CG C:ASP216 3.1 15.6 1.0 CD2 C:HIS271 3.1 11.3 1.0 CE1 C:HIS214 3.2 16.1 1.0 OD2 C:ASP216 3.2 15.5 1.0 CD2 C:HIS214 3.3 16.3 1.0 CE1 C:HIS271 3.3 11.3 1.0 O C:HOH604 4.0 37.1 1.0 O3 C:HMU403 4.0 37.9 1.0 O1 C:AKG402 4.0 22.9 1.0 C3 C:AKG402 4.3 23.0 1.0 ND1 C:HIS214 4.3 16.5 1.0 CG C:HIS271 4.3 11.3 1.0 ND1 C:HIS271 4.4 11.3 1.0 CG C:HIS214 4.4 16.6 1.0 CM5 C:HMU403 4.4 37.7 1.0 CB C:ASP216 4.5 15.7 1.0 CE1 C:PHE292 4.6 18.2 1.0 C4 C:AKG402 4.8 23.1 1.0 N C:ASP216 4.9 15.6 1.0 CZ C:PHE292 4.9 18.7 1.0 CA C:ASP216 5.0 15.8 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and 5-Hydroxymethyluracil (5HMU) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni401 b:26.5 occ:1.00 O1 D:AKG402 2.2 31.1 1.0 O5 D:AKG402 2.2 32.3 1.0 O D:HOH537 2.2 31.4 1.0 NE2 D:HIS214 2.2 21.3 1.0 OD1 D:ASP216 2.3 23.0 1.0 NE2 D:HIS271 2.3 17.7 1.0 C2 D:AKG402 2.9 32.9 1.0 C1 D:AKG402 2.9 32.4 1.0 CE1 D:HIS214 3.1 21.9 1.0 CD2 D:HIS271 3.2 18.0 1.0 CG D:ASP216 3.2 22.9 1.0 CD2 D:HIS214 3.2 21.4 1.0 CE1 D:HIS271 3.2 17.6 1.0 OD2 D:ASP216 3.4 23.5 1.0 O3 D:HMU403 3.9 51.9 1.0 O2 D:AKG402 4.1 31.7 1.0 ND1 D:HIS214 4.3 21.9 1.0 ND1 D:HIS271 4.3 17.9 1.0 CG D:HIS271 4.3 18.0 1.0 C3 D:AKG402 4.3 33.2 1.0 CG D:HIS214 4.3 21.8 1.0 CM5 D:HMU403 4.4 52.8 1.0 CB D:ASP216 4.6 22.4 1.0 O D:HOH583 4.6 36.0 1.0 CE1 D:PHE292 4.7 19.9 1.0 C4 D:AKG402 4.8 34.0 1.0 N D:ASP216 4.9 21.6 1.0 CA D:ASP216 5.0 22.2 1.0

W.Li, T.Zhang, J.Ding. Molecular Basis For the Substrate Specificity and Catalytic Mechanism of Thymine-7-Hydroxylase in Fungi Nucleic Acids Res. V. 43 10026 2015.
ISSN: ESSN 1362-4962
PubMed: 26429971
DOI: 10.1093/NAR/GKV979