Nickel in PDB 5c3q: Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and Thymine (T)

The structure of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and Thymine (T), PDB code: 5c3q 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 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.900, 156.318, 76.028, 90.00, 91.77, 90.00
R / Rfree (%)	18.4 / 21.5

The binding sites of Nickel atom in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg and Thymine (T) (pdb code 5c3q). 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 Thymine (T), PDB code: 5c3q:
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 Thymine (T)


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 Thymine (T) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:24.4 occ:1.00 O A:HOH503 2.2 27.8 1.0 NE2 A:HIS214 2.2 17.8 1.0 OD1 A:ASP216 2.2 18.6 1.0 O5 A:AKG402 2.2 25.6 1.0 NE2 A:HIS271 2.2 17.1 1.0 O1 A:AKG402 2.3 24.9 1.0 C2 A:AKG402 2.9 26.4 1.0 C1 A:AKG402 3.0 26.3 1.0 CD2 A:HIS271 3.1 17.3 1.0 CG A:ASP216 3.1 18.4 1.0 CE1 A:HIS214 3.1 17.8 1.0 CD2 A:HIS214 3.2 17.8 1.0 CE1 A:HIS271 3.3 17.2 1.0 OD2 A:ASP216 3.3 18.9 1.0 O A:HOH651 4.1 40.1 1.0 O2 A:AKG402 4.2 25.9 1.0 CG A:HIS271 4.2 17.4 1.0 ND1 A:HIS214 4.2 18.2 1.0 CG A:HIS214 4.3 18.2 1.0 ND1 A:HIS271 4.3 17.6 1.0 C3 A:AKG402 4.4 26.7 1.0 O A:HOH640 4.4 35.7 1.0 CB A:ASP216 4.5 18.1 1.0 CM5 A:TDR403 4.6 26.6 1.0 CE1 A:PHE292 4.7 19.4 1.0 N A:ASP216 4.9 18.1 1.0 C4 A:AKG402 4.9 26.7 1.0 CA A:ASP216 4.9 18.2 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 Thymine (T)


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 Thymine (T) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:27.8 occ:1.00 O2 B:AKG402 2.1 30.2 1.0 OD1 B:ASP216 2.2 21.6 1.0 O B:HOH516 2.2 26.9 1.0 NE2 B:HIS271 2.2 19.8 1.0 O5 B:AKG402 2.3 29.0 1.0 NE2 B:HIS214 2.3 22.9 1.0 C1 B:AKG402 2.9 30.5 1.0 C2 B:AKG402 3.0 29.6 1.0 CG B:ASP216 3.1 21.7 1.0 CD2 B:HIS214 3.2 22.3 1.0 CE1 B:HIS271 3.2 19.6 1.0 CD2 B:HIS271 3.2 19.7 1.0 OD2 B:ASP216 3.2 22.1 1.0 CE1 B:HIS214 3.3 22.8 1.0 O1 B:AKG402 4.1 30.1 1.0 O B:HOH622 4.2 40.0 1.0 O B:HOH613 4.2 51.5 1.0 ND1 B:HIS271 4.3 19.8 1.0 CG B:HIS271 4.3 20.0 1.0 CG B:HIS214 4.3 22.6 1.0 ND1 B:HIS214 4.4 23.0 1.0 C3 B:AKG402 4.4 29.6 1.0 CB B:ASP216 4.5 21.5 1.0 CM5 B:TDR403 4.5 31.6 1.0 CE1 B:PHE292 4.7 23.9 1.0 N B:ASP216 4.9 21.9 1.0 CA B:ASP216 4.9 21.9 1.0 C4 B:AKG402 4.9 29.1 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 Thymine (T)


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 Thymine (T) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni401 b:26.2 occ:1.00 O2 C:AKG402 2.1 27.4 1.0 O C:HOH504 2.2 30.3 1.0 OD1 C:ASP216 2.2 21.8 1.0 NE2 C:HIS214 2.3 22.2 1.0 O5 C:AKG402 2.3 27.9 1.0 NE2 C:HIS271 2.3 18.2 1.0 C1 C:AKG402 2.9 28.1 1.0 C2 C:AKG402 2.9 28.5 1.0 CG C:ASP216 3.1 21.6 1.0 CD2 C:HIS271 3.1 18.3 1.0 CE1 C:HIS214 3.2 22.3 1.0 OD2 C:ASP216 3.2 21.4 1.0 CD2 C:HIS214 3.2 22.4 1.0 CE1 C:HIS271 3.3 18.1 1.0 O C:HOH619 4.0 39.7 1.0 O1 C:AKG402 4.1 27.9 1.0 O C:HOH611 4.2 47.9 1.0 ND1 C:HIS214 4.3 22.8 1.0 CG C:HIS271 4.3 18.2 1.0 C3 C:AKG402 4.4 28.6 1.0 CG C:HIS214 4.4 22.8 1.0 ND1 C:HIS271 4.4 18.2 1.0 CM5 C:TDR403 4.5 36.2 1.0 CB C:ASP216 4.5 21.4 1.0 CE1 C:PHE292 4.6 24.6 1.0 N C:ASP216 4.9 21.2 1.0 C4 C:AKG402 4.9 28.6 1.0 CA C:ASP216 4.9 21.4 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 Thymine (T)


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 Thymine (T) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni401 b:32.4 occ:1.00 O D:HOH506 2.2 35.9 1.0 O5 D:AKG402 2.2 34.6 1.0 OD1 D:ASP216 2.2 27.2 1.0 NE2 D:HIS214 2.3 26.8 1.0 O2 D:AKG402 2.3 35.2 1.0 NE2 D:HIS271 2.3 23.3 1.0 C2 D:AKG402 2.9 35.8 1.0 C1 D:AKG402 3.0 36.0 1.0 CG D:ASP216 3.1 27.5 1.0 CD2 D:HIS271 3.2 23.5 1.0 CE1 D:HIS214 3.2 26.8 1.0 CD2 D:HIS214 3.2 26.1 1.0 CE1 D:HIS271 3.3 22.9 1.0 OD2 D:ASP216 3.3 27.5 1.0 O D:HOH590 4.1 43.4 1.0 O1 D:AKG402 4.2 35.8 1.0 ND1 D:HIS214 4.3 26.9 1.0 CG D:HIS271 4.3 23.4 1.0 ND1 D:HIS271 4.3 23.4 1.0 CG D:HIS214 4.4 26.6 1.0 C3 D:AKG402 4.4 35.9 1.0 CB D:ASP216 4.5 27.1 1.0 CE1 D:PHE292 4.7 28.0 1.0 CM5 D:TDR403 4.7 57.8 1.0 C4 D:AKG402 4.9 36.3 1.0 N D:ASP216 4.9 26.8 1.0 CA D:ASP216 4.9 27.4 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