Nickel in PDB 5c3p: Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg

The structure of Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg, PDB code: 5c3p 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 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.185, 154.726, 75.434, 90.00, 90.60, 90.00
R / Rfree (%)	18.5 / 22.2

The binding sites of Nickel atom in the Crystal Structure of the Full-Length Neurospora Crassa T7H in Complex with Alpha-Kg (pdb code 5c3p). 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, PDB code: 5c3p:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:40.0 occ:1.00 O5 A:AKG402 2.2 43.2 1.0 OD1 A:ASP216 2.2 28.7 1.0 NE2 A:HIS271 2.2 26.4 1.0 O1 A:AKG402 2.3 43.7 1.0 O A:HOH510 2.3 38.4 1.0 NE2 A:HIS214 2.3 29.1 1.0 C2 A:AKG402 2.9 44.3 1.0 C1 A:AKG402 3.0 43.5 1.0 CG A:ASP216 3.1 27.5 1.0 CE1 A:HIS271 3.2 24.5 1.0 CD2 A:HIS271 3.2 25.8 1.0 CD2 A:HIS214 3.2 28.1 1.0 OD2 A:ASP216 3.2 27.8 1.0 CE1 A:HIS214 3.3 27.3 1.0 O A:HOH529 4.1 62.8 1.0 O A:HOH639 4.1 50.2 1.0 O2 A:AKG402 4.2 43.0 1.0 ND1 A:HIS271 4.3 25.8 1.0 CG A:HIS271 4.3 25.8 1.0 C3 A:AKG402 4.4 43.4 1.0 CG A:HIS214 4.4 28.2 1.0 ND1 A:HIS214 4.4 29.5 1.0 CB A:ASP216 4.5 27.8 1.0 CE1 A:PHE292 4.7 29.4 1.0 N A:ASP216 4.8 27.3 1.0 C4 A:AKG402 4.8 41.8 1.0 CA A:ASP216 4.9 27.8 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:43.4 occ:1.00 OD1 B:ASP216 2.2 35.9 1.0 O5 B:AKG402 2.2 45.5 1.0 O B:HOH506 2.2 43.9 1.0 NE2 B:HIS214 2.3 33.8 1.0 O2 B:AKG402 2.3 41.3 1.0 NE2 B:HIS271 2.3 30.1 1.0 C2 B:AKG402 2.9 48.2 1.0 C1 B:AKG402 3.0 45.1 1.0 CG B:ASP216 3.1 33.8 1.0 CE1 B:HIS214 3.2 33.5 1.0 CE1 B:HIS271 3.2 28.7 1.0 CD2 B:HIS271 3.2 28.9 1.0 OD2 B:ASP216 3.3 33.5 1.0 CD2 B:HIS214 3.3 33.4 1.0 O B:HOH577 4.1 64.1 1.0 O1 B:AKG402 4.2 45.8 1.0 ND1 B:HIS214 4.3 35.3 1.0 ND1 B:HIS271 4.3 30.6 1.0 CG B:HIS271 4.4 30.4 1.0 C3 B:AKG402 4.4 50.0 1.0 CG B:HIS214 4.4 33.6 1.0 CB B:ASP216 4.5 32.9 1.0 CE1 B:PHE292 4.6 37.1 1.0 N B:ASP216 4.8 32.1 1.0 C4 B:AKG402 4.9 51.4 1.0 CZ B:PHE292 4.9 35.7 1.0 CA B:ASP216 4.9 32.8 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni401 b:42.4 occ:1.00 OD1 C:ASP216 2.2 32.5 1.0 O2 C:AKG402 2.2 46.0 1.0 O5 C:AKG402 2.2 47.3 1.0 NE2 C:HIS271 2.2 25.9 1.0 NE2 C:HIS214 2.3 32.4 1.0 O C:HOH527 2.3 40.8 1.0 C2 C:AKG402 2.9 49.0 1.0 C1 C:AKG402 2.9 46.1 1.0 CG C:ASP216 3.0 31.9 1.0 CE1 C:HIS271 3.1 25.9 1.0 OD2 C:ASP216 3.2 33.3 1.0 CD2 C:HIS214 3.2 30.5 1.0 CD2 C:HIS271 3.2 26.6 1.0 CE1 C:HIS214 3.3 32.4 1.0 O C:HOH564 4.1 65.6 1.0 O1 C:AKG402 4.1 46.2 1.0 ND1 C:HIS271 4.2 26.9 1.0 CG C:HIS271 4.3 26.8 1.0 CG C:HIS214 4.4 31.6 1.0 ND1 C:HIS214 4.4 33.1 1.0 C3 C:AKG402 4.4 48.5 1.0 CB C:ASP216 4.5 30.9 1.0 CE1 C:PHE292 4.6 32.5 1.0 N C:ASP216 4.8 30.9 1.0 C4 C:AKG402 4.9 48.7 1.0 CA C:ASP216 4.9 31.1 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni401 b:47.8 occ:1.00 NE2 D:HIS271 2.2 34.1 1.0 NE2 D:HIS214 2.2 35.2 1.0 O D:HOH512 2.2 48.2 1.0 O5 D:AKG402 2.2 55.5 1.0 OD1 D:ASP216 2.3 36.5 1.0 O1 D:AKG402 2.3 55.1 1.0 C2 D:AKG402 3.0 60.5 1.0 C1 D:AKG402 3.0 59.4 1.0 CE1 D:HIS271 3.1 33.3 1.0 CD2 D:HIS214 3.1 34.5 1.0 CG D:ASP216 3.2 37.1 1.0 CD2 D:HIS271 3.2 32.6 1.0 CE1 D:HIS214 3.2 34.9 1.0 OD2 D:ASP216 3.3 38.8 1.0 O D:HOH579 4.1 59.4 1.0 ND1 D:HIS271 4.2 34.4 1.0 O2 D:AKG402 4.2 59.5 1.0 ND1 D:HIS214 4.3 35.4 1.0 CG D:HIS271 4.3 33.3 1.0 CG D:HIS214 4.3 35.0 1.0 C3 D:AKG402 4.4 61.2 1.0 CB D:ASP216 4.6 36.9 1.0 CE1 D:PHE292 4.8 41.0 1.0 N D:ASP216 4.9 35.9 1.0 C4 D:AKG402 4.9 61.2 1.0 CA D:ASP216 4.9 36.8 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