Nickel in PDB 4nc8: N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with Nickel Ions

The structure of N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with Nickel Ions, PDB code: 4nc8 was solved by G.Demo, V.Papouskova, J.Komarek, H.Sanderova, A.Rabatinova, L.Krasny, L.Zidek, V.Sklenar, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.50 / 2.17
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	39.462, 109.636, 82.928, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 28.3

The binding sites of Nickel atom in the N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with Nickel Ions (pdb code 4nc8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with Nickel Ions, PDB code: 4nc8:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni101 b:45.9 occ:0.80 O A:LEU61 2.7 27.3 1.0 O A:PHE67 2.8 35.6 1.0 O B:ASN62 2.9 35.5 1.0 O A:ASN62 2.9 36.1 1.0 O A:ASP64 3.0 30.4 1.0 C A:ASN62 3.5 39.0 1.0 C A:PHE67 3.8 28.3 1.0 CA A:ASN62 3.8 39.6 1.0 C A:ASP64 3.8 30.4 1.0 C A:LEU61 3.8 37.9 1.0 C B:ASN62 3.8 38.6 1.0 N A:ASP64 4.2 31.6 1.0 CB A:PHE67 4.2 33.3 1.0 N A:ASN62 4.3 39.7 1.0 CA A:PHE67 4.3 31.8 1.0 N A:ILE63 4.3 42.2 1.0 N A:PHE67 4.4 31.9 1.0 O A:HOH204 4.4 38.6 1.0 C A:ILE63 4.5 40.7 1.0 ND2 B:ASN62 4.5 30.9 1.0 NI B:NI101 4.5 59.2 1.0 CA B:ASN62 4.5 37.7 1.0 CA A:GLY65 4.5 32.9 1.0 N A:GLY65 4.5 35.4 1.0 CB B:ASN62 4.6 36.1 1.0 CA A:ASP64 4.6 34.7 1.0 N B:ILE63 4.7 28.4 0.5 N A:LEU68 4.8 32.0 1.0 CA B:ILE63 4.8 29.2 0.5 O A:ILE63 4.8 51.3 1.0 C A:GLY65 4.9 32.3 1.0 CA A:ILE63 4.9 44.4 1.0

Nickel binding site 2 out of 2 in the N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:59.2 occ:1.00 O B:ASN62 2.6 35.5 1.0 O B:ASP64 2.6 29.6 1.0 O B:LEU61 2.7 31.5 1.0 O B:PHE67 2.7 29.9 1.0 O A:ASN62 2.8 36.1 1.0 O A:HOH204 2.9 38.6 1.0 C B:ASN62 3.3 38.6 1.0 C B:ASP64 3.6 31.2 1.0 CA B:ASN62 3.8 37.7 1.0 C B:LEU61 3.8 32.5 1.0 C B:PHE67 3.8 28.6 1.0 C A:ASN62 3.8 39.0 1.0 O B:HOH208 4.0 52.6 1.0 N B:ASP64 4.0 32.4 1.0 N B:ILE63 4.2 28.4 0.5 N B:ASN62 4.3 33.6 1.0 C B:ILE63 4.3 27.0 0.5 CB B:PHE67 4.3 36.8 1.0 N B:PHE67 4.4 33.1 1.0 CA B:PHE67 4.4 32.2 1.0 N B:GLY65 4.4 35.9 1.0 CA B:ASP64 4.4 32.5 1.0 CA B:GLY65 4.5 36.1 1.0 CA A:ASN62 4.5 39.6 1.0 NI A:NI101 4.5 45.9 0.8 CB A:ASN62 4.6 32.6 1.0 CA B:ILE63 4.6 29.2 0.5 OD1 A:ASN62 4.8 24.9 1.0 O B:ILE63 4.8 27.0 0.5 N A:ILE63 4.9 42.2 1.0 C B:GLY65 4.9 35.3 1.0 N B:LEU68 4.9 29.4 1.0

G.Demo, V.Papouskova, J.Komarek, P.Kaderavek, O.Otrusinova, P.Srb, A.Rabatinova, L.Krasny, L.Zidek, V.Sklenar, M.Wimmerova. X-Ray Vs. uc(Nmr) Structure of N-Terminal Domain of Delta-Subunit of Rna Polymerase. J.Struct.Biol. V. 187 174 2014.
ISSN: ISSN 1047-8477
PubMed: 24937760
DOI: 10.1016/J.JSB.2014.06.001