Nickel in PDB 4nc7: N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with I3C and Nickel Ions

The structure of N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with I3C and Nickel Ions, PDB code: 4nc7 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)	27.50 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	41.650, 110.200, 85.260, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.9

The structure of N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with I3C and Nickel Ions also contains other interesting chemical elements:

Iodine

(I)

3 atoms

The binding sites of Nickel atom in the N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with I3C and Nickel Ions (pdb code 4nc7). 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 I3C and Nickel Ions, PDB code: 4nc7:
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 I3C and 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 I3C and Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni102 b:42.3 occ:0.80 O B:HOH226 2.6 36.5 1.0 O A:ASN62 2.7 33.1 1.0 O A:LEU61 2.7 28.0 1.0 O A:ASP64 2.7 37.6 1.0 O B:ASN62 2.8 27.9 1.0 O A:PHE67 2.8 30.0 1.0 C A:ASN62 3.3 38.6 1.0 C A:ASP64 3.7 42.3 1.0 C B:ASN62 3.7 25.1 1.0 CA A:ASN62 3.7 35.7 1.0 C A:LEU61 3.8 28.3 1.0 C A:PHE67 3.9 31.1 1.0 O A:HOH243 4.0 34.4 1.0 O A:HOH229 4.0 42.1 1.0 N A:ASP64 4.2 40.8 1.0 N A:ILE63 4.2 36.7 1.0 N A:ASN62 4.2 28.3 1.0 CA A:GLY65 4.4 35.1 1.0 NI B:NI101 4.4 40.2 0.8 C A:ILE63 4.4 41.3 1.0 CA B:ASN62 4.4 25.5 1.0 CB A:PHE67 4.4 31.3 1.0 N A:GLY65 4.4 34.8 1.0 N A:PHE67 4.5 29.7 1.0 CA A:PHE67 4.5 30.2 1.0 CB B:ASN62 4.6 25.6 1.0 CA A:ASP64 4.6 42.2 1.0 N B:ILE63 4.7 27.5 1.0 ND2 B:ASN62 4.7 26.0 1.0 CA A:ILE63 4.8 36.7 1.0 O A:ILE63 4.8 38.1 1.0 CA B:ILE63 4.9 35.9 1.0 N A:LEU68 4.9 30.5 1.0 C A:GLY65 5.0 35.9 1.0

Nickel binding site 2 out of 2 in the N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with I3C and 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 I3C and Nickel Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:40.2 occ:0.80 O A:HOH243 2.6 34.4 1.0 O B:ASN62 2.8 27.9 1.0 O B:PHE67 2.8 30.3 1.0 O B:LEU61 2.8 26.6 1.0 O B:ASP64 2.8 31.5 1.0 O A:ASN62 2.9 33.1 1.0 O B:HOH225 3.3 47.0 1.0 C B:ASN62 3.4 25.1 1.0 C B:ASP64 3.7 30.1 1.0 CA B:ASN62 3.8 25.5 1.0 C B:PHE67 3.8 29.8 1.0 C A:ASN62 3.9 38.6 1.0 C B:LEU61 3.9 25.4 1.0 O B:HOH226 4.1 36.5 1.0 N B:ASP64 4.2 30.4 1.0 N B:ILE63 4.2 27.5 1.0 CB B:PHE67 4.3 29.1 1.0 N B:ASN62 4.3 23.5 1.0 NI A:NI102 4.4 42.3 0.8 CA B:GLY65 4.4 32.4 1.0 N B:GLY65 4.4 33.9 1.0 N B:PHE67 4.4 28.4 1.0 C B:ILE63 4.4 38.0 1.0 CA B:PHE67 4.4 26.7 1.0 CA A:ASN62 4.5 35.7 1.0 OD1 A:ASN62 4.5 32.5 1.0 CB A:ASN62 4.6 31.3 1.0 CA B:ASP64 4.6 31.4 1.0 CA B:ILE63 4.8 35.9 1.0 C B:GLY65 4.8 33.9 1.0 N B:LEU68 4.9 30.2 1.0 O B:ILE63 4.9 39.9 1.0 N A:ILE63 4.9 36.7 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