Iodine 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:

Nickel

(Ni)

2 atoms

The binding sites of Iodine 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 Iodine atom.
In total 3 binding sites of Iodine where determined in the N-Terminal Domain of Delta-Subunit of Rna Polymerase Complexed with I3C and Nickel Ions, PDB code: 4nc7:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 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 Iodine with other atoms in the I 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:I101 b:40.5 occ:0.70 I3 A:I3C101 0.0 40.5 0.7 C6 A:I3C101 2.1 41.3 1.0 OE1 A:GLU34 2.1 59.8 1.0 C1 A:I3C101 3.0 41.4 1.0 C5 A:I3C101 3.0 35.6 1.0 CD A:GLU34 3.1 64.3 1.0 N13 A:I3C101 3.2 37.5 1.0 C7 A:I3C101 3.3 45.7 1.0 O9 A:I3C101 3.6 49.0 1.0 CG A:GLU34 3.7 55.5 1.0 ND2 A:ASN37 3.7 42.3 1.0 O8 A:I3C101 3.8 46.2 1.0 O A:HOH223 4.0 31.9 1.0 OE2 A:GLU34 4.1 61.6 1.0 C4 A:I3C101 4.4 39.1 1.0 C2 A:I3C101 4.4 44.6 1.0 N A:GLU34 4.5 30.5 1.0 CB A:GLN33 4.6 35.2 1.0 C A:GLN33 4.6 31.1 1.0 CA A:GLU34 4.6 33.4 1.0 CB A:GLU34 4.7 39.5 1.0 O A:GLN33 4.8 33.4 1.0 C3 A:I3C101 4.9 38.6 1.0 CG A:ASN37 5.0 39.1 1.0

Iodine binding site 2 out of 3 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 Iodine with other atoms in the I 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 A:I101 b:34.6 occ:0.70 I2 A:I3C101 0.0 34.6 0.7 C4 A:I3C101 2.1 39.1 1.0 C5 A:I3C101 3.0 35.6 1.0 C3 A:I3C101 3.0 38.6 1.0 N13 A:I3C101 3.1 37.5 1.0 C10 A:I3C101 3.3 45.1 1.0 O12 A:I3C101 3.7 57.4 1.0 O11 A:I3C101 3.8 44.8 1.0 CG A:GLN33 4.2 35.3 1.0 C2 A:I3C101 4.3 44.6 1.0 C6 A:I3C101 4.3 41.3 1.0 CG2 A:THR74 4.6 31.3 1.0 CB A:GLN33 4.7 35.2 1.0 C1 A:I3C101 4.8 41.4 1.0

Iodine binding site 3 out of 3 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 Iodine with other atoms in the I binding site number 3 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:I101 b:63.4 occ:0.70 I1 A:I3C101 0.0 63.4 0.7 C2 A:I3C101 2.1 44.6 1.0 C1 A:I3C101 3.1 41.4 1.0 C3 A:I3C101 3.1 38.6 1.0 C7 A:I3C101 3.1 45.7 1.0 C10 A:I3C101 3.2 45.1 1.0 O11 A:I3C101 3.5 44.8 1.0 O8 A:I3C101 3.5 46.2 1.0 O9 A:I3C101 3.6 49.0 1.0 O12 A:I3C101 3.6 57.4 1.0 NZ A:LYS47 3.8 62.4 1.0 C4 A:I3C101 4.4 39.1 1.0 C6 A:I3C101 4.4 41.3 1.0 CE A:LYS47 4.8 54.5 1.0 C5 A:I3C101 4.9 35.6 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