Iodine in PDB 2ram: A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer

The structure of A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer, PDB code: 2ram was solved by Y.Q.Chen, S.Ghosh, G.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.810, 80.620, 167.800, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 30.8

The binding sites of Iodine atom in the A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer (pdb code 2ram). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer, PDB code: 2ram:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ C:I12 b:39.8 occ:1.00 I5 C:5IU12 0.0 39.8 1.0 C5 C:5IU12 2.1 38.4 1.0 C6 C:5IU12 3.0 33.9 1.0 C4 C:5IU12 3.1 31.1 1.0 O4 C:5IU12 3.4 33.4 1.0 OH A:TYR36 3.6 12.5 1.0 CD A:ARG187 3.7 35.1 1.0 CG A:ARG187 3.8 41.5 1.0 C6 C:DT11 3.9 25.4 1.0 NE A:ARG187 3.9 29.9 1.0 C2' C:DT11 4.0 16.3 1.0 CE1 A:TYR36 4.2 14.8 1.0 C5 C:DT11 4.2 27.1 1.0 N1 C:DT11 4.2 25.1 1.0 CZ A:TYR36 4.3 8.1 1.0 N1 C:5IU12 4.4 27.9 1.0 N3 C:5IU12 4.4 32.2 1.0 CZ A:ARG187 4.6 29.8 1.0 C7 C:DT11 4.6 26.2 1.0 O A:HOH332 4.7 21.1 1.0 C1' C:DT11 4.7 16.3 1.0 C4 C:DT11 4.7 30.5 1.0 C2 C:DT11 4.7 30.6 1.0 I5 C:5IU13 4.7 29.8 1.0 N3 C:DT11 4.9 30.8 1.0 O4 C:5IU13 4.9 41.7 1.0 CB A:ARG187 4.9 42.0 1.0 C2 C:5IU12 4.9 32.3 1.0

Iodine binding site 2 out of 4 in the A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ C:I13 b:29.8 occ:1.00 I5 C:5IU13 0.0 29.8 1.0 C5 C:5IU13 2.1 40.9 1.0 C6 C:5IU13 3.0 38.9 1.0 C4 C:5IU13 3.1 39.9 1.0 O4 C:5IU13 3.3 41.7 1.0 CD1 A:TYR36 3.3 18.2 1.0 CE1 A:TYR36 3.6 14.8 1.0 C6 C:5IU12 3.7 33.9 1.0 OE1 A:GLU39 3.8 31.6 1.0 CG A:TYR36 3.8 17.5 1.0 C2' C:5IU12 3.8 17.9 1.0 NH1 A:ARG187 3.9 22.5 1.0 N1 C:5IU12 3.9 27.9 1.0 NH2 A:ARG187 3.9 22.7 1.0 CZ A:ARG187 4.0 29.8 1.0 C5 C:5IU12 4.0 38.4 1.0 CD A:GLU39 4.0 31.4 1.0 CB A:TYR36 4.2 26.3 1.0 SG A:CYS38 4.3 29.5 1.0 N1 C:5IU13 4.3 34.2 1.0 N3 C:5IU13 4.3 41.2 1.0 CZ A:TYR36 4.3 8.1 1.0 C2 C:5IU12 4.4 32.3 1.0 C1' C:5IU12 4.4 17.5 1.0 OE2 A:GLU39 4.4 30.3 1.0 CG A:GLU39 4.5 28.4 1.0 CD2 A:TYR36 4.5 12.9 1.0 C4 C:5IU12 4.5 31.1 1.0 N3 C:5IU12 4.6 32.2 1.0 NE A:ARG187 4.7 29.9 1.0 I5 C:5IU12 4.7 39.8 1.0 CE2 A:TYR36 4.7 11.4 1.0 N4 C:DC14 4.8 27.7 1.0 C2 C:5IU13 4.9 41.4 1.0 OP2 C:5IU13 4.9 28.5 1.0

Iodine binding site 3 out of 4 in the A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ D:I12 b:36.9 occ:1.00 I5 D:5IU12 0.0 36.9 1.0 C5 D:5IU12 2.1 43.2 1.0 C6 D:5IU12 3.0 38.7 1.0 C4 D:5IU12 3.1 36.2 1.0 OE2 B:GLU39 3.1 45.2 1.0 O4 D:5IU12 3.3 41.8 1.0 CD B:GLU39 3.7 39.1 1.0 SG B:CYS38 3.7 46.9 1.0 C6 D:DT11 3.9 23.2 1.0 CD1 B:TYR36 3.9 23.0 1.0 CG B:GLU39 4.0 41.6 1.0 C5 D:DT11 4.0 26.0 1.0 N1 D:DT11 4.2 21.6 1.0 CG B:TYR36 4.2 24.8 1.0 NH1 B:ARG187 4.2 64.2 1.0 N1 D:5IU12 4.3 32.6 1.0 N3 D:5IU12 4.3 34.8 1.0 CB B:TYR36 4.3 35.8 1.0 C4 D:DT11 4.4 28.4 1.0 C2' D:DT11 4.4 22.8 1.0 OE1 B:GLU39 4.5 28.6 1.0 C7 D:DT11 4.5 16.7 1.0 CZ B:ARG187 4.5 63.9 1.0 CE1 B:TYR36 4.5 18.1 1.0 C2 D:DT11 4.5 20.1 1.0 N3 D:DT11 4.6 19.7 1.0 NH2 B:ARG187 4.7 69.3 1.0 C1' D:DT11 4.8 20.3 1.0 C2 D:5IU12 4.9 37.2 1.0 I5 D:5IU13 4.9 59.4 1.0

Iodine binding site 4 out of 4 in the A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of A Novel Dna Recognition Mode By Nf-Kb P65 Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ D:I13 b:59.4 occ:1.00 I5 D:5IU13 0.0 59.4 1.0 C5 D:5IU13 2.1 47.2 1.0 C6 D:5IU13 3.0 42.6 1.0 C4 D:5IU13 3.0 46.0 1.0 O4 D:5IU13 3.3 46.0 1.0 C6 D:5IU12 3.8 38.7 1.0 O B:CYS38 4.0 54.2 1.0 SG B:CYS38 4.0 46.9 1.0 N1 D:5IU12 4.0 32.6 1.0 C5 D:5IU12 4.0 43.2 1.0 C B:CYS38 4.1 54.7 1.0 C2' D:5IU12 4.1 28.7 1.0 CA B:GLU39 4.2 52.5 1.0 N B:GLU39 4.2 53.2 1.0 CB B:CYS38 4.3 51.6 1.0 N1 D:5IU13 4.3 40.5 1.0 N3 D:5IU13 4.3 45.0 1.0 C2 D:5IU12 4.3 37.2 1.0 CG B:GLU39 4.4 41.6 1.0 C4 D:5IU12 4.4 36.2 1.0 N3 D:5IU12 4.5 34.8 1.0 O D:HOH336 4.6 30.5 1.0 OE2 B:GLU39 4.6 45.2 1.0 C1' D:5IU12 4.6 29.7 1.0 CB B:GLU39 4.7 48.5 1.0 OP2 D:5IU13 4.8 31.2 1.0 CA B:CYS38 4.9 54.6 1.0 C2 D:5IU13 4.9 45.0 1.0 I5 D:5IU12 4.9 36.9 1.0 O2 D:5IU12 4.9 40.6 1.0

Y.Q.Chen, S.Ghosh, G.Ghosh. A Novel Dna Recognition Mode By the Nf-Kappa B P65 Homodimer. Nat.Struct.Biol. V. 5 67 1998.
ISSN: ISSN 1072-8368
PubMed: 9437432
DOI: 10.1038/NSB0198-67