Iodine in PDB 2irf: Crystal Structure of An Irf-2/Dna Complex.

The structure of Crystal Structure of An Irf-2/Dna Complex., PDB code: 2irf was solved by Y.Fujii, T.Shimizu, M.Kusumoto, Y.Kyogoku, T.Taniguchi, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.20
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	132.300, 132.300, 296.500, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 24.3

The structure of Crystal Structure of An Irf-2/Dna Complex. also contains other interesting chemical elements:

Potassium

(K)

6 atoms

The binding sites of Iodine atom in the Crystal Structure of An Irf-2/Dna Complex. (pdb code 2irf). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of An Irf-2/Dna Complex., PDB code: 2irf:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of An Irf-2/Dna Complex. within 5.0Å range: probe atom residue distance (Å) B Occ A:I1010 b:28.1 occ:1.00 I5 A:5IU1010 0.0 28.1 1.0 C5 A:5IU1010 2.1 20.9 1.0 C6 A:5IU1010 3.0 13.2 1.0 C4 A:5IU1010 3.1 16.7 1.0 O4 A:5IU1010 3.3 14.5 1.0 NH2 I:ARG482 3.5 7.2 1.0 C8 A:DG1009 3.6 2.0 1.0 O A:HOH3026 3.7 14.9 1.0 N7 A:DG1009 3.7 3.3 1.0 O I:HOH3275 3.8 18.2 1.0 N9 A:DG1009 3.8 6.7 1.0 CB I:ALA479 4.0 5.4 1.0 C2' A:DG1009 4.0 9.3 1.0 C5 A:DG1009 4.0 3.4 1.0 O A:HOH3148 4.1 16.0 1.0 C4 A:DG1009 4.1 8.5 1.0 N1 A:5IU1010 4.3 13.9 1.0 N3 A:5IU1010 4.4 15.1 1.0 C1' A:DG1009 4.5 7.0 1.0 O F:HOH3244 4.7 15.5 1.0 CZ I:ARG482 4.8 10.1 1.0 C6 A:DG1009 4.9 7.6 1.0 O6 A:DG1011 4.9 16.4 1.0 N3 A:DG1009 4.9 8.6 1.0 C2 A:5IU1010 4.9 12.6 1.0

Iodine binding site 2 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of An Irf-2/Dna Complex. within 5.0Å range: probe atom residue distance (Å) B Occ B:I1022 b:27.2 occ:1.00 I5 B:5IU1022 0.0 27.2 1.0 C5 B:5IU1022 2.1 9.6 1.0 C6 B:5IU1022 3.0 12.8 1.0 C4 B:5IU1022 3.1 12.5 1.0 O4 B:5IU1022 3.4 15.6 1.0 O K:HOH3058 3.4 24.6 1.0 C8 B:DG1021 3.6 8.7 1.0 NH2 K:ARG882 3.6 11.1 1.0 N7 B:DG1021 3.8 6.0 1.0 N9 B:DG1021 3.9 10.6 1.0 O B:HOH3005 3.9 8.9 1.0 C2' B:DG1021 4.0 14.0 1.0 CB K:ALA879 4.0 11.7 1.0 O B:HOH3133 4.1 18.5 1.0 C5 B:DG1021 4.1 5.1 1.0 C4 B:DG1021 4.2 6.5 1.0 O B:HOH3259 4.3 25.1 1.0 N1 B:5IU1022 4.3 10.0 1.0 N3 B:5IU1022 4.4 6.1 1.0 C1' B:DG1021 4.5 12.1 1.0 O K:HOH3301 4.5 12.0 1.0 O6 B:DG1023 4.9 8.6 1.0 CZ K:ARG882 4.9 11.8 1.0 C6 B:DG1021 4.9 10.4 1.0 C2 B:5IU1022 4.9 8.1 1.0 N3 B:DG1021 5.0 6.2 1.0

Iodine binding site 3 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of An Irf-2/Dna Complex. within 5.0Å range: probe atom residue distance (Å) B Occ C:I1034 b:27.2 occ:1.00 I5 C:5IU1034 0.0 27.2 1.0 C5 C:5IU1034 2.1 12.0 1.0 C6 C:5IU1034 3.0 9.0 1.0 C4 C:5IU1034 3.1 12.5 1.0 O4 C:5IU1034 3.4 10.9 1.0 O C:HOH3119 3.4 24.3 1.0 C8 C:DG1033 3.7 8.5 1.0 N7 C:DG1033 3.8 6.6 1.0 N9 C:DG1033 3.9 6.8 1.0 C2' C:DG1033 4.0 14.7 1.0 C5 C:DG1033 4.1 5.6 1.0 C4 C:DG1033 4.1 5.2 1.0 N1 C:5IU1034 4.3 7.0 1.0 N3 C:5IU1034 4.4 4.3 1.0 C1' C:DG1033 4.5 8.5 1.0 O C:HOH3120 4.7 5.2 1.0 O D:HOH3190 4.8 17.0 1.0 O6 C:DG1035 4.8 4.9 1.0 C6 C:DG1033 4.9 7.2 1.0 N3 C:DG1033 4.9 8.2 1.0 C2 C:5IU1034 4.9 6.4 1.0 N4 D:DC1102 5.0 14.9 1.0

Iodine binding site 4 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of An Irf-2/Dna Complex. within 5.0Å range: probe atom residue distance (Å) B Occ D:I1111 b:20.5 occ:1.00 I5 D:5IU1111 0.0 20.5 1.0 C5 D:5IU1111 2.1 17.5 1.0 C6 D:5IU1111 3.1 18.0 1.0 C4 D:5IU1111 3.1 10.7 1.0 O K:CYS883 3.3 13.2 1.0 O4 D:5IU1111 3.3 13.2 1.0 C K:CYS883 3.6 10.0 1.0 C2' D:DC1110 3.7 19.9 1.0 CA K:ALA884 3.8 14.3 1.0 N K:ALA884 3.8 11.4 1.0 OG K:SER887 3.8 16.1 1.0 C6 D:DC1110 3.9 12.1 1.0 N1 D:DC1110 4.0 15.3 1.0 O K:HOH3041 4.1 12.8 1.0 CB K:SER887 4.1 15.2 1.0 CB K:CYS883 4.1 13.2 1.0 C5 D:DC1110 4.2 9.5 1.0 O D:HOH3215 4.3 5.4 1.0 C2 D:DC1110 4.4 10.5 1.0 N1 D:5IU1111 4.4 16.1 1.0 N3 D:5IU1111 4.4 12.3 1.0 CA K:CYS883 4.5 12.6 1.0 C4 D:DC1110 4.5 11.2 1.0 C1' D:DC1110 4.5 15.8 1.0 N3 D:DC1110 4.6 4.7 1.0 O4 D:DT1112 4.7 21.3 1.0 CB K:ALA884 4.7 8.3 1.0 C K:ALA884 4.8 16.6 1.0 O K:ALA884 4.9 16.5 1.0 C3' D:DC1110 4.9 17.3 1.0 C2 D:5IU1111 5.0 15.7 1.0 O2 D:DC1110 5.0 12.2 1.0

Iodine binding site 5 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of An Irf-2/Dna Complex. within 5.0Å range: probe atom residue distance (Å) B Occ E:I1123 b:21.5 occ:1.00 I5 E:5IU1123 0.0 21.5 1.0 C5 E:5IU1123 2.1 10.0 1.0 C6 E:5IU1123 3.0 13.4 1.0 C4 E:5IU1123 3.1 17.1 1.0 O I:CYS483 3.3 16.5 1.0 O4 E:5IU1123 3.3 17.1 1.0 C I:CYS483 3.5 16.0 1.0 OG I:SER487 3.7 14.6 1.0 C2' E:DC1122 3.8 14.8 1.0 O I:HOH3298 3.8 22.9 1.0 N I:ALA484 3.8 15.2 1.0 CA I:ALA484 3.9 12.5 1.0 CB I:SER487 3.9 16.6 1.0 CB I:CYS483 4.0 14.9 1.0 N1 E:DC1122 4.1 10.7 1.0 O E:HOH3299 4.1 27.5 1.0 C6 E:DC1122 4.1 14.0 1.0 O I:HOH3372 4.2 15.2 1.0 C2 E:DC1122 4.3 11.3 1.0 C5 E:DC1122 4.4 10.6 1.0 N1 E:5IU1123 4.4 12.2 1.0 N3 E:5IU1123 4.4 8.7 1.0 CA I:CYS483 4.4 14.9 1.0 C1' E:DC1122 4.5 13.2 1.0 C4 E:DC1122 4.6 11.7 1.0 N3 E:DC1122 4.6 11.2 1.0 O4 E:DT1124 4.7 16.6 1.0 CB I:ALA484 4.8 12.3 1.0 O2 E:DC1122 4.9 14.7 1.0 C I:ALA484 4.9 15.3 1.0 C3' E:DC1122 4.9 17.9 1.0 C2 E:5IU1123 4.9 10.6 1.0

Iodine binding site 6 out of 6 in the Crystal Structure of An Irf-2/Dna Complex.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of An Irf-2/Dna Complex. within 5.0Å range: probe atom residue distance (Å) B Occ F:I1135 b:18.2 occ:1.00 I5 F:5IU1135 0.0 18.2 1.0 C5 F:5IU1135 2.1 8.0 1.0 C6 F:5IU1135 3.0 7.9 1.0 C4 F:5IU1135 3.1 7.3 1.0 O4 F:5IU1135 3.3 7.5 1.0 O G:CYS83 3.5 12.8 1.0 C G:CYS83 3.6 10.4 1.0 C2' F:DC1134 3.7 15.5 1.0 N G:ALA84 3.7 14.2 1.0 OG G:SER87 3.7 18.6 1.0 CA G:ALA84 3.8 12.6 1.0 C6 F:DC1134 3.9 11.7 1.0 O G:HOH3236 4.0 15.1 1.0 N1 F:DC1134 4.0 13.3 1.0 CB G:CYS83 4.0 8.1 1.0 CB G:SER87 4.1 12.6 1.0 C5 F:DC1134 4.1 10.2 1.0 O F:HOH3033 4.2 10.0 1.0 C2 F:DC1134 4.3 8.1 1.0 N1 F:5IU1135 4.4 6.9 1.0 N3 F:5IU1135 4.4 5.4 1.0 CA G:CYS83 4.4 8.9 1.0 C1' F:DC1134 4.4 12.2 1.0 C4 F:DC1134 4.4 7.0 1.0 N3 F:DC1134 4.5 6.8 1.0 O4 F:DT1136 4.6 6.9 1.0 CB G:ALA84 4.7 9.8 1.0 C3' F:DC1134 4.8 13.6 1.0 C G:ALA84 4.9 12.3 1.0 O2 F:DC1134 4.9 11.6 1.0 C2 F:5IU1135 4.9 6.3 1.0

Y.Fujii, T.Shimizu, M.Kusumoto, Y.Kyogoku, T.Taniguchi, T.Hakoshima. Crystal Structure of An Irf-Dna Complex Reveals Novel Dna Recognition and Cooperative Binding to A Tandem Repeat of Core Sequences. Embo J. V. 18 5028 1999.
ISSN: ISSN 0261-4189
PubMed: 10487755
DOI: 10.1093/EMBOJ/18.18.5028