Iodine in PDB 1yri: Chicken Villin Subdomain Hp-35, N68H, PH6.4

The structure of Chicken Villin Subdomain Hp-35, N68H, PH6.4, PDB code: 1yri was solved by T.K.Chiu, J.Kubelka, R.Herbst-Irmer, W.A.Eaton, J.Hofrichter, D.R.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	31.980, 31.980, 57.027, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 20.5

The binding sites of Iodine atom in the Chicken Villin Subdomain Hp-35, N68H, PH6.4 (pdb code 1yri). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Chicken Villin Subdomain Hp-35, N68H, PH6.4, PDB code: 1yri:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Chicken Villin Subdomain Hp-35, N68H, PH6.4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Chicken Villin Subdomain Hp-35, N68H, PH6.4 within 5.0Å range: probe atom residue distance (Å) B Occ A:I479 b:14.0 occ:0.20 I A:IOD479 0.0 14.0 0.2 I A:IOD479 1.0 28.8 0.2 H A:ARG55 2.7 16.5 1.0 HG3 A:ARG55 2.9 18.8 1.0 HB3 A:ASP44 3.0 21.2 1.0 O A:HOH1013 3.3 20.7 1.0 HB A:THR54 3.4 18.3 1.0 HB2 A:ARG55 3.5 17.9 1.0 N A:ARG55 3.5 13.7 1.0 HA A:THR54 3.7 16.3 1.0 CG A:ARG55 3.7 15.6 1.0 CB A:ASP44 3.9 17.6 1.0 CB A:ARG55 4.0 14.9 1.0 HD2 A:ARG55 4.0 16.8 1.0 HG23 A:THR54 4.1 24.2 1.0 CB A:THR54 4.2 15.3 1.0 CG A:ASP44 4.2 18.6 1.0 CA A:THR54 4.3 13.6 1.0 HA A:ASP44 4.3 19.2 1.0 CD A:ARG55 4.3 14.0 1.0 CA A:ARG55 4.4 13.7 1.0 O A:ASP44 4.4 18.6 1.0 C A:THR54 4.4 12.9 1.0 HE A:ARG55 4.4 17.0 1.0 HG2 A:ARG55 4.5 18.8 1.0 H A:SER56 4.5 17.8 1.0 HB2 A:ASP44 4.6 21.2 1.0 OD2 A:ASP44 4.6 24.6 1.0 CA A:ASP44 4.6 16.0 1.0 HB2 A:LYS48 4.6 25.9 1.0 OD1 A:ASP44 4.6 16.4 1.0 CG2 A:THR54 4.6 16.2 1.0 NE A:ARG55 4.7 14.2 1.0 C A:ASP44 4.8 17.1 1.0 HB3 A:PHE47 4.8 16.4 1.0 HB3 A:ARG55 4.9 17.9 1.0 HD1 A:PHE47 4.9 15.9 1.0 HG21 A:THR54 4.9 24.2 1.0

Iodine binding site 2 out of 4 in the Chicken Villin Subdomain Hp-35, N68H, PH6.4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Chicken Villin Subdomain Hp-35, N68H, PH6.4 within 5.0Å range: probe atom residue distance (Å) B Occ A:I479 b:28.8 occ:0.20 I A:IOD479 0.0 28.8 0.2 I A:IOD479 1.0 14.0 0.2 HB3 A:ASP44 2.8 21.2 1.0 H A:ARG55 3.0 16.5 1.0 HG3 A:ARG55 3.4 18.8 1.0 HA A:THR54 3.4 16.3 1.0 HB A:THR54 3.6 18.3 1.0 HG23 A:THR54 3.7 24.2 1.0 HB2 A:LYS48 3.7 25.9 1.0 O A:ASP44 3.7 18.6 1.0 CB A:ASP44 3.8 17.6 1.0 N A:ARG55 3.8 13.7 1.0 O A:HOH1013 4.0 20.7 1.0 HE2 A:LYS48 4.1 47.1 1.0 CA A:THR54 4.1 13.6 1.0 HA A:ASP44 4.1 19.2 1.0 CB A:THR54 4.1 15.3 1.0 C A:ASP44 4.3 17.1 1.0 HD3 A:LYS48 4.3 43.5 1.0 CG A:ARG55 4.3 15.6 1.0 HB2 A:ARG55 4.3 17.9 1.0 CA A:ASP44 4.3 16.0 1.0 HB2 A:ASP44 4.4 21.2 1.0 CG2 A:THR54 4.4 16.2 1.0 CG A:ASP44 4.4 18.6 1.0 HB3 A:PHE47 4.5 16.4 1.0 C A:THR54 4.5 12.9 1.0 HD1 A:PHE47 4.6 15.9 1.0 CB A:LYS48 4.7 21.6 1.0 CB A:ARG55 4.7 14.9 1.0 H A:LYS48 4.7 19.2 1.0 HD2 A:ARG55 4.7 16.8 1.0 HG21 A:THR54 4.8 24.2 1.0 HE A:ARG55 4.9 17.0 1.0 CA A:ARG55 4.9 13.7 1.0 OD2 A:ASP44 4.9 24.6 1.0 HG2 A:ARG55 4.9 18.8 1.0 CE A:LYS48 4.9 39.3 1.0 OD1 A:ASP44 5.0 16.4 1.0 CD A:LYS48 5.0 36.2 1.0 CD A:ARG55 5.0 14.0 1.0

Iodine binding site 3 out of 4 in the Chicken Villin Subdomain Hp-35, N68H, PH6.4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Chicken Villin Subdomain Hp-35, N68H, PH6.4 within 5.0Å range: probe atom residue distance (Å) B Occ A:I480 b:11.3 occ:0.15 HZ3 A:LYS65 2.5 22.6 0.5 HZ3 A:LYS65 3.2 25.0 0.5 HD3 A:LYS65 3.3 15.4 0.5 NZ A:LYS65 3.4 15.1 0.5 HH2 A:TRP64 3.4 14.0 0.5 HH2 A:TRP64 3.4 18.7 0.5 HD2 A:LYS65 3.5 17.4 0.5 HZ1 A:LYS65 3.7 22.6 0.5 HZ2 A:TRP64 3.8 13.6 0.5 HZ2 A:TRP64 3.8 19.4 0.5 HZ2 A:LYS65 3.8 22.6 0.5 NZ A:LYS65 4.0 16.7 0.5 O A:HOH1035 4.0 30.0 1.0 HE3 A:LYS65 4.0 16.0 0.5 HZ2 A:LYS65 4.1 25.0 0.5 CH2 A:TRP64 4.1 11.6 0.5 CE A:LYS65 4.1 13.3 0.5 CD A:LYS65 4.2 14.5 0.5 CZ2 A:TRP64 4.2 11.3 0.5 CD A:LYS65 4.3 12.8 0.5 HD2 A:LYS65 4.6 15.4 0.5 HZ1 A:LYS65 4.6 25.0 0.5 CE A:LYS65 4.6 14.2 0.5 HD3 A:LYS65 4.7 17.4 0.5 HG2 A:PRO62 4.7 26.0 1.0 HB2 A:LYS65 4.7 13.6 0.5 HE3 A:LYS65 4.9 17.0 0.5

Iodine binding site 4 out of 4 in the Chicken Villin Subdomain Hp-35, N68H, PH6.4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Chicken Villin Subdomain Hp-35, N68H, PH6.4 within 5.0Å range:

T.K.Chiu, J.Kubelka, R.Herbst-Irmer, W.A.Eaton, J.Hofrichter, D.R.Davies. High-Resolution X-Ray Crystal Structures of the Villin Headpiece Subdomain, An Ultrafast Folding Protein. Proc.Natl.Acad.Sci.Usa V. 102 7517 2005.
ISSN: ISSN 0027-8424
PubMed: 15894611
DOI: 10.1073/PNAS.0502495102