Iodine in PDB 2x5x: The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode

The structure of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode, PDB code: 2x5x was solved by S.Wakadkar, S.Hermawan, D.Jendrossek, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	49.630, 140.580, 56.750, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 17.6

The structure of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode also contains other interesting chemical elements:

Chlorine	(Cl)	6 atoms
Sodium	(Na)	2 atoms

The binding sites of Iodine atom in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode (pdb code 2x5x). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode, PDB code: 2x5x:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:I1343 b:19.2 occ:1.00 NA A:NA1357 1.8 10.7 1.0 OG A:SER35 3.0 31.4 0.5 N A:SER35 3.6 12.7 1.0 N A:GLY20 3.9 9.0 1.0 CB A:SER35 3.9 18.8 0.5 C A:GLY34 3.9 10.1 1.0 CB A:SER35 3.9 20.4 0.5 CA A:GLY34 4.0 10.3 1.0 CA A:GLY20 4.1 9.3 1.0 CA A:SER35 4.2 15.5 0.5 CA A:SER35 4.2 15.8 0.5 O A:HOH2109 4.3 29.9 1.0 CB A:ALA19 4.4 9.1 1.0 O A:GLY34 4.6 11.2 1.0 C A:ALA19 4.9 8.1 1.0 O A:HOH2103 5.0 20.3 1.0

Iodine binding site 2 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:I1344 b:19.4 occ:1.00 O A:HOH2427 3.2 23.2 1.0 O A:HOH2328 3.5 19.5 1.0 CB A:ALA230 3.9 12.8 1.0 CA A:ARG228 3.9 8.6 1.0 N A:ALA230 3.9 9.3 1.0 C A:ARG228 4.0 8.5 1.0 CG2 A:VAL231 4.1 9.8 1.0 CB A:ARG228 4.1 9.1 1.0 N A:THR229 4.3 9.8 1.0 O A:ARG228 4.4 8.2 1.0 CA A:ALA230 4.4 10.3 1.0 CB A:TRP152 4.4 9.7 1.0 CD A:ARG228 4.4 10.0 1.0 O A:HOH2424 4.4 32.3 1.0 N A:VAL231 4.5 7.5 1.0 O A:HOH2156 4.6 31.1 1.0 C A:ALA230 4.7 8.8 1.0 O A:TRP152 4.7 8.5 1.0 C A:TRP152 4.8 8.8 1.0 CG A:ARG228 4.8 9.3 1.0 CG2 A:THR153 4.9 16.5 1.0 N A:THR153 5.0 9.0 1.0

Iodine binding site 3 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:I1345 b:28.4 occ:1.00 O A:HOH2032 2.2 37.7 1.0 O A:HOH2019 3.3 36.4 1.0 N A:GLY25 3.5 13.2 1.0 CD A:PRO24 3.9 14.6 1.0 N A:PRO24 4.0 11.9 1.0 C A:ALA23 4.0 14.9 1.0 CA A:ALA23 4.0 13.7 1.0 CB A:ALA23 4.0 16.5 1.0 CA A:GLY25 4.1 16.7 1.0 CE2 A:TYR18 4.3 8.7 1.0 CD2 A:TYR18 4.4 8.3 1.0 CG A:PRO24 4.5 15.8 1.0 O A:ALA23 4.6 20.6 1.0 C A:PRO24 4.6 12.6 1.0 O A:HOH2026 4.7 21.6 1.0 CA A:PRO24 4.9 13.1 1.0 O A:HOH2020 4.9 52.9 1.0 C A:GLY25 5.0 15.0 1.0 O A:HOH2069 5.0 13.4 1.0

Iodine binding site 4 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:I1346 b:30.7 occ:1.00 O A:HOH2079 3.1 67.7 1.0 O A:HOH2037 3.3 31.1 1.0 O A:HOH2089 3.4 53.3 1.0 O A:HOH2132 3.5 19.8 1.0 N A:GLY27 3.5 10.3 1.0 CA A:VAL26 4.0 11.0 1.0 CG1 A:ILE113 4.1 9.2 1.0 CB A:VAL26 4.1 12.2 1.0 C A:VAL26 4.3 10.4 1.0 CA A:GLY27 4.4 9.9 1.0 CD1 A:ILE113 4.4 8.8 1.0 O A:HOH2273 4.4 18.8 1.0 CG1 A:VAL26 4.5 15.3 1.0 O A:HOH2036 4.7 46.2 1.0 O A:GLY27 4.8 10.7 1.0 C A:GLY27 5.0 7.1 1.0

Iodine binding site 5 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:I1347 b:19.9 occ:1.00 N A:ALA341 3.6 8.7 1.0 CB A:ALA340 3.9 11.4 1.0 O A:HOH2557 4.0 22.5 1.0 CA A:ALA340 4.0 8.2 1.0 CB A:ALA341 4.3 13.1 1.0 C A:ALA340 4.3 8.9 1.0 CA A:ALA341 4.6 10.5 1.0 O A:HOH2554 4.8 11.8 1.0 CD1 A:LEU328 4.9 14.8 1.0

Iodine binding site 6 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:I1348 b:29.6 occ:1.00 O A:HOH2008 2.3 31.7 1.0 ND2 A:ASN6 3.4 11.9 1.0 SG A:CYS3 3.8 9.5 1.0 O A:HOH2012 3.8 17.9 1.0 CB A:CYS3 3.9 8.6 1.0 O A:HOH2009 4.0 34.9 1.0 CA A:THR5 4.0 8.9 1.0 O A:GLY4 4.1 14.2 1.0 C A:THR5 4.1 7.9 1.0 O A:HOH2013 4.1 35.2 1.0 C A:GLY4 4.1 11.7 1.0 N A:THR5 4.2 9.7 1.0 N A:ASN6 4.3 7.2 1.0 CD A:PRO59 4.3 7.5 1.0 O A:HOH2006 4.3 60.6 1.0 CG A:PRO59 4.3 13.8 1.0 N A:GLY4 4.4 8.1 1.0 CG A:ASN6 4.4 9.3 1.0 CB A:ASN6 4.5 8.6 1.0 O A:THR5 4.6 8.1 1.0 C A:CYS3 4.7 7.2 1.0 O A:HOH2147 4.8 19.4 1.0 CA A:GLY4 4.9 9.1 1.0 CA A:CYS3 4.9 7.6 1.0

Iodine binding site 7 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:I1359 b:12.6 occ:1.00 O A:HOH2129 3.6 20.2 1.0 O A:HOH2126 3.6 24.0 1.0 O A:HOH2125 3.8 36.1 1.0 CA A:LYS40 4.1 6.6 1.0 O A:THR39 4.2 7.9 1.0 CG A:LYS40 4.5 7.8 1.0 N A:LYS40 4.6 7.0 1.0 CG2 A:THR39 4.6 8.6 1.0 C A:THR39 4.6 6.7 1.0 CB A:LYS40 4.7 6.6 1.0 N A:THR41 5.0 7.2 1.0

Iodine binding site 8 out of 8 in the The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of The Crystal Structure of PHAZ7 at Atomic (1.2 Angstrom) Resolution Reveals Details of the Active Site and Suggests A Substrate Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:I1360 b:27.3 occ:1.00 O A:HOH2536 2.6 18.8 1.0 CB A:ASP329 4.0 9.1 1.0 N A:ASP329 4.0 7.5 1.0 CA A:ASP329 4.1 7.7 1.0 OD1 A:ASP329 4.5 12.7 1.0 C A:LEU328 4.6 7.3 1.0 CB A:LEU328 4.7 9.2 1.0 CG A:ASP329 4.8 10.7 1.0

S.Wakadkar, S.Hermawan, D.Jendrossek, A.C.Papageorgiou. The Structure of PHAZ7 at Atomic (1.2 A) Resolution Reveals Details of the Active Site and Suggests A Substrate-Binding Mode. Acta Crystallogr. Sect. F V. 66 648 2010STRUCT. Biol. Cryst. Commun..
ISSN: ESSN 1744-3091
PubMed: 20516591
DOI: 10.1107/S174430911001434X