Iodine in PDB 1utx: Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2

The structure of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2, PDB code: 1utx was solved by A.Razeto, S.Rumpel, C.M.Pillar, M.S.Gilmore, S.Becker, M.Zweckstetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.76 / 1.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	63.679, 63.679, 41.187, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 19.3

The structure of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iodine atom in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 (pdb code 1utx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2, PDB code: 1utx:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 15 in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1067 b:46.1 occ:0.30 NZ A:LYS38 2.3 40.2 1.0 O A:HOH2055 2.5 54.1 1.0 O A:HOH2064 3.4 27.2 1.0 CE A:LYS38 3.5 40.3 1.0 ND2 A:ASN32 3.6 24.1 1.0 CD A:LYS38 3.8 38.9 1.0 O A:GLN29 3.9 19.3 1.0 N A:GLY33 3.9 19.2 1.0 CA A:GLY33 4.0 19.0 1.0 CG A:GLN29 4.1 18.6 0.5 O A:HOH2065 4.2 33.7 1.0 CB A:ASN32 4.4 20.4 1.0 CG A:ASN32 4.4 22.1 1.0 C A:ASN32 4.5 19.9 1.0 C A:GLN29 4.8 19.6 1.0 CA A:GLN29 4.8 19.7 1.0 O A:ASN32 4.9 20.3 1.0

Iodine binding site 2 out of 15 in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1068 b:37.5 occ:0.30 O A:HOH2025 2.3 44.1 1.0 O A:HOH2055 3.1 54.1 1.0 CA A:GLN29 3.9 19.7 1.0 N A:GLN29 3.9 20.2 1.0 NE A:ARG28 4.0 27.1 1.0 CD A:ARG28 4.0 25.1 1.0 CB A:ASN32 4.1 20.4 1.0 CG A:ARG28 4.2 22.2 1.0 C A:ARG28 4.2 19.8 1.0 O A:ARG28 4.3 19.5 1.0 ND2 A:ASN32 4.3 24.1 1.0 O A:HOH2051 4.4 46.0 1.0 CB A:GLN29 4.5 20.2 1.0 CB A:ARG28 4.5 20.4 1.0 CG A:ASN32 4.5 22.1 1.0 CZ A:ARG28 4.8 30.1 1.0 O A:HOH2053 4.8 22.4 1.0 OE1 A:GLN17 4.9 20.1 1.0

Iodine binding site 3 out of 15 in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1069 b:26.3 occ:0.20 I A:IOD1069 0.0 26.3 0.2 I A:IOD1069 1.0 27.2 0.5 CD A:LYS48 3.2 24.0 1.0 NZ A:LYS48 3.5 25.2 1.0 NE2 A:GLN44 3.7 21.6 0.5 CG A:GLN44 3.9 20.9 1.0 CE A:LYS48 4.0 24.9 1.0 CA A:LEU45 4.0 17.2 1.0 O A:HOH2072 4.1 43.0 1.0 N A:LEU45 4.1 17.4 1.0 CB A:LEU45 4.2 17.6 1.0 CD1 A:LEU45 4.2 18.3 1.0 CD A:GLN44 4.3 21.2 0.5 C A:GLN44 4.4 17.1 1.0 CG A:LYS48 4.4 21.0 1.0 CB A:GLN44 4.5 17.8 1.0 O A:GLN44 4.5 17.3 1.0 CG A:LEU45 4.8 18.3 1.0 CG1 A:VAL26 4.9 22.4 1.0

Iodine binding site 4 out of 15 in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1069 b:27.2 occ:0.50 I A:IOD1069 0.0 27.2 0.5 I A:IOD1069 1.0 26.3 0.2 O A:HOH2072 3.5 43.0 1.0 CB A:LEU45 4.0 17.6 1.0 CD A:LYS48 4.1 24.0 1.0 NE2 A:GLN44 4.1 21.6 0.5 CD1 A:LEU45 4.1 18.3 1.0 NZ A:LYS48 4.2 25.2 1.0 CA A:LEU45 4.2 17.2 1.0 N A:LEU45 4.3 17.4 1.0 CG1 A:VAL26 4.4 22.4 1.0 CG A:GLN44 4.5 20.9 1.0 CG A:LEU45 4.6 18.3 1.0 CE A:LYS48 4.8 24.9 1.0 OG A:SER42 4.8 17.0 1.0 C A:GLN44 4.8 17.1 1.0 CD A:GLN44 4.9 21.2 0.5 CB A:GLN44 4.9 17.8 1.0

Iodine binding site 5 out of 15 in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1070 b:37.7 occ:0.30 O A:HOH2014 2.3 37.2 1.0 O A:HOH2087 3.1 31.7 1.0 O A:HOH2031 4.0 26.7 1.0 CE A:LYS13 4.1 17.6 1.0 CG A:LYS12 4.1 21.9 1.0 CB A:LYS12 4.2 18.8 1.0 CG2 A:ILE9 4.2 16.7 1.0 CG A:LYS13 4.3 17.9 1.0 O A:ILE9 4.4 16.9 1.0 O A:HOH2018 4.5 40.3 1.0 CA A:ILE9 4.6 17.3 1.0 O A:HOH2038 4.6 49.8 1.0 CB A:ILE9 4.7 17.0 1.0 CG1 A:ILE9 4.8 18.4 1.0 CD A:LYS13 4.8 17.4 1.0 NZ A:LYS13 4.8 16.9 1.0 C A:ILE9 5.0 16.8 1.0

Iodine binding site 6 out of 15 in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1072 b:36.1 occ:0.20 I A:IOD1072 0.0 36.1 0.2 I A:IOD1072 2.2 38.1 0.3 O B:HOH2072 3.5 31.4 1.0 O B:HOH2028 3.6 37.5 1.0 CD2 B:TYR51 3.8 17.5 1.0 CE2 B:TYR51 4.0 16.1 1.0 O B:HOH2074 4.3 37.3 1.0 O A:HOH2097 4.9 32.2 1.0 CG B:TYR51 5.0 16.5 1.0

Iodine binding site 7 out of 15 in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1072 b:38.1 occ:0.30 I A:IOD1072 0.0 38.1 0.3 I A:IOD1072 2.2 36.1 0.2 O B:HOH2074 3.2 37.3 1.0 O B:HOH2072 3.5 31.4 1.0 CE2 B:TYR51 4.3 16.1 1.0 CD2 B:TYR51 4.6 17.5 1.0 O B:HOH2035 5.0 52.6 1.0

Iodine binding site 8 out of 15 in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 within 5.0Å range: probe atom residue distance (Å) B Occ B:I1067 b:40.6 occ:0.30 I B:IOD1067 0.0 40.6 0.3 I B:IOD1067 1.3 36.0 0.3 I B:IOD1067 2.9 40.9 0.2 N B:GLN17 3.3 27.7 1.0 CB B:SER16 3.5 30.0 1.0 CA B:SER16 3.5 30.0 1.0 NH1 B:ARG10 3.8 26.6 1.0 C B:SER16 3.9 28.5 1.0 I B:IOD1068 4.2 47.4 0.3 CB B:GLN17 4.3 27.6 1.0 CA B:GLN17 4.4 27.4 1.0 O B:HOH2019 4.5 59.9 1.0 O B:HOH2027 4.5 36.2 1.0 CZ B:ARG10 4.6 26.1 1.0 CG B:GLN17 4.7 28.3 1.0 I B:IOD1068 4.7 46.0 0.2 OG B:SER16 4.8 30.7 1.0 NH2 B:ARG10 4.8 25.7 1.0 N B:SER16 4.8 30.9 1.0

Iodine binding site 9 out of 15 in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 within 5.0Å range: probe atom residue distance (Å) B Occ B:I1067 b:36.0 occ:0.30 I B:IOD1067 0.0 36.0 0.3 I B:IOD1067 1.3 40.6 0.3 I B:IOD1067 1.7 40.9 0.2 O B:HOH2027 3.5 36.2 1.0 O B:HOH2019 3.7 59.9 1.0 NH1 B:ARG10 3.9 26.6 1.0 N B:GLN17 4.0 27.7 1.0 NH2 B:ARG10 4.2 25.7 1.0 CB B:GLN17 4.3 27.6 1.0 CG B:GLN17 4.3 28.3 1.0 CZ B:ARG10 4.4 26.1 1.0 CD B:GLN17 4.5 27.4 1.0 CA B:SER16 4.7 30.0 1.0 OE1 B:GLN17 4.8 30.7 1.0 CB B:SER16 4.8 30.0 1.0 CA B:GLN17 4.8 27.4 1.0 C B:SER16 4.8 28.5 1.0 I B:IOD1068 5.0 47.4 0.3

Iodine binding site 10 out of 15 in the Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Regulation of Cytolysin Expression By Enterococcus Faecalis: Role of CYLR2 within 5.0Å range: probe atom residue distance (Å) B Occ B:I1067 b:40.9 occ:0.20 I B:IOD1067 0.0 40.9 0.2 I B:IOD1067 1.7 36.0 0.3 O B:HOH2027 2.0 36.2 1.0 I B:IOD1067 2.9 40.6 0.3 CD B:GLN17 3.6 27.4 1.0 OE1 B:GLN17 3.7 30.7 1.0 CG B:GLN17 3.9 28.3 1.0 NE2 B:GLN17 4.0 25.2 1.0 O B:HOH2019 4.0 59.9 1.0 CB B:GLN17 4.2 27.6 1.0 NH2 B:ARG10 4.4 25.7 1.0 NH1 B:ARG10 4.8 26.6 1.0 N B:GLN17 4.8 27.7 1.0 CZ B:ARG10 4.9 26.1 1.0

S.Rumpel, A.Razeto, C.M.Pillar, V.Vijayan, A.Taylor, K.Giller, M.S.Gilmore, S.Becker, M.Zweckstetter. Structure and Dna-Binding Properties of the Cytolysin Regulator CYLR2 From Enterococcus Faecalis Embo J. V. 23 3632 2004.
ISSN: ISSN 0261-4189
PubMed: 15359276
DOI: 10.1038/SJ.EMBOJ.7600367