Iodine in PDB 2vma: The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae

The structure of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae, PDB code: 2vma was solved by J.Abendroth, K.V.Korotkov, D.D.Mitchell, A.Kreger, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.32 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.816, 54.368, 88.587, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.5

The structure of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

Pages:

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

Binding sites:

The binding sites of Iodine atom in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae (pdb code 2vma). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae, PDB code: 2vma:
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 The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:I1179 b:39.5 occ:0.70 O A:HOH2087 3.5 27.8 1.0 OD1 A:ASN159 3.6 24.7 1.0 CA A:TYR156 3.8 18.9 1.0 N A:TYR156 4.0 18.0 1.0 O A:ASP155 4.2 17.2 1.0 C A:ASP155 4.2 17.2 1.0 CB A:TYR156 4.3 20.1 1.0 CD1 A:TYR156 4.5 23.0 1.0 CG A:ASN159 4.5 21.5 1.0 CB A:ASN159 4.6 21.4 1.0 CB A:ASP155 4.7 16.2 1.0 CG A:TYR156 4.8 22.0 1.0 C A:TYR156 5.0 18.8 1.0

Iodine binding site 2 out of 15 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:I1180 b:39.7 occ:0.50 O A:HOH2070 3.4 32.8 1.0 CD2 A:LEU68 3.7 18.3 1.0 O A:HOH2069 3.8 31.4 1.0 CE2 A:TYR156 3.8 21.3 1.0 CD1 A:PHE133 4.0 19.2 1.0 O A:HOH2094 4.0 37.1 1.0 CD2 A:TYR156 4.0 23.0 1.0 CD A:ARG160 4.4 26.0 1.0 CE1 A:PHE133 4.6 17.8 1.0 CB A:ALA157 4.7 17.9 1.0 CG A:LEU68 4.8 17.6 1.0 NE A:ARG160 4.8 26.4 1.0 CA A:ALA157 4.9 18.6 1.0 CG A:PHE133 4.9 17.7 1.0 CB A:PHE133 4.9 18.1 1.0 O A:HOH2010 5.0 25.1 1.0

Iodine binding site 3 out of 15 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:I1181 b:43.8 occ:0.47 NH1 A:ARG152 3.3 37.0 1.0 CB A:SER148 3.5 19.7 1.0 CD A:ARG152 4.0 28.1 1.0 C A:SER148 4.0 18.8 1.0 CZ A:ARG152 4.0 33.8 1.0 N A:VAL149 4.0 18.1 1.0 CG1 A:VAL149 4.1 18.0 1.0 O A:SER148 4.2 18.5 1.0 NE A:ARG152 4.2 31.6 1.0 CG A:ARG152 4.4 22.8 1.0 CA A:SER148 4.4 19.3 1.0 CA A:VAL149 4.4 18.0 1.0 OG A:SER148 4.5 23.1 1.0 O A:HOH2082 4.7 34.6 1.0 CB A:HIS145 4.9 21.9 1.0 O A:HIS145 4.9 22.4 1.0 NH2 A:ARG152 4.9 33.8 1.0 CB A:VAL149 4.9 18.1 1.0

Iodine binding site 4 out of 15 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:I1182 b:38.8 occ:0.40 NH1 A:ARG160 3.5 29.0 1.0 CD A:ARG160 3.9 26.0 1.0 CG A:ARG160 3.9 24.3 1.0 CB A:ARG160 4.0 22.4 1.0 OH A:TYR156 4.3 24.1 1.0 CA A:ARG160 4.3 22.3 1.0 CZ A:ARG160 4.4 29.0 1.0 NE A:ARG160 4.6 26.4 1.0 CE A:MSE163 4.6 30.3 1.0 CZ A:TYR156 4.8 22.9 1.0

Iodine binding site 5 out of 15 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:I1183 b:22.0 occ:0.30 O A:HOH2087 3.7 27.8 1.0 CD A:ARG152 3.8 28.1 1.0 CB A:ARG152 4.1 18.2 1.0 CG A:ARG152 4.5 22.8 1.0 NE A:ARG152 4.6 31.6 1.0 CE A:MSE136 4.8 31.9 1.0

Iodine binding site 6 out of 15 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:I1184 b:47.3 occ:0.34 N A:HIS127 3.8 21.5 1.0 C A:PRO126 4.0 21.3 1.0 CA A:HIS127 4.1 21.6 1.0 CB A:PRO126 4.1 21.1 1.0 CG A:PRO126 4.2 21.1 1.0 CB A:HIS127 4.2 21.8 1.0 O A:PRO126 4.2 20.3 1.0 CA A:PRO126 4.7 20.8 1.0 O A:HOH2072 4.9 29.5 1.0

Iodine binding site 7 out of 15 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:I1180 b:28.7 occ:0.70 O B:HOH2076 3.6 29.2 1.0 OD1 B:ASN159 3.6 25.0 1.0 CA B:TYR156 3.8 18.6 1.0 N B:TYR156 4.0 18.0 1.0 O B:ASP155 4.2 16.6 1.0 C B:ASP155 4.2 16.8 1.0 CB B:TYR156 4.3 20.2 1.0 CD1 B:TYR156 4.4 25.2 1.0 CG B:ASN159 4.5 23.5 1.0 CB B:ASN159 4.5 21.7 1.0 CB B:ASP155 4.6 15.9 1.0 CG B:TYR156 4.9 22.3 1.0

Iodine binding site 8 out of 15 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:I1181 b:27.8 occ:0.43 O B:HOH2085 3.3 37.2 1.0 O B:HOH2066 3.4 34.2 1.0 CD2 B:LEU68 3.5 21.2 1.0 CE2 B:TYR156 3.6 24.8 1.0 O B:HOH2086 3.6 42.1 1.0 O B:HOH2065 3.7 24.6 1.0 CD2 B:TYR156 3.7 23.5 1.0 CD1 B:PHE133 4.2 16.2 1.0 CD B:ARG160 4.3 26.7 1.0 CB B:ALA157 4.5 18.3 1.0 CA B:ALA157 4.6 17.9 1.0 CG B:LEU68 4.7 20.1 1.0 CE1 B:PHE133 4.9 15.3 1.0 CZ B:TYR156 4.9 25.2 1.0 NE B:ARG160 5.0 29.2 1.0 N B:ALA157 5.0 17.8 1.0

Iodine binding site 9 out of 15 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:I1182 b:43.2 occ:0.57 CD B:ARG152 3.1 30.4 1.0 CG B:ARG152 3.8 24.8 1.0 OG B:SER148 3.9 22.4 1.0 NH1 B:ARG152 4.0 40.2 1.0 N B:VAL149 4.1 19.1 1.0 CG2 B:VAL149 4.1 19.5 1.0 C B:SER148 4.1 19.5 1.0 O B:SER148 4.2 18.7 1.0 CB B:SER148 4.2 20.4 1.0 CA B:VAL149 4.3 18.5 1.0 NE B:ARG152 4.3 35.5 1.0 O B:HOH2073 4.5 34.8 1.0 CZ B:ARG152 4.6 37.8 1.0 CB B:ARG152 4.8 19.4 1.0 CA B:SER148 4.8 19.8 1.0 CB B:VAL149 4.9 18.6 1.0

Iodine binding site 10 out of 15 in the The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:I1183 b:44.3 occ:0.35 NE B:ARG152 2.9 35.5 1.0 NH2 B:ARG152 2.9 39.4 1.0 CZ B:ARG152 2.9 37.8 1.0 O B:HOH2076 3.2 29.2 1.0 NH1 B:ARG152 3.8 40.2 1.0 CD B:ARG152 3.8 30.4 1.0 CB B:ARG152 4.0 19.4 1.0 CG B:ARG152 4.4 24.8 1.0 CA B:ARG152 4.9 18.8 1.0 O B:HOH2080 4.9 29.4 1.0 O B:ARG152 4.9 16.9 1.0

J.Abendroth, D.D.Mitchell, K.V.Korotkov, T.L.Johnson, A.Kreger, M.Sandkvist, W.G.Hol. The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf From the Type 2 Secretion System of Vibrio Cholerae. J.Struct.Biol. V. 166 303 2009.
ISSN: ISSN 1047-8477
PubMed: 19324092
DOI: 10.1016/J.JSB.2009.03.009