Iodine in PDB 3vay: Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000

The structure of Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000, PDB code: 3vay was solved by Z.Hou, H.Zhang, M.Li, W.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.91 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.325, 92.274, 70.191, 90.00, 108.13, 90.00
R / Rfree (%)	19.3 / 22.4

The structure of Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 (pdb code 3vay). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000, PDB code: 3vay:
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 Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


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 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:43.0 occ:0.53 O A:HOH432 3.4 27.5 1.0 O A:HOH465 3.5 33.5 1.0 OD1 A:ASN130 3.8 28.5 1.0 ND2 A:ASN130 3.9 24.8 1.0 CZ A:PHE97 4.1 32.7 1.0 CE2 A:PHE97 4.1 33.6 1.0 CG A:ASN130 4.2 28.2 1.0 CG1 A:ILE64 4.4 35.8 1.0 NH2 A:ARG68 4.5 44.4 1.0 CG B:GLU44 4.8 45.7 1.0 NE A:ARG68 4.9 41.5 1.0 CD B:GLU44 4.9 47.8 1.0 CD1 A:ILE20 4.9 31.3 1.0 NE A:ARG101 4.9 27.0 1.0 OE1 B:GLU44 4.9 46.7 1.0 CG2 A:ILE64 5.0 29.4 1.0

Iodine binding site 2 out of 15 in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


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 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:47.6 occ:0.48 O A:HOH449 2.9 36.7 1.0 CD2 A:LEU138 3.4 32.0 1.0 O A:GLY137 3.8 37.9 1.0 CG A:GLN111 3.9 29.9 1.0 C A:GLY137 3.9 36.7 1.0 CB A:GLN111 4.0 28.0 1.0 CG A:LEU138 4.3 30.7 1.0 N A:LEU138 4.3 34.5 1.0 CA A:GLY137 4.4 37.8 1.0 CE2 A:TYR141 4.5 29.9 1.0 CA A:LEU138 4.6 33.2 1.0 CD1 A:ILE106 4.6 28.4 1.0 O A:HOH542 4.8 35.6 1.0 CA A:GLN111 5.0 24.4 1.0 CB A:LEU138 5.0 30.7 1.0

Iodine binding site 3 out of 15 in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


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 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:41.0 occ:0.31 NH2 A:ARG50 3.3 44.3 1.0 NE A:ARG50 3.7 43.2 1.0 CA A:LYS61 3.9 34.5 1.0 CD2 A:LEU67 3.9 35.9 1.0 CD1 A:LEU54 3.9 30.1 1.0 CZ A:ARG50 4.0 44.8 1.0 CB A:LYS61 4.0 37.2 1.0 CD2 A:LEU54 4.1 36.8 1.0 O A:HOH526 4.4 42.0 1.0 O A:LYS61 4.5 33.0 1.0 CD1 A:ILE64 4.5 37.6 1.0 CG A:LEU54 4.6 36.5 1.0 C A:LYS61 4.7 34.5 1.0 N A:LYS61 4.8 35.0 1.0 CD A:ARG50 5.0 40.2 1.0

Iodine binding site 4 out of 15 in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


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 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:33.4 occ:0.44 I B:IOD302 2.4 40.4 0.5 NH1 A:ARG50 2.6 46.5 1.0 CZ A:ARG50 3.5 44.8 1.0 CD A:ARG50 3.9 40.2 1.0 CA A:ARG68 4.0 30.6 1.0 NE A:ARG50 4.0 43.2 1.0 CZ A:ARG68 4.1 39.4 1.0 CB A:ARG68 4.1 25.0 1.0 CG2 A:VAL71 4.1 31.7 1.0 CG A:ARG68 4.1 33.8 1.0 CZ3 B:TRP47 4.2 47.9 1.0 NH2 A:ARG68 4.2 44.4 1.0 NE A:ARG68 4.2 41.5 1.0 CG A:ARG50 4.3 36.8 1.0 NH2 A:ARG50 4.4 44.3 1.0 CB A:VAL71 4.4 34.6 1.0 NH1 A:ARG68 4.5 44.7 1.0 N A:ARG68 4.5 27.2 1.0 CG1 A:VAL71 4.6 32.9 1.0 CB A:ARG50 4.7 34.1 1.0 CG A:LEU67 4.8 34.7 1.0 CD A:ARG68 4.8 33.9 1.0 CH2 B:TRP47 4.9 44.8 1.0 C A:LEU67 5.0 31.5 1.0 O A:LEU67 5.0 33.8 1.0

Iodine binding site 5 out of 15 in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


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 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:40.4 occ:0.51 I A:IOD305 2.4 33.4 0.4 CZ3 B:TRP47 2.9 47.9 1.0 CH2 B:TRP47 3.1 44.8 1.0 CB A:LEU46 3.7 40.2 1.0 NH1 A:ARG50 3.7 46.5 1.0 CE3 B:TRP47 4.2 45.0 1.0 CG1 A:VAL71 4.3 32.9 1.0 NH1 A:ARG68 4.3 44.7 1.0 CZ2 B:TRP47 4.4 41.7 1.0 CD A:ARG50 4.4 40.2 1.0 O A:LEU46 4.5 34.2 1.0 CZ A:ARG68 4.6 39.4 1.0 C A:LEU46 4.6 35.0 1.0 CG A:LEU46 4.6 40.9 1.0 NH2 A:ARG68 4.6 44.4 1.0 CD1 A:LEU46 4.7 43.5 1.0 CA A:LEU46 4.7 39.6 1.0 CZ A:ARG50 4.8 44.8 1.0 CB A:VAL71 4.8 34.6 1.0 CB A:ARG50 4.8 34.1 1.0 CG2 A:VAL71 4.9 31.7 1.0 CD2 A:LEU46 4.9 37.4 1.0 CG A:ARG50 5.0 36.8 1.0

Iodine binding site 6 out of 15 in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


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 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ B:I303 b:37.3 occ:0.49 I B:IOD306 2.3 38.1 0.4 NH1 B:ARG50 3.1 46.3 1.0 CD B:ARG50 3.6 38.3 1.0 NE B:ARG68 3.6 45.4 1.0 NH2 B:ARG68 3.6 49.1 1.0 CZ B:ARG50 3.9 45.1 1.0 CZ B:ARG68 4.0 42.9 1.0 CA B:ARG68 4.0 30.6 1.0 NE B:ARG50 4.1 44.7 1.0 CB B:ARG68 4.1 28.7 1.0 CG2 B:VAL71 4.1 32.0 1.0 O B:HOH548 4.4 45.9 1.0 CG B:ARG50 4.4 38.3 1.0 CB B:VAL71 4.4 34.3 1.0 CG B:ARG68 4.5 34.7 1.0 CG1 B:VAL71 4.6 36.1 1.0 N B:ARG68 4.6 28.2 1.0 CD B:ARG68 4.6 32.7 1.0 CB B:ARG50 4.8 34.5 1.0 OE1 A:GLU44 4.9 45.9 1.0 NH2 B:ARG50 4.9 49.4 1.0

Iodine binding site 7 out of 15 in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ B:I304 b:44.4 occ:0.54 O B:HOH493 3.4 33.2 1.0 O B:HOH496 3.6 32.5 1.0 NH1 B:ARG68 3.8 45.5 1.0 ND2 B:ASN130 3.9 30.1 1.0 CE2 B:PHE97 4.0 37.0 1.0 OD1 B:ASN130 4.1 29.3 1.0 CZ B:PHE97 4.1 39.9 1.0 CG1 B:ILE64 4.3 37.4 1.0 CD1 B:ILE20 4.4 33.4 1.0 CG B:ASN130 4.4 28.8 1.0 O B:HOH550 4.6 41.5 1.0 CG2 B:ILE64 4.7 30.7 1.0 CG A:GLU44 4.7 41.8 1.0 CD A:GLU44 4.9 47.0 1.0 CZ B:ARG68 4.9 42.9 1.0

Iodine binding site 8 out of 15 in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ B:I305 b:35.7 occ:0.42 O B:HOH502 2.9 32.6 1.0 NH1 B:ARG167 3.2 38.0 1.0 CD B:ARG167 3.9 38.0 1.0 O B:HOH532 4.0 36.6 1.0 CB B:ARG167 4.1 27.0 1.0 CZ B:ARG167 4.3 42.4 1.0 CB B:PHE144 4.4 25.5 1.0 O B:ALA143 4.6 27.2 1.0 NE B:ARG167 4.6 36.9 1.0 CG B:ARG167 4.6 31.0 1.0 O B:ARG167 4.7 25.3 1.0 CD2 B:PHE144 4.8 24.5 1.0 CA B:ARG167 4.9 27.1 1.0 CG B:PHE144 5.0 24.0 1.0

Iodine binding site 9 out of 15 in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ B:I306 b:38.1 occ:0.43 I B:IOD303 2.3 37.3 0.5 O B:HOH548 3.4 45.9 1.0 CB B:LEU46 3.5 38.1 1.0 NH2 B:ARG68 3.9 49.1 1.0 NH1 B:ARG50 3.9 46.3 1.0 CD B:ARG50 4.0 38.3 1.0 CD1 B:TRP47 4.1 41.3 1.0 CG1 B:VAL71 4.3 36.1 1.0 CG B:LEU46 4.3 40.1 1.0 C B:LEU46 4.4 36.2 1.0 O B:LEU46 4.4 38.7 1.0 NE1 B:TRP47 4.4 40.6 1.0 CA B:LEU46 4.5 39.9 1.0 NE B:ARG68 4.5 45.4 1.0 CZ B:ARG68 4.7 42.9 1.0 O B:HOH510 4.7 41.5 1.0 CB B:ARG50 4.8 34.5 1.0 N B:TRP47 4.8 35.9 1.0 CB B:VAL71 4.9 34.3 1.0 CG B:ARG50 4.9 38.3 1.0 CZ B:ARG50 4.9 45.1 1.0 CG2 B:VAL71 4.9 32.0 1.0 NE B:ARG50 4.9 44.7 1.0

Iodine binding site 10 out of 15 in the Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 within 5.0Å range: probe atom residue distance (Å) B Occ B:I307 b:41.0 occ:0.28 O B:HOH414 2.8 25.4 1.0 O B:HOH451 2.9 35.2 1.0 CA B:THR122 4.0 20.7 1.0 OG1 B:THR122 4.0 23.2 1.0 CG2 B:THR122 4.0 23.5 1.0 O B:HOH555 4.0 40.9 1.0 CB B:ALA143 4.2 23.8 1.0 CB B:THR122 4.2 24.5 1.0 N B:LEU123 4.5 17.0 1.0 O B:PHE121 4.5 19.3 1.0 N B:ALA143 4.7 24.3 1.0 CA B:ALA143 4.8 28.7 1.0 C B:THR122 4.8 18.3 1.0 N B:THR122 4.9 17.1 1.0

Z.Hou, H.Zhang, M.Li, W.Chang. Structure of 2-Haloacid Dehalogenase From Pseudomonas Syringae Pv. Tomato DC3000 Acta Crystallogr.,Sect.D V. 69 1108 2013.
ISSN: ISSN 0907-4449
PubMed: 23695255
DOI: 10.1107/S0907444913006021