Iodine in PDB 3lmt: Crystal Strucutre of Dtd From Plasmodium Falciparum

The structure of Crystal Strucutre of Dtd From Plasmodium Falciparum, PDB code: 3lmt was solved by Y.Manickam, T.K.Bhatt, S.Khan, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.67 / 2.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.340, 57.880, 91.630, 102.80, 105.90, 99.60
R / Rfree (%)	18.1 / 23.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Iodine atom in the Crystal Strucutre of Dtd From Plasmodium Falciparum (pdb code 3lmt). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 29 binding sites of Iodine where determined in the Crystal Strucutre of Dtd From Plasmodium Falciparum, PDB code: 3lmt:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 29 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:I165 b:38.8 occ:1.00 N A:GLY135 3.4 35.4 1.0 OH A:TYR116 3.4 38.2 1.0 C A:GLY135 3.4 40.1 1.0 CA A:GLY135 3.4 36.1 1.0 N A:PHE137 3.7 37.1 1.0 N A:SER87 3.7 31.6 1.0 O A:GLY135 3.8 38.9 1.0 N A:LYS136 3.8 34.2 1.0 OG A:SER87 3.8 34.7 0.0 CA A:PHE137 3.8 36.8 1.0 CZ A:TYR116 3.9 35.3 1.0 C A:LYS136 4.0 38.9 1.0 CA A:VAL86 4.1 33.0 1.0 CE2 A:TYR116 4.2 33.7 1.0 O A:ILE85 4.2 35.2 1.0 CE A:MET141 4.4 35.0 1.0 CG1 A:VAL86 4.4 29.6 1.0 CB A:SER87 4.4 32.8 0.0 CB A:SER87 4.4 32.7 1.0 CB A:PHE137 4.4 36.0 1.0 CA A:LYS136 4.4 36.8 1.0 C A:VAL86 4.4 33.0 1.0 O A:LYS136 4.5 38.4 1.0 C A:ILE134 4.6 36.4 1.0 CA A:SER87 4.6 32.8 1.0 CA A:SER87 4.6 32.8 0.0 SD A:MET141 4.7 38.7 1.0 CE1 A:TYR116 4.7 32.7 1.0 CD1 A:PHE137 4.8 39.3 1.0 CB A:VAL86 4.8 32.4 1.0 CB A:ILE134 4.9 38.1 1.0

Iodine binding site 2 out of 29 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:I166 b:56.9 occ:0.87 ND2 A:ASN147 3.5 38.1 1.0 ND2 B:ASN147 3.6 39.4 1.0 NE2 A:GLN6 3.7 36.1 1.0 NE2 B:GLN6 3.8 39.7 1.0 OD1 A:ASN147 4.1 38.9 1.0 CG A:GLN6 4.1 31.5 1.0 CD A:GLN6 4.2 37.3 1.0 CG A:ASN147 4.2 33.7 1.0 OD1 B:ASN147 4.2 41.1 1.0 CG B:GLN6 4.3 34.8 1.0 CG1 A:VAL145 4.3 31.4 1.0 CD B:GLN6 4.3 41.4 1.0 CG B:ASN147 4.3 34.4 1.0 CB A:VAL145 4.4 32.1 1.0 CG1 B:VAL145 4.4 31.1 1.0 CB B:VAL145 4.4 30.3 1.0 CG2 A:VAL145 4.5 32.1 1.0 CE2 A:PHE40 4.5 32.6 1.0 CE2 B:PHE40 4.6 33.5 1.0 CZ A:PHE40 4.6 28.5 1.0 CG2 B:VAL145 4.6 32.4 1.0 CZ B:PHE40 4.6 29.2 1.0 CB A:GLN6 4.9 31.4 1.0

Iodine binding site 3 out of 29 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:I167 b:78.1 occ:0.65 C A:GLU26 3.7 55.0 1.0 CD A:ARG16 3.7 41.1 1.0 NE A:ARG16 3.8 51.4 1.0 O A:LYS25 3.8 59.6 1.0 CA A:GLU26 3.8 59.0 1.0 O A:GLU26 3.9 45.9 1.0 N A:LEU27 4.0 54.6 1.0 C A:LYS25 4.0 59.1 1.0 N A:GLU26 4.0 58.7 1.0 CD1 A:LEU27 4.0 34.8 1.0 CG A:LYS25 4.1 63.6 1.0 CB A:ARG16 4.1 39.4 1.0 CG A:ARG16 4.2 43.6 1.0 CA A:ARG16 4.3 41.7 1.0 CA A:LEU27 4.7 40.7 1.0 N A:LYS17 4.7 52.2 1.0 CA A:LYS25 4.9 56.6 1.0 CB A:LYS25 4.9 46.7 1.0

Iodine binding site 4 out of 29 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:I168 b:61.0 occ:0.43 CG A:GLU28 3.9 36.4 1.0 CD A:LYS17 4.0 42.6 1.0 CG A:LYS17 4.2 48.9 1.0 CE A:LYS17 4.3 50.0 1.0 CB A:LYS17 4.6 47.6 1.0 NZ A:LYS17 4.9 48.0 1.0

Iodine binding site 5 out of 29 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:I169 b:75.8 occ:0.65 NH1 A:ARG2 3.5 41.3 1.0 CD2 A:LEU105 3.5 43.5 1.0 NH2 A:ARG2 3.8 39.5 1.0 O A:HOH203 3.9 32.0 1.0 N A:ASN94 4.0 34.4 1.0 CB A:ASN94 4.0 29.4 1.0 CA A:ASN94 4.1 32.6 1.0 CZ A:ARG2 4.1 41.6 1.0 C A:PHE92 4.1 33.1 1.0 O A:PHE92 4.2 34.6 1.0 CA A:PHE92 4.3 32.5 1.0 C A:GLY93 4.3 30.4 1.0 ND2 A:ASN94 4.3 43.6 1.0 O A:GLY93 4.4 31.3 1.0 CD1 A:PHE92 4.4 33.2 1.0 N A:GLY93 4.6 30.1 1.0 CG A:ASN94 4.6 33.4 1.0 CG A:LEU105 4.6 46.1 1.0 CB A:LEU105 4.7 38.5 1.0 CB A:PHE92 4.8 24.2 1.0 O A:LEU91 4.9 34.5 1.0

Iodine binding site 6 out of 29 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ B:I165 b:38.0 occ:0.72 OG B:SER87 3.4 40.6 1.0 OH B:TYR116 3.5 44.0 1.0 C B:GLY135 3.6 39.2 1.0 N B:PHE137 3.6 37.1 1.0 N B:SER87 3.6 31.0 1.0 CA B:PHE137 3.7 36.0 1.0 CA B:GLY135 3.7 35.2 1.0 N B:GLY135 3.7 37.4 1.0 O B:HOH197 3.8 35.0 1.0 N B:LYS136 3.9 35.6 1.0 CZ B:TYR116 3.9 37.8 1.0 O B:GLY135 3.9 40.4 1.0 C B:LYS136 4.0 38.8 1.0 CE2 B:TYR116 4.1 37.4 1.0 CA B:VAL86 4.2 34.2 1.0 CB B:PHE137 4.2 36.2 1.0 CE B:MET141 4.2 36.0 1.0 O B:ILE85 4.4 35.4 1.0 O B:LYS136 4.4 39.7 1.0 C B:VAL86 4.4 30.8 1.0 CG1 B:VAL86 4.4 29.9 1.0 CB B:SER87 4.4 33.3 1.0 CA B:LYS136 4.5 36.2 1.0 CD1 B:PHE137 4.6 39.3 1.0 CA B:SER87 4.6 36.3 1.0 CE1 B:TYR116 4.7 31.4 1.0 SD B:MET141 4.7 40.4 1.0 CG B:PHE137 4.8 38.8 1.0 O B:SER87 4.9 34.4 1.0 CB B:VAL86 4.9 30.9 1.0 C B:ILE134 4.9 35.0 1.0 C B:PHE137 5.0 42.7 1.0

Iodine binding site 7 out of 29 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ B:I166 b:45.8 occ:0.59 O B:HOH199 3.0 30.9 1.0 N B:ILE43 3.9 33.9 1.0 N B:PHE89 3.9 34.8 1.0 CA B:PHE89 3.9 34.6 1.0 CB B:PHE89 4.0 29.9 1.0 CD1 B:ILE43 4.0 40.2 1.0 CB B:SER87 4.0 33.3 1.0 O B:LEU41 4.1 35.2 1.0 N B:GLN88 4.1 31.3 1.0 CG1 B:ILE43 4.2 35.9 1.0 C B:GLN88 4.3 35.4 1.0 CB B:ILE43 4.3 40.0 1.0 CA B:GLY42 4.6 28.9 1.0 C B:SER87 4.6 32.4 1.0 CA B:ILE43 4.6 38.6 1.0 CA B:SER87 4.7 36.3 1.0 C B:GLY42 4.8 34.1 1.0 O B:ILE43 4.8 38.0 1.0 CB B:ALA112 4.8 47.5 1.0 O B:GLN88 4.8 34.5 1.0 CA B:GLN88 4.8 32.5 1.0 CE1 B:PHE137 4.8 39.7 1.0 OG B:SER87 4.9 40.6 1.0

Iodine binding site 8 out of 29 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ B:I167 b:66.3 occ:0.42 OD1 B:ASN99 2.3 28.5 1.0 O A:HOH177 2.9 33.5 1.0 CG B:ASN99 3.0 36.1 1.0 ND2 B:ASN99 3.1 43.9 1.0 CG A:ARG57 3.3 33.8 0.4 CD A:ARG57 3.5 34.9 0.4 CB A:ASN61 3.8 27.3 1.0 CG A:ARG57 3.8 33.7 0.6 NE A:ARG57 3.9 34.9 0.4 NZ A:LYS58 4.2 38.7 1.0 O A:ARG57 4.2 34.6 1.0 NH1 A:ARG57 4.2 40.0 0.4 CZ A:ARG57 4.3 32.8 0.4 CG A:ASN61 4.4 34.5 1.0 CE A:LYS58 4.4 36.9 1.0 CD A:LYS58 4.5 33.0 1.0 ND2 A:ASN61 4.5 36.0 1.0 CB B:ASN99 4.5 28.9 1.0 C A:ARG57 4.6 36.4 1.0 CD A:ARG57 4.7 36.0 0.6 CB A:ARG57 4.7 33.9 0.4 CB A:ARG57 4.8 34.1 0.6 N A:LYS58 4.9 31.6 1.0 CA A:LYS58 5.0 30.7 1.0

Iodine binding site 9 out of 29 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ B:I168 b:95.8 occ:0.54 N B:GLU26 3.4 35.9 1.0 CB B:ARG16 3.6 43.4 1.0 CA B:ARG16 3.9 46.6 1.0 O B:GLU26 4.1 48.4 1.0 C B:GLU26 4.2 47.5 1.0 CD2 B:LEU27 4.3 36.2 1.0 CA B:GLU26 4.4 48.1 1.0 C B:ARG16 4.4 38.0 1.0 N B:LEU27 4.7 41.0 1.0 CG B:LEU27 4.7 45.2 1.0

Iodine binding site 10 out of 29 in the Crystal Strucutre of Dtd From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Strucutre of Dtd From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ B:I169 b:53.2 occ:0.51 O B:HOH195 2.7 42.9 1.0 O B:PHE92 3.2 39.8 1.0 CD2 B:LEU105 3.4 56.9 1.0 NH1 B:ARG2 3.6 38.6 1.0 C B:PHE92 3.6 37.3 1.0 CA B:PHE92 3.9 34.0 1.0 N B:ASN94 3.9 33.9 1.0 CB B:ASN94 4.0 37.0 1.0 CA B:ASN94 4.0 36.0 1.0 NH2 B:ARG2 4.1 38.8 1.0 C B:GLY93 4.3 37.3 1.0 CZ B:ARG2 4.3 41.3 1.0 CD1 B:PHE92 4.3 31.3 1.0 ND2 B:ASN94 4.3 47.6 1.0 CB B:LEU105 4.4 43.1 1.0 CB B:PHE92 4.4 32.8 1.0 CG B:LEU105 4.4 46.6 1.0 O B:GLY93 4.5 42.0 1.0 N B:GLY93 4.5 32.3 1.0 CG B:ASN94 4.7 48.1 1.0 CG B:PHE92 4.8 31.7 1.0 O B:LEU91 4.9 35.2 1.0 CA B:GLY93 5.0 34.7 1.0

M.Yogavel, S.Khan, T.K.Bhatt, A.Sharma. Structure of D-Tyrosyl-Trnatyr Deacylase Using Home-Source Cu Kalpha and Moderate-Quality Iodide-Sad Data: Structural Polymorphism and Hepes-Bound Enzyme States Acta Crystallogr.,Sect.D V. 66 584 2010.
ISSN: ISSN 0907-4449
PubMed: 20445234
DOI: 10.1107/S0907444910006062