Iodine in PDB 2gq2: Mycobacterium Tuberculosis Thyx-Nadp Complex

All present enzymatic activity of Mycobacterium Tuberculosis Thyx-Nadp Complex:
2.1.1.148;

The structure of Mycobacterium Tuberculosis Thyx-Nadp Complex, PDB code: 2gq2 was solved by P.Sampathkumar, S.Turley, C.H.Sibley, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.20 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.007, 78.090, 88.514, 90.00, 95.67, 90.00
R / Rfree (%)	21.2 / 25.5

The structure of Mycobacterium Tuberculosis Thyx-Nadp Complex also contains other interesting chemical elements:

Potassium

(K)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iodine atom in the Mycobacterium Tuberculosis Thyx-Nadp Complex (pdb code 2gq2). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 18 binding sites of Iodine where determined in the Mycobacterium Tuberculosis Thyx-Nadp Complex, PDB code: 2gq2:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 18 in the Mycobacterium Tuberculosis Thyx-Nadp Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Mycobacterium Tuberculosis Thyx-Nadp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:22.2 occ:0.70 NH1 A:ARG115 3.2 38.5 1.0 CG A:LYS112 3.7 31.4 1.0 N A:GLU111 3.9 29.8 1.0 CB A:PRO110 3.9 29.6 1.0 NH2 A:ARG115 4.0 36.4 1.0 CZ A:ARG115 4.0 37.2 1.0 N A:LYS112 4.0 29.6 1.0 CA A:PRO110 4.2 29.8 1.0 OH A:TYR108 4.2 39.1 1.0 C A:PRO110 4.3 29.7 1.0 CE A:LYS112 4.5 30.9 1.0 CB A:LYS112 4.6 30.6 1.0 CD A:LYS112 4.6 31.5 1.0 CA A:GLU111 4.8 30.2 1.0 CA A:LYS112 4.9 30.4 1.0 C A:GLU111 4.9 29.7 1.0 CB A:GLU111 5.0 31.0 1.0

Iodine binding site 2 out of 18 in the Mycobacterium Tuberculosis Thyx-Nadp Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Mycobacterium Tuberculosis Thyx-Nadp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:28.1 occ:0.50 I A:IOD502 0.0 28.1 0.5 I A:IOD502 1.6 26.9 0.5 NH2 D:ARG87 3.6 34.4 1.0 NE D:ARG87 3.7 32.8 1.0 CB A:HIS91 3.9 17.9 1.0 O A:ARG87 4.1 19.4 1.0 CG A:HIS91 4.1 20.7 1.0 CZ D:ARG87 4.1 34.2 1.0 ND1 A:HIS91 4.1 20.8 1.0 O D:HOH657 4.2 30.4 1.0 O A:HOH719 4.3 29.7 1.0 O D:ARG87 4.4 19.8 1.0 C A:ARG87 4.4 19.3 1.0 CB D:ARG87 4.4 20.9 1.0 OD1 A:ASN177 4.5 26.8 1.0 CA A:SER88 4.6 19.7 1.0 CB D:HIS91 4.6 18.3 1.0 N A:SER88 4.6 19.6 1.0 ND1 D:HIS91 4.6 19.9 1.0 C D:ARG87 4.6 19.8 1.0 NH2 A:ARG87 4.7 34.7 1.0 CB A:ARG87 4.8 20.4 1.0 CG D:HIS91 4.8 19.5 1.0 NE A:ARG87 4.8 33.2 1.0 CD D:ARG87 4.8 29.8 1.0 CD2 A:HIS91 4.9 22.0 1.0 CE1 A:HIS91 4.9 22.5 1.0

Iodine binding site 3 out of 18 in the Mycobacterium Tuberculosis Thyx-Nadp Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Mycobacterium Tuberculosis Thyx-Nadp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:26.9 occ:0.50 I A:IOD502 0.0 26.9 0.5 I A:IOD502 1.6 28.1 0.5 NH2 A:ARG87 3.2 34.7 1.0 NE A:ARG87 3.6 33.2 1.0 CZ A:ARG87 3.7 34.3 1.0 O A:HOH719 3.8 29.7 1.0 CB D:HIS91 3.9 18.3 1.0 O D:ARG87 4.1 19.8 1.0 CG D:HIS91 4.1 19.5 1.0 OD1 D:ASN177 4.2 27.5 1.0 CA D:SER88 4.3 20.1 1.0 C D:ARG87 4.3 19.8 1.0 ND1 D:HIS91 4.3 19.9 1.0 N D:SER88 4.4 19.9 1.0 CB A:ARG87 4.5 20.4 1.0 O A:ARG87 4.5 19.4 1.0 ND1 A:HIS91 4.7 20.8 1.0 CD A:ARG87 4.7 29.6 1.0 CB D:ARG87 4.7 20.9 1.0 CD2 D:HIS91 4.8 18.8 1.0 C A:ARG87 4.8 19.3 1.0 O D:HOH657 4.9 30.4 1.0 NH1 A:ARG87 4.9 32.6 1.0 CB A:HIS91 4.9 17.9 1.0 NE D:ARG87 4.9 32.8 1.0 CB D:SER88 4.9 20.2 1.0 CG A:ARG87 5.0 24.1 1.0

Iodine binding site 4 out of 18 in the Mycobacterium Tuberculosis Thyx-Nadp Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Mycobacterium Tuberculosis Thyx-Nadp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I515 b:49.9 occ:0.60 CG1 A:VAL206 3.0 27.7 1.0 N A:GLY121 3.2 34.6 1.0 CA A:GLY121 3.7 36.4 1.0 CB D:ALA170 4.0 27.7 1.0 CD A:PRO120 4.0 30.2 1.0 N A:PRO120 4.0 29.9 1.0 CB A:PRO119 4.1 26.8 1.0 C A:PRO120 4.3 33.1 1.0 C A:PRO119 4.4 28.1 1.0 CB A:PRO120 4.4 31.7 1.0 CA A:PRO120 4.5 31.6 1.0 O D:GLN166 4.5 35.5 1.0 CA D:ALA170 4.5 28.0 1.0 CB A:VAL206 4.5 26.4 1.0 CG A:PRO120 4.6 30.3 1.0 N D:ALA170 4.6 29.1 1.0 CA A:PRO119 4.6 26.8 1.0 CG D:GLN169 4.8 33.5 1.0 C A:GLY121 4.9 37.7 1.0

Iodine binding site 5 out of 18 in the Mycobacterium Tuberculosis Thyx-Nadp Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Mycobacterium Tuberculosis Thyx-Nadp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I516 b:30.1 occ:0.30 N A:TYR60 3.8 23.7 1.0 C A:GLY59 3.9 23.9 1.0 CA A:TYR60 4.0 23.9 1.0 O A:GLY59 4.0 24.1 1.0 O A:HOH747 4.1 27.0 1.0 CD1 A:TYR60 4.4 23.8 1.0 CB A:TYR60 4.4 23.6 1.0 CA A:GLY59 4.5 24.1 1.0 O A:THR56 4.7 25.6 1.0 O A:HOH798 4.8 36.8 1.0 O A:HOH738 4.8 37.5 1.0 NH2 A:ARG41 4.9 23.9 1.0 CG A:TYR60 5.0 24.2 1.0

Iodine binding site 6 out of 18 in the Mycobacterium Tuberculosis Thyx-Nadp Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Mycobacterium Tuberculosis Thyx-Nadp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:I504 b:22.6 occ:0.50 NE C:ARG87 4.0 32.7 1.0 NH2 C:ARG87 4.1 34.8 1.0 O B:ARG87 4.1 20.6 1.0 CB B:HIS91 4.2 18.4 1.0 NH2 B:ARG87 4.2 34.9 1.0 CB C:HIS91 4.2 18.7 1.0 NE B:ARG87 4.2 32.8 1.0 O B:HOH639 4.3 33.2 1.0 O C:ARG87 4.3 19.5 1.0 ND1 C:HIS91 4.4 21.8 1.0 CG B:HIS91 4.4 19.7 1.0 ND1 B:HIS91 4.5 19.8 1.0 C B:ARG87 4.5 19.8 1.0 CG C:HIS91 4.5 19.6 1.0 CZ C:ARG87 4.5 34.5 1.0 CB C:ARG87 4.5 20.5 1.0 C C:ARG87 4.6 19.4 1.0 CB B:ARG87 4.6 20.3 1.0 CZ B:ARG87 4.7 34.3 1.0 CA B:SER88 4.8 19.6 1.0 N B:SER88 4.8 19.4 1.0 N C:SER88 4.9 20.0 1.0 OD1 B:ASN177 5.0 31.1 1.0 CD C:ARG87 5.0 29.6 1.0 CA C:SER88 5.0 20.3 1.0

Iodine binding site 7 out of 18 in the Mycobacterium Tuberculosis Thyx-Nadp Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Mycobacterium Tuberculosis Thyx-Nadp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:I510 b:46.0 occ:0.50 NH1 B:ARG172 2.5 43.6 1.0 CD B:ARG87 3.4 30.0 1.0 CZ B:ARG172 3.7 42.1 1.0 ND2 C:ASN177 3.8 26.1 1.0 NE B:ARG87 4.1 32.8 1.0 CG2 B:THR179 4.2 19.5 1.0 CG B:ARG172 4.2 31.7 1.0 CB B:MSE175 4.2 25.0 1.0 NE B:ARG172 4.4 40.0 1.0 CD B:ARG172 4.4 36.8 1.0 NH2 B:ARG172 4.4 42.1 1.0 CG B:ARG87 4.6 24.2 1.0 CZ B:ARG87 4.6 34.3 1.0 CB B:THR179 4.6 17.1 1.0 NH1 B:ARG87 4.7 34.9 1.0 CG C:ASN177 4.7 24.5 1.0 OD1 C:ASN177 4.7 29.6 1.0 CG B:MSE175 4.7 28.3 1.0 O B:GLN106 4.8 37.0 1.0 OG1 B:THR179 4.8 20.2 1.0

Iodine binding site 8 out of 18 in the Mycobacterium Tuberculosis Thyx-Nadp Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Mycobacterium Tuberculosis Thyx-Nadp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:I506 b:39.8 occ:0.40 N C:ALA225 3.8 25.5 1.0 CA C:ALA225 3.8 25.6 1.0 CB C:ALA58 3.9 25.1 1.0 CB C:ALA225 4.0 26.0 1.0 CB C:PRO224 4.1 24.9 1.0 C C:PRO224 4.3 25.0 1.0 O C:PRO224 4.7 24.8 1.0 CA C:ALA58 4.8 24.9 1.0 CA C:PRO224 4.9 24.9 1.0

Iodine binding site 9 out of 18 in the Mycobacterium Tuberculosis Thyx-Nadp Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Mycobacterium Tuberculosis Thyx-Nadp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:I509 b:24.9 occ:0.50 NE C:ARG172 3.2 39.6 1.0 ND2 B:ASN177 3.6 26.4 1.0 CD C:ARG87 3.7 29.6 1.0 CG C:GLN106 3.7 40.6 1.0 NH2 C:ARG172 3.8 42.9 1.0 CZ C:ARG172 3.9 42.7 1.0 CB C:MSE175 4.0 24.6 1.0 CD C:ARG172 4.1 35.2 1.0 NH1 C:ARG87 4.1 34.2 1.0 CG2 C:THR179 4.2 18.7 1.0 CG C:MSE175 4.3 28.3 1.0 NE C:ARG87 4.3 32.7 1.0 NE2 C:GLN106 4.4 44.6 1.0 CD C:GLN106 4.4 43.8 1.0 CB C:ARG172 4.4 25.9 1.0 CZ C:ARG87 4.5 34.5 1.0 CB C:THR179 4.7 18.1 1.0 O C:GLN106 4.7 40.1 1.0 CG C:ARG172 4.7 28.9 1.0 CG B:ASN177 4.7 25.8 1.0 CG C:ARG87 4.7 22.9 1.0 OG1 C:THR179 4.8 18.1 1.0 O C:ARG172 4.9 24.5 1.0 CB C:GLN106 5.0 38.2 1.0 OD1 B:ASN177 5.0 31.1 1.0

Iodine binding site 10 out of 18 in the Mycobacterium Tuberculosis Thyx-Nadp Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Mycobacterium Tuberculosis Thyx-Nadp Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:I511 b:40.5 occ:0.50 I C:IOD511 0.0 40.5 0.5 I C:IOD511 2.9 47.3 0.5 N B:HIS98 3.5 20.1 1.0 O B:HOH683 3.6 33.2 1.0 ND1 B:HIS98 3.9 20.3 1.0 CB B:ARG97 4.2 20.7 1.0 CE1 B:HIS98 4.2 21.9 1.0 CA B:HIS98 4.2 19.2 1.0 CG B:ARG97 4.3 21.5 1.0 CG C:ARG97 4.4 21.5 1.0 CB C:ARG97 4.4 19.9 1.0 CA B:ARG97 4.5 20.1 1.0 C B:ARG97 4.5 19.9 1.0 CG B:HIS98 4.5 20.6 1.0 CD C:ARG97 4.5 22.9 1.0 NE2 D:HIS98 4.7 19.3 1.0 CD2 D:HIS98 4.8 19.9 1.0 NE2 B:HIS98 4.8 19.0 1.0 I D:IOD512 4.9 52.3 0.5 CB B:HIS98 5.0 18.9 1.0

P.Sampathkumar, S.Turley, C.H.Sibley, W.G.Hol. Nadp+ Expels Both the Co-Factor and A Substrate Analog From the Mycobacterium Tuberculosis Thyx Active Site: Opportunities For Anti-Bacterial Drug Design. J.Mol.Biol. V. 360 1 2006.
ISSN: ISSN 0022-2836
PubMed: 16730023
DOI: 10.1016/J.JMB.2006.04.061