Iodine in PDB 4y0l: Mycobacterial Membrane Protein MMPL11D2

The structure of Mycobacterial Membrane Protein MMPL11D2, PDB code: 4y0l was solved by R.Torres, N.Chim, C.W.Goulding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.36 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	65.600, 91.730, 32.850, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.4

The binding sites of Iodine atom in the Mycobacterial Membrane Protein MMPL11D2 (pdb code 4y0l). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Mycobacterial Membrane Protein MMPL11D2, PDB code: 4y0l:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in the Mycobacterial Membrane Protein MMPL11D2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Mycobacterial Membrane Protein MMPL11D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I601 b:52.7 occ:0.55 HG2 A:ARG449 3.0 40.7 1.0 HA A:HIS450 3.5 31.1 1.0 O A:HOH711 3.7 70.4 1.0 HB2 A:ALA453 3.7 34.3 1.0 NH1 A:ARG449 3.8 34.5 1.0 HH11 A:ARG449 3.8 41.4 1.0 O A:HOH716 3.8 46.8 1.0 HH12 A:ARG449 4.0 41.4 1.0 CG A:ARG449 4.0 33.9 1.0 CZ A:ARG449 4.0 39.2 1.0 HB A:VAL461 4.1 52.5 1.0 HB3 A:ALA453 4.2 34.3 1.0 O A:ARG449 4.3 24.4 1.0 HG3 A:ARG449 4.3 40.7 1.0 CB A:ALA453 4.3 28.6 1.0 NE A:ARG449 4.3 44.2 1.0 CA A:HIS450 4.4 25.9 1.0 C A:ARG449 4.5 21.7 1.0 HD3 A:ARG449 4.5 52.4 1.0 NH2 A:ARG449 4.5 32.4 1.0 HB1 A:ALA453 4.5 34.3 1.0 CD A:ARG449 4.5 43.7 1.0 N A:HIS450 4.6 30.3 1.0 HB2 A:HIS450 4.6 41.4 1.0 HH22 A:ARG449 4.7 38.8 1.0 HD2 A:HIS450 4.7 46.5 1.0 HG21 A:VAL461 4.8 55.0 1.0 HB3 A:ARG449 4.8 30.2 1.0 HE A:ARG449 4.8 53.1 1.0 CB A:ARG449 4.9 25.2 1.0 HH21 A:ARG449 5.0 38.8 1.0 CB A:VAL461 5.0 43.8 1.0 CB A:HIS450 5.0 34.5 1.0

Iodine binding site 2 out of 9 in the Mycobacterial Membrane Protein MMPL11D2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Mycobacterial Membrane Protein MMPL11D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I602 b:23.8 occ:1.00 H A:ASP432 2.7 29.8 1.0 HD1 A:PHE431 3.1 27.1 1.0 O A:HOH703 3.2 39.0 1.0 HB2 A:ASP432 3.3 55.6 1.0 HA A:PHE431 3.3 25.4 1.0 HA A:ALA506 3.5 22.5 1.0 N A:ASP432 3.5 24.8 1.0 O A:HOH709 3.6 18.2 1.0 HB3 A:ALA505 3.7 24.7 1.0 HB3 A:PHE431 3.7 22.9 1.0 HE1 A:HIS441 3.8 18.2 1.0 CD1 A:PHE431 4.0 22.6 1.0 HB2 A:ALA506 4.0 22.1 1.0 HB1 A:ALA505 4.0 24.7 1.0 H A:ALA433 4.1 33.4 1.0 CA A:PHE431 4.1 21.1 1.0 N A:ALA506 4.1 19.4 1.0 CA A:ALA506 4.1 18.8 1.0 CB A:ASP432 4.2 46.3 1.0 C A:ALA505 4.2 17.8 1.0 O A:ALA505 4.3 22.3 1.0 CB A:PHE431 4.3 19.1 1.0 CB A:ALA505 4.3 20.6 1.0 C A:PHE431 4.3 28.6 1.0 H A:ALA506 4.4 23.3 1.0 HB3 A:ASP432 4.4 55.6 1.0 CA A:ASP432 4.4 30.1 1.0 CE1 A:HIS441 4.4 15.2 1.0 CB A:ALA506 4.6 18.4 1.0 CG A:PHE431 4.6 18.4 1.0 N A:ALA433 4.8 27.8 1.0 CA A:ALA505 4.9 26.6 1.0 HE1 A:PHE431 4.9 18.4 1.0 HB1 A:ALA506 4.9 22.1 1.0 CE1 A:PHE431 4.9 15.3 1.0

Iodine binding site 3 out of 9 in the Mycobacterial Membrane Protein MMPL11D2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Mycobacterial Membrane Protein MMPL11D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I603 b:84.6 occ:0.52 HA A:TRP494 3.3 56.1 1.0 HD1 A:TRP494 3.4 55.8 1.0 HE21 A:GLN498 3.5 66.2 1.0 HG21 A:THR497 3.6 56.2 1.0 HB A:THR497 3.8 65.6 1.0 CD1 A:TRP494 3.9 46.5 1.0 CA A:TRP494 4.2 46.7 1.0 NE2 A:GLN498 4.3 55.2 1.0 CB A:THR497 4.4 54.7 1.0 CG2 A:THR497 4.4 46.9 1.0 HG2 A:GLN498 4.4 53.6 1.0 HB2 A:TRP494 4.4 56.1 1.0 OG1 A:THR497 4.4 61.1 1.0 CG A:TRP494 4.5 45.0 1.0 CB A:TRP494 4.6 46.8 1.0 HG22 A:THR497 4.7 56.2 1.0 NE1 A:TRP494 4.7 44.2 1.0 HG1 A:THR497 4.7 73.3 1.0 HE22 A:GLN498 4.7 66.2 1.0 HE1 A:TRP494 4.8 53.0 1.0 O A:TRP494 4.8 58.4 1.0 O A:THR493 4.9 49.2 1.0 HG23 A:THR493 4.9 79.9 1.0 N A:TRP494 4.9 48.9 1.0

Iodine binding site 4 out of 9 in the Mycobacterial Membrane Protein MMPL11D2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Mycobacterial Membrane Protein MMPL11D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I604 b:78.0 occ:0.56 HB2 A:PRO500 3.2 37.5 1.0 HG2 A:ARG501 3.6 72.9 1.0 HA A:ARG501 3.7 32.8 1.0 CB A:PRO500 4.0 31.2 1.0 N A:ARG501 4.0 33.9 1.0 HB3 A:PRO500 4.1 37.5 1.0 H A:ARG501 4.2 40.7 1.0 C A:PRO500 4.2 25.5 1.0 CA A:ARG501 4.3 27.3 1.0 HH11 A:ARG501 4.4 66.3 1.0 CG A:ARG501 4.5 60.8 1.0 O A:PRO500 4.5 23.2 1.0 HG3 A:ARG501 4.7 72.9 1.0 CA A:PRO500 4.8 32.5 1.0 CB A:ARG501 4.8 38.5 1.0 HG2 A:PRO500 5.0 40.4 1.0 NH1 A:ARG501 5.0 55.2 1.0 HB3 A:ARG501 5.0 46.2 1.0

Iodine binding site 5 out of 9 in the Mycobacterial Membrane Protein MMPL11D2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Mycobacterial Membrane Protein MMPL11D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I605 b:37.7 occ:0.25 HE22 A:GLN443 3.1 48.5 1.0 HA A:ALA447 3.2 20.1 1.0 O A:HOH708 3.4 29.1 1.0 HB2 A:HIS450 3.7 41.4 1.0 HB3 A:HIS450 3.8 41.4 1.0 NE2 A:GLN443 3.8 40.4 1.0 O A:ALA446 4.0 26.9 1.0 CA A:ALA447 4.1 16.8 1.0 HE21 A:GLN443 4.1 48.5 1.0 CB A:HIS450 4.1 34.5 1.0 HB1 A:ALA446 4.2 27.1 1.0 C A:ALA446 4.2 16.7 1.0 N A:ALA447 4.3 15.3 1.0 HB2 A:ALA447 4.3 20.0 1.0 CG A:HIS450 4.4 43.3 1.0 HB3 A:ALA446 4.5 27.1 1.0 CB A:ALA447 4.7 16.6 1.0 ND1 A:HIS450 4.8 51.3 1.0 CB A:ALA446 4.8 22.6 1.0 H A:ALA447 4.8 18.4 1.0 O A:HOH711 4.8 70.4 1.0 CD A:GLN443 4.8 42.7 1.0 CD2 A:HIS450 4.9 38.8 1.0 HB1 A:ALA447 4.9 20.0 1.0 OE1 A:GLN443 5.0 34.1 1.0

Iodine binding site 6 out of 9 in the Mycobacterial Membrane Protein MMPL11D2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Mycobacterial Membrane Protein MMPL11D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I606 b:45.5 occ:0.32 HH22 A:ARG449 3.1 38.8 1.0 HH12 A:ARG449 3.2 41.4 1.0 I A:IOD609 3.7 67.9 0.3 NH2 A:ARG449 3.9 32.4 1.0 NH1 A:ARG449 4.0 34.5 1.0 CZ A:ARG449 4.5 39.2 1.0 HH21 A:ARG449 4.6 38.8 1.0 HH11 A:ARG449 4.7 41.4 1.0

Iodine binding site 7 out of 9 in the Mycobacterial Membrane Protein MMPL11D2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Mycobacterial Membrane Protein MMPL11D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I607 b:32.3 occ:0.31 HD3 A:ARG449 3.0 52.4 1.0 HD3 A:PRO464 3.0 21.3 1.0 HA A:ALA446 3.1 30.6 1.0 HG22 A:ILE445 3.3 20.8 1.0 I A:IOD608 3.5 42.8 0.3 HG3 A:PRO464 3.6 20.1 1.0 HB2 A:ALA446 3.6 27.1 1.0 HD2 A:ARG449 3.6 52.4 1.0 HH11 A:ARG449 3.7 41.4 1.0 CD A:PRO464 3.7 17.8 1.0 HD2 A:PRO464 3.7 21.3 1.0 CD A:ARG449 3.7 43.7 1.0 CA A:ALA446 3.9 25.5 1.0 CB A:ALA446 4.1 22.6 1.0 CG A:PRO464 4.1 16.8 1.0 N A:ALA446 4.2 17.5 1.0 CG2 A:ILE445 4.2 17.3 1.0 HG21 A:ILE445 4.2 20.8 1.0 HB3 A:ARG449 4.3 30.2 1.0 HB2 A:ARG449 4.3 30.2 1.0 NH1 A:ARG449 4.3 34.5 1.0 HB1 A:ALA446 4.3 27.1 1.0 C A:ILE445 4.5 24.6 1.0 H A:ALA446 4.5 21.0 1.0 O A:ILE445 4.5 22.1 1.0 HB A:ILE445 4.6 16.4 1.0 NE A:ARG449 4.6 44.2 1.0 HA A:PRO463 4.6 34.5 1.0 CB A:ARG449 4.6 25.2 1.0 HG2 A:PRO464 4.7 20.1 1.0 CG A:ARG449 4.8 33.9 1.0 HH12 A:ARG449 4.8 41.4 1.0 O A:HOH711 4.8 70.4 1.0 CZ A:ARG449 4.9 39.2 1.0 O A:SER442 4.9 17.1 1.0 HG23 A:ILE445 4.9 20.8 1.0 CB A:ILE445 4.9 13.6 1.0 HD21 A:LEU475 5.0 45.7 1.0

Iodine binding site 8 out of 9 in the Mycobacterial Membrane Protein MMPL11D2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Mycobacterial Membrane Protein MMPL11D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I608 b:42.8 occ:0.30 HB1 A:ALA446 3.1 27.1 1.0 O A:HOH711 3.2 70.4 1.0 HH11 A:ARG449 3.3 41.4 1.0 HB2 A:ALA446 3.5 27.1 1.0 I A:IOD607 3.5 32.3 0.3 I A:IOD609 3.5 67.9 0.3 CB A:ALA446 3.7 22.6 1.0 HA A:ALA446 3.8 30.6 1.0 NH1 A:ARG449 4.0 34.5 1.0 HH12 A:ARG449 4.0 41.4 1.0 HD3 A:ARG449 4.2 52.4 1.0 CA A:ALA446 4.3 25.5 1.0 HB3 A:ALA446 4.6 27.1 1.0 O A:HOH708 4.8 29.1 1.0 O A:ALA446 4.9 26.9 1.0 HB3 A:ARG449 5.0 30.2 1.0

Iodine binding site 9 out of 9 in the Mycobacterial Membrane Protein MMPL11D2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Mycobacterial Membrane Protein MMPL11D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:I609 b:67.9 occ:0.33 I A:IOD608 3.5 42.8 0.3 HH12 A:ARG449 3.5 41.4 1.0 I A:IOD606 3.7 45.5 0.3 NH1 A:ARG449 4.2 34.5 1.0 HH11 A:ARG449 4.2 41.4 1.0

N.Chim, R.Torres, Y.Liu, J.Capri, G.Batot, J.P.Whitelegge, C.W.Goulding. The Structure and Interactions of Periplasmic Domains of Crucial Mmpl Membrane Proteins From Mycobacterium Tuberculosis. Chem.Biol. V. 22 1098 2015.
ISSN: ISSN 1074-5521
PubMed: 26278184
DOI: 10.1016/J.CHEMBIOL.2015.07.013