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Iodine in PDB 4y0l: Mycobacterial Membrane Protein MMPL11D2

Protein crystallography data

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

Iodine Binding Sites:

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 4y0l

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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 4y0l

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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 4y0l

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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 4y0l

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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 4y0l

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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 4y0l

Go back to Iodine Binding Sites List in 4y0l
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 4y0l

Go back to Iodine Binding Sites List in 4y0l
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 4y0l

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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 4y0l

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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

Reference:

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
Page generated: Sun Aug 11 20:24:05 2024

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