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Iodine in PDB 3ol3: Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased

Protein crystallography data

The structure of Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased, PDB code: 3ol3 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.870, 72.900, 45.140, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.6

Iodine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased (pdb code 3ol3). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 21 binding sites of Iodine where determined in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased, PDB code: 3ol3:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 21 in 3ol3

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Iodine binding site 1 out of 21 in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased


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 A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I104

b:34.5
occ:0.45
O B:HOH186 3.4 31.2 1.0
CD2 A:PHE8 3.4 38.1 1.0
CE2 A:PHE8 3.6 39.0 1.0
SD A:MET9 4.1 27.5 0.8
CG2 A:VAL12 4.1 22.1 1.0
CA A:MET9 4.2 31.9 1.0
CB A:VAL12 4.3 21.6 1.0
CE A:MET9 4.3 29.4 1.0
N A:MET9 4.5 33.3 1.0
CB A:MET9 4.6 33.3 1.0
CG1 A:VAL12 4.6 20.5 1.0
CB B:LEU33 4.6 14.7 1.0
CG A:PHE8 4.6 37.6 1.0
O A:PHE8 4.7 32.7 1.0
O B:LEU33 4.7 14.4 1.0
C A:PHE8 4.7 33.9 1.0
CB B:LYS37 4.7 22.6 1.0

Iodine binding site 2 out of 21 in 3ol3

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Iodine binding site 2 out of 21 in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased


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 A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I105

b:35.5
occ:0.51
O B:HOH186 2.9 31.2 1.0
NZ A:LYS37 3.2 30.9 1.0
CE A:LYS37 3.7 27.5 1.0
CB B:LEU36 3.9 18.2 1.0
CD A:LYS37 4.3 28.4 1.0
CB A:LEU36 4.3 18.5 1.0
O A:LEU36 4.3 18.9 1.0
O B:LEU36 4.4 20.2 1.0
C B:LEU36 4.5 20.0 1.0
CD1 B:LEU36 4.7 19.0 1.0
N B:LYS37 4.7 20.2 1.0
CD1 A:LEU36 4.7 18.7 1.0
C A:LEU36 4.8 19.9 1.0
CA B:LEU36 4.8 18.9 1.0
CG B:LEU36 4.9 18.0 1.0
CG A:LEU36 4.9 17.2 1.0

Iodine binding site 3 out of 21 in 3ol3

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Iodine binding site 3 out of 21 in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased


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 A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I106

b:48.1
occ:0.57
O A:HOH169 3.4 35.3 1.0
CE A:LYS18 3.8 40.9 1.0
NZ A:LYS18 3.9 43.4 1.0
CA A:TRP15 4.0 21.8 1.0
CB A:TRP15 4.2 21.7 1.0
CD1 A:TRP15 4.2 26.3 1.0
N A:TRP15 4.4 22.1 1.0
CG A:TRP15 4.6 23.6 1.0
CD A:LYS18 4.7 39.1 1.0
C A:GLY14 4.8 23.1 1.0
O A:GLY14 4.9 23.0 1.0
O1 A:PGE116 5.0 42.8 1.0

Iodine binding site 4 out of 21 in 3ol3

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Iodine binding site 4 out of 21 in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased


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 A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I107

b:31.9
occ:0.59
NH1 A:ARG47 3.2 35.0 1.0
O A:HOH131 3.3 32.2 1.0
CD A:ARG47 3.8 28.2 1.0
CB A:ASP43 3.9 31.5 1.0
CG A:GLU44 4.3 26.6 1.0
CZ A:ARG47 4.3 32.9 1.0
C A:ASP43 4.3 25.8 1.0
N A:GLU44 4.4 24.0 1.0
NE A:ARG47 4.5 29.6 1.0
O A:ASP43 4.6 24.7 1.0
CA A:ASP43 4.7 27.9 1.0
OG1 A:THR41 4.8 26.9 1.0
CA A:GLU44 4.8 22.4 1.0
OD2 A:ASP43 5.0 41.4 1.0

Iodine binding site 5 out of 21 in 3ol3

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Iodine binding site 5 out of 21 in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased


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 A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I108

b:31.8
occ:0.29
OG A:SER55 3.4 35.5 1.0
O A:HOH181 3.4 31.0 1.0
O A:HOH132 3.5 33.8 1.0
CD1 A:ILE52 3.5 18.1 0.4
CG2 A:THR56 3.9 34.4 1.0
CG A:ASP66 4.1 27.8 1.0
CB A:ASP66 4.1 24.2 1.0
OD1 A:ASP66 4.2 29.2 1.0
CB A:SER55 4.3 34.8 1.0
CG2 A:ILE52 4.5 18.8 0.6
CA A:ILE52 4.5 19.1 0.6
OD2 A:ASP66 4.5 27.9 1.0
CA A:ILE52 4.5 19.2 0.4
O A:ILE52 4.6 19.3 1.0
O A:SER55 4.6 36.6 1.0
CG1 A:ILE52 4.7 17.5 0.6
CG2 A:ILE52 4.7 19.1 0.4
CA A:ASP66 4.8 24.6 1.0
C A:SER55 4.8 34.6 1.0
CB A:ILE52 4.8 18.0 0.6
CG1 A:ILE52 4.8 18.6 0.4
O A:ASP66 4.8 22.6 1.0
CB A:ILE52 5.0 18.2 0.4

Iodine binding site 6 out of 21 in 3ol3

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Iodine binding site 6 out of 21 in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased


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 A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I109

b:34.4
occ:0.47
O A:ASP57 2.6 36.2 1.0
O A:HOH179 2.8 41.5 1.0
CG A:GLN59 3.6 37.8 1.0
O A:HOH151 3.6 48.5 1.0
C A:ASP57 3.6 35.5 1.0
O A:HOH140 3.9 23.2 1.0
N A:GLN59 3.9 34.8 1.0
CB A:ASP57 4.3 36.7 1.0
C A:GLY58 4.3 34.3 1.0
CG A:ASP57 4.3 38.1 1.0
CA A:GLY58 4.3 33.6 1.0
N A:GLY58 4.4 34.2 1.0
OD2 A:ASP57 4.4 35.8 1.0
CD A:GLN59 4.5 39.1 1.0
CB A:GLN59 4.5 37.4 1.0
NE2 A:GLN59 4.6 39.5 1.0
CA A:ASP57 4.6 35.6 1.0
CA A:GLN59 4.6 37.0 1.0
OD1 A:ASP57 4.8 39.1 1.0

Iodine binding site 7 out of 21 in 3ol3

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Iodine binding site 7 out of 21 in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased


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 A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I110

b:28.6
occ:0.74
O A:HOH122 3.5 16.9 1.0
NE A:ARG90 3.6 16.4 1.0
CA A:ARG90 3.9 15.4 1.0
N A:ARG90 4.0 15.0 1.0
O A:ALA89 4.0 16.2 1.0
C A:ALA89 4.0 15.0 1.0
NH2 A:ARG90 4.1 16.9 1.0
O A:HOH166 4.2 30.2 1.0
CB A:ALA89 4.3 16.2 1.0
CZ A:ARG90 4.3 18.5 1.0
CD A:ARG90 4.5 15.4 1.0
O A:HOH128 4.5 15.8 1.0
CB A:ARG90 4.5 14.8 1.0
CB A:SER93 4.6 17.9 1.0
OG A:SER93 4.8 18.1 1.0
CA A:ALA89 4.8 15.2 1.0
O A:HOH135 4.9 28.9 1.0

Iodine binding site 8 out of 21 in 3ol3

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Iodine binding site 8 out of 21 in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased


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 A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I111

b:43.8
occ:0.45
NZ A:LYS77 3.6 38.8 1.0
NH1 A:ARG38 3.7 20.5 1.0
O A:HOH133 3.8 36.5 1.0
CD A:ARG38 4.3 24.7 1.0
CD A:LYS77 4.4 34.3 1.0
CE A:LYS77 4.5 34.2 1.0
CZ A:ARG38 4.7 20.0 1.0
NE A:ARG38 4.9 21.1 1.0

Iodine binding site 9 out of 21 in 3ol3

Go back to Iodine Binding Sites List in 3ol3
Iodine binding site 9 out of 21 in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased


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 A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I112

b:64.4
occ:0.51
CD2 A:HIS72 3.8 33.3 1.0
CA A:GLU76 3.9 32.7 1.0
CG A:GLU76 4.1 38.0 1.0
O A:HIS72 4.2 30.5 1.0
CB A:GLU76 4.2 36.0 1.0
NE2 A:HIS72 4.2 34.0 1.0
C A:GLU76 4.4 32.2 1.0
O A:GLU76 4.6 33.5 1.0
OE2 A:GLU76 4.8 48.0 1.0
C A:HIS72 4.9 29.0 1.0
N A:GLU76 5.0 30.6 1.0
CD A:GLU76 5.0 45.7 1.0

Iodine binding site 10 out of 21 in 3ol3

Go back to Iodine Binding Sites List in 3ol3
Iodine binding site 10 out of 21 in the Crystal Structure of A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased


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 A Putative Uncharacterized Protein From Mycobacterium Smegamtis, An Ortholog of RV0543C, Iodide Phased within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I113

b:48.8
occ:0.37
N A:GLU42 3.4 26.9 1.0
O A:HOH130 3.6 37.0 1.0
O A:HOH119 3.9 19.0 1.0
CB A:GLU42 3.9 28.2 1.0
CA A:THR41 4.0 26.3 1.0
O A:HOH190 4.1 35.1 1.0
CB A:THR41 4.1 28.4 1.0
C A:THR41 4.2 26.4 1.0
CA A:GLU42 4.2 26.6 1.0
CG2 A:THR41 4.9 29.0 1.0

Reference:

L.Baugh, I.Phan, D.W.Begley, M.C.Clifton, B.Armour, D.M.Dranow, B.M.Taylor, M.M.Muruthi, J.Abendroth, J.W.Fairman, D.Fox, S.H.Dieterich, B.L.Staker, A.S.Gardberg, R.Choi, S.N.Hewitt, A.J.Napuli, J.Myers, L.K.Barrett, Y.Zhang, M.Ferrell, E.Mundt, K.Thompkins, N.Tran, S.Lyons-Abbott, A.Abramov, A.Sekar, D.Serbzhinskiy, D.Lorimer, G.W.Buchko, R.Stacy, L.J.Stewart, T.E.Edwards, W.C.Van Voorhis, P.J.Myler. Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003
Page generated: Sun Dec 13 19:28:48 2020

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