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Iodine in PDB 3tur: Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment

Protein crystallography data

The structure of Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment, PDB code: 3tur was solved by M.A.Bianchet, S.B.Erdemli, R.Gupta, G.Lamichhane, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.69 / 1.72
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119.132, 120.829, 122.847, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.5

Other elements in 3tur:

The structure of Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment also contains other interesting chemical elements:

Platinum (Pt) 12 atoms

Iodine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment (pdb code 3tur). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment, PDB code: 3tur:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 3tur

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Iodine binding site 1 out of 11 in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:59.3
occ:0.30
I1 A:0JC501 0.0 59.3 0.3
PT1 A:0JC501 2.4 49.9 0.3
ND1 A:HIS347 2.9 48.6 1.0
CG A:HIS347 3.4 40.3 1.0
CB A:HIS347 3.4 31.7 1.0
N1 A:0JC501 3.4 55.7 0.3
CE1 A:HIS347 3.8 50.1 1.0
CD2 A:HIS347 4.4 44.9 1.0
CA A:HIS347 4.4 30.4 1.0
N2 A:0JC501 4.4 52.5 0.3
NE2 A:HIS347 4.6 47.4 1.0
O A:HOH637 4.6 54.6 1.0
C1 A:0JC501 4.7 56.1 0.3
C2 A:0JC501 4.9 52.8 0.3
C A:HIS347 5.0 30.4 1.0
O A:HIS347 5.0 30.4 1.0

Iodine binding site 2 out of 11 in 3tur

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Iodine binding site 2 out of 11 in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment


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 M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:0.1
occ:0.50
I1 A:0JC502 0.0 0.1 0.5
N2 A:0JC502 0.7 61.4 0.5
PT1 A:0JC502 1.8 54.6 0.5
C2 A:0JC502 1.8 57.6 0.5
PT1 A:0JC502 2.7 0.8 0.5
N1 A:0JC502 2.8 59.9 0.5
C1 A:0JC502 2.8 57.7 0.5
SD A:MET157 3.0 63.9 0.5
O A:HOH737 3.3 35.1 1.0
SD A:MET157 3.4 85.5 0.5
CB A:ALA171 3.5 31.8 1.0
CB A:MET157 3.5 33.1 0.5
N1 A:0JC502 3.5 1.0 0.5
CG A:MET157 3.6 57.2 0.5
CB A:MET157 3.7 39.8 0.5
CG A:MET157 3.8 42.7 0.5
I1 A:0JC502 4.4 88.5 0.5
NH2 A:ARG209 4.4 30.7 1.0
OE1 A:GLU207 4.4 37.6 1.0
CE A:MET157 4.7 58.4 0.5
CZ A:ARG209 4.7 34.3 1.0
N2 A:0JC502 4.7 0.8 0.5
OE2 A:GLU168 4.7 37.8 1.0
C1 A:0JC502 4.7 0.7 0.5
NE A:ARG209 4.8 28.6 1.0
OH A:TYR330 4.8 55.8 1.0
CA A:MET157 4.9 32.8 0.5
CA A:ALA171 5.0 31.6 1.0

Iodine binding site 3 out of 11 in 3tur

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Iodine binding site 3 out of 11 in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment


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 M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:88.5
occ:0.50
I1 A:0JC502 0.0 88.5 0.5
PT1 A:0JC502 2.7 54.6 0.5
SD A:MET157 3.0 85.5 0.5
CE A:MET157 3.3 58.4 0.5
SD A:MET157 3.4 63.9 0.5
PT1 A:0JC502 3.5 0.8 0.5
CE A:MET157 3.5 84.1 0.5
N1 A:0JC502 3.6 59.9 0.5
N2 A:0JC502 4.0 0.8 0.5
I1 A:0JC502 4.4 0.1 0.5
OH A:TYR330 4.4 55.8 1.0
CD A:ARG371 4.6 58.1 1.0
CG A:MET157 4.7 57.2 0.5
N2 A:0JC502 4.7 61.4 0.5
NE A:ARG371 4.9 67.0 1.0
N1 A:0JC502 4.9 1.0 0.5
NH1 A:ARG371 4.9 77.1 1.0
CG A:MET157 4.9 42.7 0.5
C2 A:0JC502 5.0 0.9 0.5

Iodine binding site 4 out of 11 in 3tur

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Iodine binding site 4 out of 11 in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment


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 M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:78.8
occ:0.30
I1 A:0JC503 0.0 78.8 0.3
PT1 A:0JC503 2.5 69.4 0.3
CG A:MET237 2.9 62.8 1.0
SD A:MET237 3.2 79.3 1.0
CE A:MET237 3.5 65.8 1.0
O A:GLU235 3.5 52.5 1.0
N1 A:0JC503 3.6 71.9 0.3
CB A:MET237 4.3 55.8 1.0
CB A:GLU235 4.5 54.4 1.0
C A:GLU235 4.5 53.0 1.0
N2 A:0JC503 4.5 72.4 0.3
C1 A:0JC503 4.6 70.9 0.3
N A:MET237 4.7 53.9 1.0
CA A:MET237 4.9 55.2 1.0
C A:GLY236 4.9 54.1 1.0

Iodine binding site 5 out of 11 in 3tur

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Iodine binding site 5 out of 11 in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment


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 M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:0.3
occ:0.50
I1 A:0JC504 0.0 0.3 0.5
C2 A:0JC504 1.0 0.5 0.5
C1 A:0JC504 1.4 0.0 0.5
N2 A:0JC504 2.1 0.6 0.5
N1 A:0JC504 2.2 0.7 0.5
PT1 A:0JC504 2.7 0.4 0.5
PT1 A:0JC504 3.1 0.0 0.5
O A:HOH652 3.5 52.5 1.0
N A:PHE215 3.6 33.2 1.0
ND1 A:HIS214 3.7 87.1 1.0
O A:HOH763 3.7 54.2 1.0
N1 A:0JC504 3.7 99.0 0.5
CB A:HIS214 3.8 41.9 1.0
CD2 A:PHE215 3.8 31.5 1.0
CG A:HIS214 4.0 62.4 1.0
CG A:PHE215 4.0 28.4 1.0
CB A:PHE215 4.1 30.8 1.0
CA A:HIS214 4.3 37.9 1.0
C A:HIS214 4.5 34.8 1.0
CA A:PHE215 4.5 31.4 1.0
CE2 A:PHE215 4.5 34.7 1.0
CE1 A:HIS214 4.7 79.5 1.0
N2 A:0JC504 4.9 97.6 0.5
CD1 A:PHE215 4.9 31.0 1.0
O A:PHE215 5.0 33.1 1.0

Iodine binding site 6 out of 11 in 3tur

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Iodine binding site 6 out of 11 in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment


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 M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:0.8
occ:0.50
I1 A:0JC504 0.0 0.8 0.5
C2 A:0JC504 0.7 96.2 0.5
C1 A:0JC504 0.9 95.8 0.5
N2 A:0JC504 2.0 97.6 0.5
N1 A:0JC504 2.1 99.0 0.5
PT1 A:0JC504 2.7 0.0 0.5
PT1 A:0JC504 3.1 0.4 0.5
N1 A:0JC504 3.7 0.7 0.5
O A:HOH811 3.8 43.9 1.0
CD1 A:ILE291 4.0 37.8 1.0
CE3 A:TRP394 4.5 34.5 1.0
O A:TRP394 4.5 31.6 1.0
ND1 A:HIS214 4.6 87.1 1.0
O A:GLU213 4.6 38.1 1.0
O A:HOH759 4.6 39.1 1.0
N2 A:0JC504 4.8 0.6 0.5

Iodine binding site 7 out of 11 in 3tur

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Iodine binding site 7 out of 11 in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment


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 M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I502

b:85.1
occ:0.60
I1 B:0JC502 0.0 85.1 0.6
PT1 B:0JC502 2.6 61.9 0.6
ND1 B:HIS347 3.3 50.5 1.0
N1 B:0JC502 3.5 68.2 0.6
CB B:HIS347 3.7 33.0 1.0
CG B:HIS347 3.8 37.9 1.0
O A:HOH749 3.9 68.6 1.0
CE1 B:HIS347 4.3 48.9 1.0
CA B:HIS347 4.6 31.5 1.0
N2 B:0JC502 4.7 66.5 0.6
O B:HIS347 4.7 30.7 1.0
O B:HOH812 4.9 48.2 1.0
C1 B:0JC502 5.0 66.3 0.6
CD2 B:HIS347 5.0 42.4 1.0
C B:HIS347 5.0 30.7 1.0

Iodine binding site 8 out of 11 in 3tur

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Iodine binding site 8 out of 11 in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment


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 M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I503

b:0.5
occ:1.00
I1 B:0JC503 0.0 0.5 1.0
PT1 B:0JC503 2.6 0.6 0.3
N1 B:0JC503 3.4 0.3 0.3
CB B:HIS214 3.5 37.6 1.0
N B:PHE215 3.5 33.2 1.0
ND1 B:HIS214 3.5 48.2 1.0
CD2 B:PHE215 3.9 34.4 1.0
CG B:HIS214 3.9 45.1 1.0
CA B:HIS214 3.9 35.9 1.0
CG B:PHE215 4.0 31.1 1.0
C B:HIS214 4.3 33.7 1.0
CE2 B:PHE215 4.3 33.6 1.0
CB B:PHE215 4.3 32.2 1.0
CA B:PHE215 4.6 31.8 1.0
N2 B:0JC503 4.6 0.4 0.3
O B:HOH711 4.6 60.6 1.0
CD1 B:PHE215 4.7 30.8 1.0
CE1 B:HIS214 4.7 53.8 1.0
O B:HOH691 4.7 52.7 1.0
C1 B:0JC503 4.8 0.1 0.3
CZ B:PHE215 4.9 28.1 1.0

Iodine binding site 9 out of 11 in 3tur

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Iodine binding site 9 out of 11 in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment


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 M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I504

b:28.5
occ:0.10
I1 B:0JC504 0.0 28.5 0.1
O B:HOH838 2.3 0.8 1.0
PT1 B:0JC504 2.6 13.9 0.1
O B:HOH782 2.7 74.8 1.0
N2 B:0JC504 2.8 14.4 0.5
SD B:MET157 3.4 57.0 1.0
PT1 B:0JC504 3.5 63.0 0.5
N1 B:0JC504 3.5 41.9 0.1
C2 B:0JC504 3.8 45.0 0.5
CE B:MET157 4.0 54.4 1.0
NE B:ARG371 4.0 58.0 1.0
CD B:ARG371 4.2 51.8 1.0
OG B:SER296 4.3 48.3 1.0
CZ B:ARG371 4.6 55.2 1.0
N2 B:0JC504 4.7 34.3 0.1
N1 B:0JC504 4.7 67.8 0.5
C1 B:0JC504 4.8 40.1 0.1
CB B:LEU131 4.8 56.2 1.0
OH B:TYR330 4.9 59.7 1.0
NH1 B:ARG371 4.9 58.6 1.0
CG B:ARG371 4.9 41.6 1.0

Iodine binding site 10 out of 11 in 3tur

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Iodine binding site 10 out of 11 in the Crystal Structure of M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment


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 M. Tuberculosis Ld-Transpeptidase Type 2 Complexed with A Peptidoglycan Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I504

b:83.8
occ:0.50
I1 B:0JC504 0.0 83.8 0.5
PT1 B:0JC504 2.7 63.0 0.5
NH1 B:ARG173 2.7 78.6 1.0
CZ B:ARG173 3.2 78.7 1.0
CE B:MET157 3.3 54.4 1.0
N1 B:0JC504 3.4 67.8 0.5
SD B:MET157 3.5 57.0 1.0
N2 B:0JC504 3.6 34.3 0.1
NH2 B:ARG173 3.6 79.7 1.0
OE1 B:GLU207 3.7 36.5 1.0
O B:HOH772 3.9 53.1 1.0
PT1 B:0JC504 3.9 13.9 0.1
CB B:ALA171 4.0 33.8 1.0
NE B:ARG173 4.0 73.5 1.0
CG B:MET157 4.2 47.2 1.0
CB B:MET157 4.3 34.9 1.0
CD B:GLU207 4.4 41.8 1.0
N2 B:0JC504 4.4 14.4 0.5
OE2 B:GLU207 4.6 43.5 1.0
C2 B:0JC504 4.6 45.0 0.1
C1 B:0JC504 4.6 35.5 0.5
CB B:ARG173 4.8 44.3 1.0
C1 B:0JC504 4.8 40.1 0.1

Reference:

S.B.Erdemli, R.Gupta, W.R.Bishai, G.Lamichhane, L.M.Amzel, M.A.Bianchet. Targeting the Cell Wall of Mycobacterium Tuberculosis: Structure and Mechanism of L,D-Transpeptidase 2. Structure V. 20 2103 2012.
ISSN: ISSN 0969-2126
PubMed: 23103390
DOI: 10.1016/J.STR.2012.09.016
Page generated: Sun Dec 13 19:30:33 2020

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