Atomistry » Iodine » PDB 3ru1-3unh » 3tur
Atomistry »
  Iodine »
    PDB 3ru1-3unh »
      3tur »

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

Go back to Iodine Binding Sites List in 3tur
Iodine binding site 1 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 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

Go back to Iodine Binding Sites List in 3tur
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

Go back to Iodine Binding Sites List in 3tur
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

Go back to Iodine Binding Sites List in 3tur
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

Go back to Iodine Binding Sites List in 3tur
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

Go back to Iodine Binding Sites List in 3tur
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

Go back to Iodine Binding Sites List in 3tur
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

Go back to Iodine Binding Sites List in 3tur
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

Go back to Iodine Binding Sites List in 3tur
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

Go back to Iodine Binding Sites List in 3tur
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 Aug 11 16:51:42 2024

Last articles

Ca in 5OWO
Ca in 5OWR
Ca in 5OWC
Ca in 5OW8
Ca in 5OTJ
Ca in 5OSQ
Ca in 5OTN
Ca in 5OV7
Ca in 5OT1
Ca in 5ONR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy