Iodine in PDB 7kem: Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis

Protein crystallography data

The structure of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis, PDB code: 7kem was solved by G.A.Libreros, M.V.B.Dias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.66 / 1.77
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.528, 121.051, 122.699, 90.00, 90.00, 90.00
R / Rfree (%) 26.1 / 27.5

Other elements in 7kem:

The structure of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis 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 Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis (pdb code 7kem). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis, PDB code: 7kem:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in 7kem

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Iodine binding site 1 out of 11 in the Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:50.5
occ:0.00
I1 A:0JC501 0.0 50.5 0.0
PT1 A:0JC501 2.4 41.1 0.0
ND1 A:HIS347 2.8 32.6 1.0
CG A:HIS347 3.4 27.2 1.0
N1 A:0JC501 3.4 46.9 0.0
CB A:HIS347 3.5 22.5 1.0
CE1 A:HIS347 3.7 32.1 1.0
N2 A:0JC501 4.4 43.7 0.0
CA A:HIS347 4.4 23.0 1.0
CD2 A:HIS347 4.4 31.2 1.0
NE2 A:HIS347 4.6 35.2 1.0
C1 A:0JC501 4.7 47.3 0.0
C2 A:0JC501 4.9 44.0 0.0
C A:HIS347 5.0 22.4 1.0
O A:HIS347 5.0 23.7 1.0

Iodine binding site 2 out of 11 in 7kem

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Iodine binding site 2 out of 11 in the Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:0.3
occ:0.00
I1 A:0JC502 0.0 0.3 0.0
N2 A:0JC502 0.7 52.6 0.0
PT1 A:0JC502 1.8 45.8 0.0
C2 A:0JC502 1.8 48.8 0.0
PT1 A:0JC502 2.7 0.9 0.0
N1 A:0JC502 2.8 51.1 0.0
C1 A:0JC502 2.8 48.9 0.0
SD A:MET157 3.0 35.6 0.5
CB A:MET157 3.2 27.2 0.5
CB A:ALA171 3.3 23.0 1.0
CB A:MET157 3.3 27.8 0.5
N1 A:0JC502 3.5 96.2 0.0
CG A:MET157 3.7 29.1 0.5
CG A:MET157 3.9 30.1 0.5
CE A:MET157 4.1 35.3 0.5
OE1 A:GLU207 4.3 23.4 1.0
NH2 A:ARG371 4.3 43.8 1.0
NH2 A:ARG209 4.3 22.1 1.0
I1 A:0JC502 4.4 79.7 0.0
CA A:MET157 4.6 24.9 0.5
CZ A:ARG209 4.6 21.9 1.0
CA A:MET157 4.6 25.1 0.5
N2 A:0JC502 4.7 94.0 0.0
NE A:ARG209 4.7 18.6 1.0
CA A:ALA171 4.7 21.3 1.0
C1 A:0JC502 4.7 93.9 0.0
OH A:TYR330 4.8 41.2 1.0
C A:MET157 4.9 24.8 0.5
C A:MET157 4.9 24.6 0.5

Iodine binding site 3 out of 11 in 7kem

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Iodine binding site 3 out of 11 in the Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:79.7
occ:0.00
I1 A:0JC502 0.0 79.7 0.0
CE A:MET157 2.5 35.3 0.5
PT1 A:0JC502 2.7 45.8 0.0
PT1 A:0JC502 3.5 0.9 0.0
N1 A:0JC502 3.6 51.1 0.0
SD A:MET157 3.8 35.6 0.5
NH2 A:ARG371 3.8 43.8 1.0
N2 A:0JC502 4.0 94.0 0.0
CZ A:ARG371 4.0 52.1 1.0
SD A:MET157 4.2 36.8 0.5
NE A:ARG371 4.2 48.7 1.0
I1 A:0JC502 4.4 0.3 0.0
CG A:MET157 4.5 30.1 0.5
NH1 A:ARG371 4.5 39.7 1.0
CG A:MET157 4.6 29.1 0.5
N2 A:0JC502 4.7 52.6 0.0
N1 A:0JC502 4.9 96.2 0.0
C2 A:0JC502 5.0 93.1 0.0

Iodine binding site 4 out of 11 in 7kem

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Iodine binding site 4 out of 11 in the Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:70.0
occ:0.00
I1 A:0JC503 0.0 70.0 0.0
PT1 A:0JC503 2.5 60.6 0.0
O A:GLU235 3.1 39.3 1.0
N1 A:0JC503 3.6 63.1 0.0
CG A:MET237 3.6 62.1 1.0
CE A:MET237 3.9 71.0 1.0
C A:GLU235 4.1 39.9 1.0
CB A:GLU235 4.3 49.6 1.0
N2 A:0JC503 4.5 63.6 0.0
N A:MET237 4.6 43.2 1.0
C1 A:0JC503 4.6 62.1 0.0
C A:GLY236 4.6 44.0 1.0
SD A:MET237 4.7 84.0 1.0
CB A:MET237 4.7 52.7 1.0
O A:GLY234 4.8 34.0 1.0
CA A:GLU235 4.8 43.9 1.0
O A:GLY236 4.9 41.1 1.0
N A:GLY236 5.0 39.8 1.0
CA A:MET237 5.0 46.2 1.0

Iodine binding site 5 out of 11 in 7kem

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Iodine binding site 5 out of 11 in the Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:0.5
occ:0.00
I1 A:0JC504 0.0 0.5 0.0
C2 A:0JC504 1.0 92.7 0.0
C1 A:0JC504 1.4 92.2 0.0
N2 A:0JC504 2.1 94.8 0.0
N1 A:0JC504 2.2 95.9 0.0
PT1 A:0JC504 2.7 0.6 0.0
PT1 A:0JC504 3.1 0.2 0.0
N A:PHE215 3.7 22.8 1.0
CD2 A:PHE215 3.7 22.4 1.0
N1 A:0JC504 3.7 90.2 0.0
CG A:PHE215 3.9 21.9 1.0
CB A:HIS214 4.0 29.0 1.0
CB A:PHE215 4.0 23.3 1.0
ND1 A:HIS214 4.1 39.3 1.0
CA A:HIS214 4.4 26.1 1.0
CE2 A:PHE215 4.4 24.4 1.0
CA A:PHE215 4.4 23.6 1.0
C A:HIS214 4.5 23.8 1.0
CG A:HIS214 4.6 38.8 1.0
CD1 A:PHE215 4.8 21.3 1.0
N2 A:0JC504 4.9 88.8 0.0

Iodine binding site 6 out of 11 in 7kem

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Iodine binding site 6 out of 11 in the Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:1.0
occ:0.00
I1 A:0JC504 0.0 1.0 0.0
C2 A:0JC504 0.7 87.4 0.0
C1 A:0JC504 0.9 87.0 0.0
N2 A:0JC504 2.0 88.8 0.0
N1 A:0JC504 2.1 90.2 0.0
PT1 A:0JC504 2.7 0.2 0.0
PT1 A:0JC504 3.1 0.6 0.0
N1 A:0JC504 3.7 95.9 0.0
CD1 A:ILE291 4.0 23.8 1.0
O A:TRP394 4.5 22.2 1.0
CE3 A:TRP394 4.5 23.4 1.0
O A:GLU213 4.7 27.9 1.0
N2 A:0JC504 4.8 94.8 0.0

Iodine binding site 7 out of 11 in 7kem

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Iodine binding site 7 out of 11 in the Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis


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Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I503

b:76.3
occ:0.00
I1 B:0JC503 0.0 76.3 0.0
PT1 B:0JC503 2.6 53.1 0.0
ND1 B:HIS347 3.2 33.2 1.0
N1 B:0JC503 3.5 59.4 0.0
CB B:HIS347 3.7 24.1 1.0
CG B:HIS347 3.8 27.5 1.0
CE1 B:HIS347 4.2 33.9 1.0
CA B:HIS347 4.5 22.9 1.0
N2 B:0JC503 4.7 57.7 0.0
O B:HIS347 4.8 20.2 1.0
C1 B:0JC503 5.0 57.5 0.0
CD2 B:HIS347 5.0 28.7 1.0
C B:HIS347 5.0 21.9 1.0

Iodine binding site 8 out of 11 in 7kem

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Iodine binding site 8 out of 11 in the Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I504

b:0.7
occ:0.00
I1 B:0JC504 0.0 0.7 0.0
PT1 B:0JC504 2.6 0.8 0.0
N1 B:0JC504 3.4 0.5 0.0
N B:PHE215 3.5 25.6 1.0
ND1 B:HIS214 3.6 40.2 1.0
CB B:HIS214 3.6 33.1 1.0
CA B:HIS214 3.8 29.4 1.0
CD2 B:PHE215 3.9 26.3 1.0
CG B:PHE215 4.0 26.2 1.0
CG B:HIS214 4.1 42.4 1.0
C B:HIS214 4.2 27.9 1.0
CB B:PHE215 4.3 25.5 1.0
CE2 B:PHE215 4.4 26.4 1.0
CA B:PHE215 4.5 24.6 1.0
CD1 B:PHE215 4.5 25.2 1.0
N2 B:0JC504 4.6 0.6 0.0
CE1 B:HIS214 4.7 46.8 1.0
C1 B:0JC504 4.8 0.3 0.0
CZ B:PHE215 4.9 25.3 1.0
CE1 B:PHE215 4.9 26.4 1.0

Iodine binding site 9 out of 11 in 7kem

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Iodine binding site 9 out of 11 in the Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I505

b:19.7
occ:0.00
I1 B:0JC505 0.0 19.7 0.0
PT1 B:0JC505 2.6 5.1 0.0
N2 B:0JC505 2.8 5.7 0.0
PT1 B:0JC505 3.5 54.2 0.0
N1 B:0JC505 3.5 33.1 0.0
C2 B:0JC505 3.8 36.2 0.0
CD B:ARG371 3.8 51.7 1.0
NE B:ARG371 3.8 57.7 1.0
SD B:MET157 3.9 63.6 1.0
OG B:SER296 4.2 30.8 1.0
CZ B:ARG371 4.2 67.3 1.0
CE B:MET157 4.3 54.2 1.0
CB B:LEU131 4.3 52.0 1.0
NH2 B:ARG371 4.6 71.6 1.0
N2 B:0JC505 4.7 25.5 0.0
N1 B:0JC505 4.7 59.0 0.0
C1 B:0JC505 4.8 31.3 0.0
NH1 B:ARG371 4.8 67.3 1.0

Iodine binding site 10 out of 11 in 7kem

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Iodine binding site 10 out of 11 in the Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I505

b:75.0
occ:0.00
I1 B:0JC505 0.0 75.0 0.0
NH1 B:ARG173 2.3 44.6 1.0
PT1 B:0JC505 2.7 54.2 0.0
CZ B:ARG173 3.1 59.9 1.0
CE B:MET157 3.3 54.2 1.0
CG B:MET157 3.4 42.6 1.0
N1 B:0JC505 3.4 59.0 0.0
N2 B:0JC505 3.6 25.5 0.0
OE1 B:GLU207 3.7 25.1 1.0
NE B:ARG173 3.7 54.0 1.0
SD B:MET157 3.9 63.6 1.0
PT1 B:0JC505 3.9 5.1 0.0
NH2 B:ARG173 3.9 57.9 1.0
CB B:ALA171 4.0 21.3 1.0
CB B:MET157 4.1 28.1 1.0
CD B:GLU207 4.3 26.4 1.0
OE2 B:GLU207 4.4 29.3 1.0
N2 B:0JC505 4.4 5.7 0.0
C2 B:0JC505 4.6 36.2 0.0
C1 B:0JC505 4.6 26.7 0.0
OH B:TYR330 4.7 30.1 1.0
CB B:ARG173 4.8 31.9 1.0
C1 B:0JC505 4.8 31.3 0.0

Reference:

G.A.Libreros, M.V.B.Dias. Crystallographic Structure of L,D-Transpeptidase 2 From Mycobacterium Tuberculosis. To Be Published.
Page generated: Sun Dec 13 20:04:03 2020

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