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Iodine in PDB 7nnw: Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.:
2.1.3.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate., PDB code: 7nnw was solved by V.Mendes, P.Gupta, A.Burgess, V.Sebastian-Perez, E.Cattermole, C.Meghir, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.80 / 1.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.802, 143.512, 97.524, 90, 117.69, 90
R / Rfree (%) 18.1 / 20.6

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. (pdb code 7nnw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate., PDB code: 7nnw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 7nnw

Go back to Iodine Binding Sites List in 7nnw
Iodine binding site 1 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.


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 Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I402

b:106.0
occ:1.00
 I11 B:98T402 0.0 106.0 1.0
C10 B:98T402 2.1 75.4 1.0
C08 B:98T402 3.1 71.4 1.0
C12 B:98T402 3.2 66.3 1.0
O09 B:98T402 3.2 75.9 1.0
CD1 B:ILE45 3.8 36.7 1.0
CG B:LEU78 3.9 63.8 1.0
CG2 A:THR51 4.1 46.4 1.0
CD1 B:LEU78 4.2 54.0 1.0
CG2 B:THR87 4.3 48.3 1.0
CG1 B:ILE45 4.4 32.2 1.0
C07 B:98T402 4.4 68.9 1.0
CG2 B:ILE45 4.5 33.9 1.0
C05 B:98T402 4.5 55.7 1.0
CE1 A:PHE55 4.6 33.0 1.0
CD2 B:LEU78 4.7 68.6 1.0
CG1 B:VAL71 4.8 41.4 1.0
CG2 B:VAL71 4.9 43.1 1.0
CB B:LEU78 4.9 67.7 1.0
CD1 B:LEU91 4.9 40.3 1.0
CD2 B:LEU91 5.0 40.3 1.0
C06 B:98T402 5.0 65.6 1.0

Iodine binding site 2 out of 6 in 7nnw

Go back to Iodine Binding Sites List in 7nnw
Iodine binding site 2 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.


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 Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I703

b:76.1
occ:1.00
 I11 C:98T703 0.0 76.1 1.0
C10 C:98T703 2.1 43.6 1.0
O C:HOH991 2.9 53.3 1.0
C08 C:98T703 3.0 52.8 1.0
O09 C:98T703 3.1 60.0 1.0
C12 C:98T703 3.1 41.2 1.0
CD2 A:LEU78 3.8 60.2 1.0
CD1 A:ILE45 3.8 32.0 1.0
CG1 A:ILE45 3.9 32.2 1.0
C07 C:98T703 4.3 51.4 1.0
CG2 A:VAL71 4.3 32.5 1.0
CG1 A:VAL71 4.4 40.8 1.0
CG2 A:ILE45 4.4 29.6 1.0
CE1 C:PHE55 4.4 41.0 1.0
C05 C:98T703 4.4 39.4 1.0
CD1 A:LEU78 4.5 50.3 1.0
CB A:VAL71 4.5 34.2 1.0
CG A:LEU78 4.5 61.9 1.0
CG2 C:THR51 4.5 37.4 1.0
CD1 A:LEU91 4.6 29.6 1.0
CG2 A:THR87 4.6 35.4 1.0
CD2 A:LEU91 4.7 33.3 1.0
CB A:ILE45 4.8 28.1 1.0
C06 C:98T703 4.9 52.8 1.0
CZ C:PHE55 4.9 36.5 1.0
CG A:LEU91 5.0 33.8 1.0

Iodine binding site 3 out of 6 in 7nnw

Go back to Iodine Binding Sites List in 7nnw
Iodine binding site 3 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.


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 Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I704

b:94.6
occ:1.00
 I11 C:98T704 0.0 94.6 1.0
C10 C:98T704 2.1 55.9 1.0
C08 C:98T704 3.0 60.2 1.0
C12 C:98T704 3.1 50.5 1.0
O09 C:98T704 3.2 59.4 1.0
CD1 C:LEU78 3.6 60.3 1.0
CD1 C:ILE45 3.8 35.2 1.0
CG1 C:ILE45 4.1 29.7 1.0
CG2 B:THR51 4.2 49.7 1.0
CE1 B:PHE55 4.3 48.8 1.0
CG2 C:ILE45 4.3 33.4 1.0
CD2 C:LEU78 4.3 50.5 1.0
CG2 C:VAL71 4.3 38.8 1.0
C07 C:98T704 4.3 54.8 1.0
CG C:LEU78 4.4 52.2 1.0
C05 C:98T704 4.4 49.4 1.0
CD2 C:LEU91 4.5 41.9 1.0
CD1 C:LEU91 4.5 37.3 1.0
CG2 C:THR87 4.6 43.4 1.0
CZ B:PHE55 4.7 41.6 1.0
CG1 C:VAL71 4.8 41.9 1.0
CB C:VAL71 4.8 36.4 1.0
CG C:LEU91 4.8 37.0 1.0
CB C:ILE45 4.9 31.6 1.0
C06 C:98T704 4.9 56.9 1.0

Iodine binding site 4 out of 6 in 7nnw

Go back to Iodine Binding Sites List in 7nnw
Iodine binding site 4 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.


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 Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I502

b:72.5
occ:1.00
 I11 D:98T502 0.0 72.5 1.0
C10 D:98T502 2.1 47.5 1.0
C08 D:98T502 3.0 53.0 1.0
O09 D:98T502 3.1 52.9 1.0
C12 D:98T502 3.2 45.7 1.0
CD1 E:ILE45 3.6 31.8 1.0
CD2 E:LEU78 3.9 61.4 1.0
CG1 E:ILE45 3.9 30.9 1.0
C07 D:98T502 4.3 51.7 1.0
CG2 E:VAL71 4.3 36.7 1.0
CD1 E:LEU78 4.4 54.9 1.0
CG1 E:VAL71 4.4 39.8 1.0
CG E:LEU78 4.4 59.2 1.0
CG2 D:THR51 4.5 42.3 1.0
CE1 D:PHE55 4.5 36.5 1.0
C05 D:98T502 4.5 43.8 1.0
CG2 E:ILE45 4.5 27.5 1.0
CD1 E:LEU91 4.5 35.4 1.0
CB E:VAL71 4.6 36.6 1.0
CG2 E:THR87 4.7 42.4 1.0
CD2 E:LEU91 4.8 36.3 1.0
CB E:ILE45 4.9 28.3 1.0
C06 D:98T502 4.9 47.5 1.0
CZ D:PHE55 4.9 31.2 1.0
CG E:LEU91 5.0 32.7 1.0

Iodine binding site 5 out of 6 in 7nnw

Go back to Iodine Binding Sites List in 7nnw
Iodine binding site 5 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.


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 Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I503

b:101.5
occ:1.00
 I11 D:98T503 0.0 101.5 1.0
C10 D:98T503 2.1 57.3 1.0
O D:HOH805 2.8 52.2 1.0
C08 D:98T503 3.0 60.0 1.0
C12 D:98T503 3.0 48.2 1.0
O09 D:98T503 3.1 52.2 1.0
CD1 D:ILE45 3.7 40.3 1.0
CD1 D:LEU78 3.8 61.5 1.0
CG1 D:ILE45 4.0 40.3 1.0
CG2 D:THR87 4.3 47.3 1.0
CD2 D:LEU91 4.3 38.0 1.0
C07 D:98T503 4.3 54.2 1.0
C05 D:98T503 4.4 40.0 1.0
CG2 D:VAL71 4.4 40.1 1.0
CD1 D:LEU91 4.4 33.8 1.0
CG2 F:THR51 4.5 44.1 1.0
CE1 F:PHE55 4.5 41.8 1.0
CG2 D:ILE45 4.5 36.9 1.0
CG D:LEU91 4.7 36.5 1.0
CG D:LEU78 4.8 56.2 1.0
CB D:VAL71 4.8 44.0 1.0
C06 D:98T503 4.8 54.9 1.0
CG1 D:VAL71 4.9 46.7 1.0
CB D:ILE45 4.9 34.6 1.0
CD2 D:LEU78 4.9 59.9 1.0

Iodine binding site 6 out of 6 in 7nnw

Go back to Iodine Binding Sites List in 7nnw
Iodine binding site 6 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate.


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 Mycobacterium Tuberculosis Argf in Complex with Methyl 4-Hydroxy-3-Iodobenzoate. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I402

b:86.4
occ:1.00
 I11 E:98T402 0.0 86.4 1.0
C10 E:98T402 2.1 45.0 1.0
C08 E:98T402 3.0 50.9 1.0
C12 E:98T402 3.1 39.2 1.0
O09 E:98T402 3.2 59.4 1.0
CD1 F:LEU78 3.5 61.7 1.0
CD1 F:ILE45 3.8 31.3 1.0
CG1 F:ILE45 4.0 31.0 1.0
CG2 F:VAL71 4.2 37.1 1.0
CG F:LEU78 4.4 53.8 1.0
C07 E:98T402 4.4 53.9 1.0
CD2 F:LEU78 4.4 45.9 1.0
C05 E:98T402 4.5 36.7 1.0
CG2 F:ILE45 4.5 30.8 1.0
CG2 E:THR51 4.5 37.3 1.0
CG1 F:VAL71 4.5 39.6 1.0
CE2 E:PHE55 4.6 40.5 1.0
CB F:VAL71 4.6 35.5 1.0
CD2 F:LEU91 4.6 31.2 1.0
CD1 F:LEU91 4.6 28.3 1.0
CG2 F:THR87 4.7 39.2 1.0
CB F:ILE45 4.9 28.4 1.0
C06 E:98T402 4.9 50.9 1.0
CG F:LEU91 5.0 28.9 1.0

Reference:

P.Gupta, S.E.Thomas, S.A.Zaidan, M.A.Pasillas, J.Cory-Wright, V.Sebastian-Perez, A.Burgess, E.Cattermole, C.Meghir, C.Abell, A.G.Coyne, W.R.Jacobs, T.L.Blundell, S.Tiwari, V.Mendes. A Fragment-Based Approach to Assess the Ligandability of Argb, Argc, Argd and Argf in the L-Arginine Biosynthetic Pathway of Mycobacterium Tuberculosis Comput Struct Biotechnol J V. 19 3491 2021.
ISSN: ESSN 2001-0370
DOI: 10.1016/J.CSBJ.2021.06.006
Page generated: Mon Aug 12 01:49:32 2024

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