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Iodine in PDB 5ijw: Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction

Enzymatic activity of Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction

All present enzymatic activity of Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction:
5.1.1.3;

Protein crystallography data

The structure of Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction, PDB code: 5ijw was solved by S.Poen, Y.Nakatani, K.Krause, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.40 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.100, 90.100, 101.700, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.5

Iodine Binding Sites:

The binding sites of Iodine atom in the Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction (pdb code 5ijw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction, PDB code: 5ijw:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 5ijw

Go back to Iodine Binding Sites List in 5ijw
Iodine binding site 1 out of 3 in the Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:28.0
occ:0.28
 O A:HOH491 3.0 17.1 1.0
N A:GLN121 3.4 13.5 1.0
C A:GLY45 3.6 17.2 1.0
CB A:PRO147 3.6 17.3 1.0
O A:HOH643 3.7 19.3 1.0
CB A:GLN121 3.8 14.6 1.0
O A:GLY45 3.8 15.6 1.0
CA A:GLY45 3.8 16.3 1.0
CA A:PRO147 3.9 16.0 1.0
O A:HOH454 3.9 20.0 1.0
CB A:THR120 3.9 15.2 1.0
N A:PRO46 4.0 14.7 1.0
CG A:PRO147 4.1 17.1 1.0
CA A:THR120 4.2 13.5 1.0
CA A:GLN121 4.2 15.5 1.0
C A:THR120 4.3 14.0 1.0
CD A:PRO46 4.4 17.0 1.0
CG2 A:THR120 4.5 14.2 1.0
O A:PRO147 4.5 20.3 1.0
CA A:PRO46 4.5 17.6 1.0
O A:HOH520 4.6 24.8 1.0
C A:PRO147 4.7 15.2 1.0
CB A:PRO46 4.8 17.3 1.0
N A:PRO147 4.9 17.2 1.0

Iodine binding site 2 out of 3 in 5ijw

Go back to Iodine Binding Sites List in 5ijw
Iodine binding site 2 out of 3 in the Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:44.7
occ:0.33
 CB A:PRO261 3.2 39.4 1.0
NH1 B:ARG240 3.5 26.1 1.0
O B:HOH582 3.7 27.8 1.0
CD B:ARG240 3.8 19.2 1.0
CB B:ARG240 4.0 16.2 1.0
CG B:ARG240 4.2 18.1 1.0
CA A:PRO261 4.2 34.3 1.0
CG A:PRO261 4.3 38.7 1.0
CZ B:ARG240 4.5 22.8 1.0
NE B:ARG240 4.6 17.5 1.0
CE1 B:PHE242 4.6 20.1 1.0
CG2 A:VAL266 4.8 45.6 1.0

Iodine binding site 3 out of 3 in 5ijw

Go back to Iodine Binding Sites List in 5ijw
Iodine binding site 3 out of 3 in the Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Glutamate Racemase (Muri) From Mycobacterium Smegmatis with Bound D- Glutamate, 1.8 Angstrom Resolution, X-Ray Diffraction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:27.9
occ:0.32
 O A:HOH657 3.1 30.8 1.0
O A:HOH434 3.2 26.7 1.0
O A:ALA250 3.6 29.6 1.0
C A:ALA250 3.7 28.3 1.0
N A:PHE251 3.8 26.9 1.0
CB A:ALA250 3.8 28.2 1.0
CG2 A:THR39 3.9 19.3 1.0
CA A:PHE251 4.0 21.1 1.0
CG2 A:VAL15 4.1 22.0 1.0
CD2 A:LEU254 4.1 29.1 1.0
CB A:THR39 4.3 21.9 1.0
O A:HOH514 4.4 31.0 1.0
CA A:ALA250 4.4 28.9 1.0
CB A:LEU254 4.5 25.2 1.0
O A:HOH449 4.6 25.8 1.0
CB A:PHE251 4.8 23.9 1.0
O A:HOH607 4.8 39.1 1.0
OG1 A:THR39 4.9 21.7 1.0
CG A:LEU254 4.9 28.9 1.0

Reference:

S.Poen, Y.Nakatani, H.K.Opel-Reading, M.Lasse, R.C.Dobson, K.L.Krause. Exploring the Structure of Glutamate Racemase From Mycobacterium Tuberculosis As A Template For Anti-Mycobacterial Drug Discovery. Biochem. J. V. 473 1267 2016.
ISSN: ESSN 1470-8728
PubMed: 26964898
DOI: 10.1042/BCJ20160186
Page generated: Sun Dec 13 19:39:30 2020

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