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Iodine in PDB 3da8: Crystal Structure of Purn From Mycobacterium Tuberculosis

Enzymatic activity of Crystal Structure of Purn From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of Purn From Mycobacterium Tuberculosis:
2.1.2.2;

Protein crystallography data

The structure of Crystal Structure of Purn From Mycobacterium Tuberculosis, PDB code: 3da8 was solved by Z.Zhang, C.J.Squire, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.69 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.273, 73.366, 77.246, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 18.6

Other elements in 3da8:

The structure of Crystal Structure of Purn From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Purn From Mycobacterium Tuberculosis (pdb code 3da8). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of Purn From Mycobacterium Tuberculosis, PDB code: 3da8:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 3da8

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Iodine binding site 1 out of 9 in the Crystal Structure of Purn From Mycobacterium Tuberculosis


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 Purn From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I602

b:12.2
occ:1.00
 N A:PRO165 3.9 8.4 1.0
CD A:PRO165 3.9 9.1 1.0
CB A:PRO163 4.1 7.2 1.0
C A:VAL164 4.1 8.4 1.0
CB A:PRO165 4.2 9.5 1.0
CA A:PRO165 4.2 8.3 1.0
N A:VAL164 4.3 7.6 1.0
CG A:PRO163 4.4 8.8 1.0
CG2 A:VAL141 4.4 7.2 1.0
C A:PRO163 4.4 7.0 1.0
CG A:PRO165 4.5 10.0 1.0
CG1 A:VAL141 4.5 7.6 1.0
CA A:VAL164 4.5 8.5 1.0
O A:PRO163 4.6 7.9 1.0
O A:VAL164 4.6 7.8 1.0
CA A:PRO163 4.9 6.7 1.0

Iodine binding site 2 out of 9 in 3da8

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Iodine binding site 2 out of 9 in the Crystal Structure of Purn From Mycobacterium Tuberculosis


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 Purn From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I603

b:12.1
occ:1.00
 O A:HOH615 3.3 13.6 1.0
O A:HOH661 3.3 19.4 1.0
O A:HOH620 3.5 10.0 1.0
N A:LEU26 3.7 9.7 1.0
CB A:ALA19 3.9 9.3 1.0
CA A:GLY23 3.9 11.9 1.0
CB A:LEU25 4.0 12.2 1.0
CB A:LEU26 4.1 9.8 1.0
CA A:GLY97 4.1 10.3 1.0
CG1 A:VAL17 4.3 8.9 1.0
N A:LEU25 4.3 11.0 1.0
C A:GLY23 4.3 11.7 1.0
CA A:LEU26 4.4 9.7 1.0
N A:GLY97 4.4 10.3 1.0
C A:LEU25 4.5 10.5 1.0
CA A:LEU25 4.5 11.2 1.0
N A:GLY23 4.6 12.1 1.0
CA A:ALA19 4.7 8.0 1.0
O A:GLY23 4.8 11.1 1.0
N A:SER24 4.8 12.2 1.0
CG A:LEU25 4.8 13.6 1.0
CD2 A:LEU25 4.8 15.9 1.0
O A:LEU18 4.8 7.8 1.0
C A:GLY97 5.0 9.5 1.0
O A:HOH815 5.0 28.3 1.0

Iodine binding site 3 out of 9 in 3da8

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Iodine binding site 3 out of 9 in the Crystal Structure of Purn 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 Crystal Structure of Purn From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I606

b:12.5
occ:0.50
 OE1 A:GLU177 1.3 12.3 0.5
CD A:GLU177 1.4 9.4 0.5
OE2 A:GLU177 1.5 9.1 0.5
CG A:GLU177 3.0 8.0 0.5
O A:HOH714 3.3 14.0 1.0
CB A:GLU177 3.8 7.7 0.5
C A:GLU177 3.9 9.0 1.0
N A:ARG178 3.9 8.7 1.0
O A:GLU177 3.9 10.3 1.0
CA A:ARG178 4.0 8.9 1.0
CG2 A:VAL181 4.3 11.0 1.0
CA A:GLU177 4.5 8.8 1.0
CB A:ARG178 4.6 9.2 1.0
O A:HOH718 4.7 21.9 1.0
O A:HOH733 4.8 19.4 1.0
O A:HOH753 4.8 31.5 1.0

Iodine binding site 4 out of 9 in 3da8

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Iodine binding site 4 out of 9 in the Crystal Structure of Purn From Mycobacterium Tuberculosis


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 Purn From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I609

b:16.4
occ:0.33
 O A:HOH739 2.9 18.2 1.0
C A:GLY215 3.3 15.7 1.0
O A:GLY215 3.3 17.0 1.0
CA A:GLY215 3.9 15.2 1.0
CB A:THR213 4.0 5.9 1.0
CG2 A:THR213 4.0 6.7 1.0
OG1 A:THR213 4.1 8.4 1.0

Iodine binding site 5 out of 9 in 3da8

Go back to Iodine Binding Sites List in 3da8
Iodine binding site 5 out of 9 in the Crystal Structure of Purn From Mycobacterium Tuberculosis


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 Purn From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:18.2
occ:0.50
 O A:HOH814 2.9 19.6 1.0
CB A:ALA69 4.0 8.8 1.0
CA A:ALA69 4.0 7.9 1.0
N A:ALA69 4.2 8.2 1.0
CB A:LEU68 4.6 10.5 1.0
C A:LEU68 4.6 8.4 1.0
O A:HOH700 4.6 10.6 1.0
O A:LEU68 5.0 8.8 1.0

Iodine binding site 6 out of 9 in 3da8

Go back to Iodine Binding Sites List in 3da8
Iodine binding site 6 out of 9 in the Crystal Structure of Purn From Mycobacterium Tuberculosis


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 Purn From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I604

b:11.3
occ:1.00
 N B:PRO165 3.9 7.5 1.0
CD B:PRO165 3.9 8.9 1.0
CB B:PRO163 4.1 6.9 1.0
C B:VAL164 4.2 7.6 1.0
CB B:PRO165 4.2 9.1 1.0
CA B:PRO165 4.2 8.2 1.0
CG2 B:VAL141 4.3 5.7 1.0
N B:VAL164 4.3 7.5 1.0
CG B:PRO163 4.4 7.0 1.0
C B:PRO163 4.4 7.5 1.0
CG1 B:VAL141 4.5 6.1 1.0
CG B:PRO165 4.6 9.2 1.0
CA B:VAL164 4.6 8.2 1.0
O B:PRO163 4.7 8.4 1.0
O B:VAL164 4.7 7.5 1.0
CA B:PRO163 4.9 6.8 1.0
CB B:VAL141 5.0 5.3 1.0

Iodine binding site 7 out of 9 in 3da8

Go back to Iodine Binding Sites List in 3da8
Iodine binding site 7 out of 9 in the Crystal Structure of Purn From Mycobacterium Tuberculosis


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 Purn From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I605

b:11.5
occ:1.00
 O B:HOH611 3.4 11.2 1.0
O B:HOH615 3.5 9.2 1.0
O B:HOH775 3.6 27.5 1.0
N B:LEU26 3.7 9.6 1.0
CB B:LEU25 4.0 12.8 1.0
CB B:ALA19 4.0 8.8 1.0
CA B:GLY23 4.0 9.5 1.0
CB B:LEU26 4.0 9.7 1.0
CA B:GLY97 4.1 9.1 1.0
CA B:LEU26 4.4 8.8 1.0
CD2 B:LEU25 4.4 16.8 1.0
CG1 B:VAL17 4.4 8.8 1.0
N B:GLY97 4.4 9.2 1.0
C B:GLY23 4.4 9.9 1.0
N B:LEU25 4.5 11.4 1.0
CG B:LEU25 4.5 15.0 1.0
C B:LEU25 4.5 10.5 1.0
CA B:LEU25 4.6 11.4 1.0
N B:GLY23 4.6 9.2 1.0
CA B:ALA19 4.8 7.3 1.0
O B:GLY23 4.8 10.1 1.0
N B:SER24 4.9 11.6 1.0
C B:GLY97 5.0 7.9 1.0
O B:LEU18 5.0 7.6 1.0

Iodine binding site 8 out of 9 in 3da8

Go back to Iodine Binding Sites List in 3da8
Iodine binding site 8 out of 9 in the Crystal Structure of Purn 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 Crystal Structure of Purn From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I608

b:25.9
occ:0.33
 O B:HOH692 3.9 27.1 1.0
C B:ALA189 4.0 8.9 1.0
O B:ALA189 4.0 9.4 1.0
N B:ALA190 4.0 8.5 1.0
CA B:ALA190 4.0 8.7 1.0
CB B:ALA160 4.1 8.6 1.0
CB B:ALA189 4.1 9.8 1.0
CB B:ALA193 4.4 10.0 1.0
O B:HOH809 4.4 20.6 1.0
CB B:ALA190 4.5 9.6 1.0
O B:HOH657 4.6 16.0 1.0
CA B:ALA189 4.7 9.2 1.0

Iodine binding site 9 out of 9 in 3da8

Go back to Iodine Binding Sites List in 3da8
Iodine binding site 9 out of 9 in the Crystal Structure of Purn 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 Crystal Structure of Purn From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I610

b:22.6
occ:0.33
 N B:ARG51 3.6 10.3 1.0
C B:GLY21 3.8 8.9 1.0
O B:GLY21 3.8 9.4 1.0
O B:HOH648 4.0 18.9 1.0
CA B:CYS50 4.1 11.1 1.0
N B:THR22 4.1 9.7 1.0
CB B:CYS50 4.1 10.8 1.0
CG2 B:THR22 4.2 14.5 1.0
CB B:ARG51 4.2 10.9 1.0
CA B:THR22 4.3 10.7 1.0
CA B:GLY21 4.3 9.2 1.0
C B:CYS50 4.4 10.5 1.0
CA B:ARG51 4.5 10.3 1.0
CB B:THR22 4.9 12.1 1.0

Reference:

Z.Zhang, T.T.Caradoc-Davies, J.M.Dickson, E.N.Baker, C.J.Squire. Structures of Glycinamide Ribonucleotide Transformylase (Purn) From Mycobacterium Tuberculosis Reveal A Novel Dimer with Relevance to Drug Discovery. J.Mol.Biol. V. 389 722 2009.
ISSN: ISSN 0022-2836
PubMed: 19394344
DOI: 10.1016/J.JMB.2009.04.044
Page generated: Sun Dec 13 19:26:50 2020

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