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Iodine in PDB 2af6: Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump):
2.1.1.148;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump), PDB code: 2af6 was solved by P.Sampathkumar, S.Turley, J.E.Ulmer, H.G.Rhie, C.H.Sibley, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.95 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.090, 78.300, 168.720, 90.00, 96.80, 90.00
R / Rfree (%) 19.5 / 24.3

Other elements in 2af6:

The structure of Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) also contains other interesting chemical elements:

Bromine (Br) 8 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) (pdb code 2af6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump), PDB code: 2af6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 2af6

Go back to Iodine Binding Sites List in 2af6
Iodine binding site 1 out of 10 in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)


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 Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I3001

b:42.0
occ:0.30
 O A:HOH4737 2.9 30.1 1.0
O A:HOH4723 3.2 22.7 1.0
CB A:ALA247 3.3 35.6 1.0
O A:HOH4724 3.7 31.1 1.0
O A:ARG193 3.8 12.7 1.0
C A:ARG193 3.9 12.2 1.0
N A:HIS194 4.0 12.1 1.0
CB A:ARG193 4.0 12.2 1.0
CA A:HIS194 4.1 12.3 1.0
CB A:ALA197 4.3 15.5 1.0
CA A:ALA247 4.3 35.9 1.0
NE A:ARG193 4.4 19.0 1.0
NH2 A:ARG193 4.5 19.9 1.0
O A:HOH4729 4.5 35.1 1.0
O A:LEU246 4.6 35.8 1.0
CA A:ARG193 4.6 12.4 1.0
CZ A:PHE230 4.7 25.1 1.0
O A:HOH4732 4.8 44.4 1.0
CB A:HIS194 4.8 13.2 1.0
O A:HOH4728 4.8 27.0 1.0
CZ A:ARG193 4.8 20.8 1.0

Iodine binding site 2 out of 10 in 2af6

Go back to Iodine Binding Sites List in 2af6
Iodine binding site 2 out of 10 in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)


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 Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I3008

b:34.2
occ:0.40
 OG1 A:THR4 3.3 28.3 1.0
N A:PRO6 4.0 23.2 1.0
CB A:THR4 4.1 27.9 1.0
CB A:PRO6 4.1 22.6 1.0
O A:HOH4660 4.1 26.2 1.0
C A:ALA5 4.3 24.1 1.0
CD A:PRO6 4.3 23.6 1.0
O A:THR4 4.3 26.7 1.0
CA A:PRO6 4.3 22.5 1.0
C A:THR4 4.3 27.1 1.0
N A:ALA5 4.5 25.9 1.0
CG A:PRO6 4.6 23.0 1.0
O A:ALA5 4.6 24.1 1.0
CA A:ALA5 4.8 24.7 1.0
CA A:THR4 4.8 27.9 1.0

Iodine binding site 3 out of 10 in 2af6

Go back to Iodine Binding Sites List in 2af6
Iodine binding site 3 out of 10 in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)


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 Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I3009

b:20.2
occ:0.40
 OG1 C:THR4 3.2 27.9 1.0
N C:THR4 3.6 27.4 1.0
CA C:GLU3 4.3 29.2 1.0
CB C:THR4 4.3 27.2 1.0
O C:THR4 4.4 26.1 1.0
CA C:THR4 4.4 26.9 1.0
C C:GLU3 4.5 28.4 1.0
CG2 C:THR4 4.8 27.4 1.0
CB C:GLU3 4.8 29.7 1.0
C C:THR4 4.8 26.3 1.0

Iodine binding site 4 out of 10 in 2af6

Go back to Iodine Binding Sites List in 2af6
Iodine binding site 4 out of 10 in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)


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 Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I3002

b:49.2
occ:0.30
 O3 D:GOL2012 3.2 27.7 0.5
C3 D:GOL2012 3.2 26.9 0.5
N D:SER71 3.3 21.9 1.0
CB D:SER71 3.6 20.7 1.0
O1P C:FAD2600 3.6 23.8 1.0
N D:PHE70 3.7 26.9 1.0
O2' C:FAD2600 3.7 17.4 1.0
CE C:MSE198 3.8 23.3 0.3
OG D:SER71 3.9 22.9 1.0
O D:GLY68 3.9 32.7 1.0
NH2 D:ARG190 4.0 16.2 1.0
CA D:SER71 4.0 20.5 1.0
C2' C:FAD2600 4.1 15.0 1.0
C D:HIS69 4.2 28.5 1.0
C D:PHE70 4.2 23.4 1.0
C3' C:FAD2600 4.2 16.6 1.0
CA D:PHE70 4.3 25.2 1.0
NH1 D:ARG190 4.4 13.7 1.0
CZ D:ARG190 4.4 16.7 1.0
CA D:HIS69 4.4 29.6 0.5
P C:FAD2600 4.6 20.3 1.0
CB D:PHE70 4.6 25.6 1.0
SE C:MSE198 4.6 24.9 0.3
O2P C:FAD2600 4.7 24.5 1.0
C2 D:GOL2012 4.7 26.8 0.5
O5' C:FAD2600 4.9 21.4 1.0
O D:HIS69 5.0 28.6 1.0
C D:GLY68 5.0 32.5 1.0
O4' C:FAD2600 5.0 19.4 1.0

Iodine binding site 5 out of 10 in 2af6

Go back to Iodine Binding Sites List in 2af6
Iodine binding site 5 out of 10 in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)


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 Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I3004

b:66.7
occ:0.30
 O D:HOH3123 2.2 21.4 1.0
O D:HOH3122 2.2 15.8 1.0
CG1 D:VAL222 2.5 28.4 1.0
O D:HOH3124 2.7 32.5 1.0
OH D:TYR189 3.0 15.1 1.0
CB D:LYS14 3.9 18.2 1.0
CB D:VAL222 4.0 27.7 1.0
N D:GLY32 4.1 16.9 1.0
CD D:LYS14 4.1 22.7 1.0
CZ D:TYR189 4.1 14.2 1.0
CA D:GLY32 4.3 16.3 1.0
CG D:LYS14 4.3 19.7 1.0
O D:VAL222 4.3 28.3 1.0
CD D:PRO33 4.3 15.1 1.0
CG2 D:VAL78 4.4 14.6 1.0
CE1 D:TYR189 4.4 15.3 1.0
O D:HOH3114 4.5 35.1 1.0
CE D:LYS14 4.5 23.4 1.0
CG2 D:VAL222 4.6 27.6 1.0
C D:VAL222 4.7 27.3 1.0
N D:THR15 4.7 18.6 1.0
O D:THR15 4.9 20.0 1.0
CA D:VAL222 4.9 27.4 1.0
O D:SER77 4.9 15.7 1.0

Iodine binding site 6 out of 10 in 2af6

Go back to Iodine Binding Sites List in 2af6
Iodine binding site 6 out of 10 in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)


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 Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I3006

b:37.0
occ:0.40
 CG2 E:VAL23 3.0 28.6 1.0
O E:HOH8710 3.2 29.9 1.0
NE2 G:GLN10 3.5 20.6 1.0
N E:VAL23 3.9 30.2 1.0
C E:ASP22 3.9 31.0 1.0
CE2 G:TYR81 4.0 16.7 1.0
O G:HOH6701 4.0 35.9 1.0
O E:ASP22 4.1 31.5 1.0
CB E:ASP22 4.1 31.7 1.0
CB E:VAL23 4.2 29.2 1.0
CA E:VAL23 4.2 29.2 1.0
CD2 G:TYR81 4.4 15.4 1.0
CB E:PRO20 4.4 28.0 1.0
CA E:ASP22 4.5 31.6 1.0
CD G:GLN10 4.6 22.5 1.0
N E:ASP22 4.8 31.1 1.0
OE1 G:GLN10 4.9 24.2 1.0
O G:HOH6639 4.9 17.2 1.0

Iodine binding site 7 out of 10 in 2af6

Go back to Iodine Binding Sites List in 2af6
Iodine binding site 7 out of 10 in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)


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 Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I3007

b:16.5
occ:0.40
 OG1 E:THR4 3.3 27.2 1.0
N E:THR4 3.6 27.1 1.0
CB E:THR4 4.2 26.7 1.0
CA E:GLU3 4.3 28.9 1.0
CA E:THR4 4.4 26.5 1.0
C E:GLU3 4.4 28.0 1.0
O E:THR4 4.5 25.6 1.0
CG2 E:THR4 4.5 26.5 1.0
CB E:GLU3 4.9 29.4 1.0
C E:THR4 4.9 25.9 1.0

Iodine binding site 8 out of 10 in 2af6

Go back to Iodine Binding Sites List in 2af6
Iodine binding site 8 out of 10 in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)


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 Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I3005

b:38.5
occ:0.50
 O F:HOH7704 1.9 25.3 1.0
OH F:TYR189 2.9 13.7 1.0
CG1 F:VAL222 3.4 28.7 1.0
CB F:LYS14 3.6 18.6 1.0
N F:GLY32 3.6 16.5 1.0
N F:THR15 3.7 20.0 1.0
O F:HOH7678 3.7 29.8 1.0
CA F:GLY32 3.7 16.2 1.0
CZ F:TYR189 3.9 14.8 1.0
CG F:LYS14 4.1 20.6 1.0
CE1 F:TYR189 4.2 13.0 1.0
O F:THR15 4.2 20.9 1.0
CB F:THR15 4.3 20.3 1.0
CD F:PRO33 4.4 15.9 1.0
CG2 F:VAL78 4.4 14.8 1.0
O F:SER77 4.4 14.9 1.0
CA F:LYS14 4.4 18.7 1.0
CD F:LYS14 4.5 23.6 1.0
CA F:THR15 4.5 20.3 1.0
C F:LYS14 4.6 19.3 1.0
OG1 F:THR15 4.8 21.0 1.0
C F:THR15 4.8 21.0 1.0
C F:GLY32 4.9 15.9 1.0
C F:GLY31 4.9 17.3 1.0
CE F:LYS14 4.9 24.3 1.0
CB F:VAL222 4.9 27.8 1.0

Iodine binding site 9 out of 10 in 2af6

Go back to Iodine Binding Sites List in 2af6
Iodine binding site 9 out of 10 in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)


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 Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I3010

b:45.8
occ:0.40
 O3 F:GOL2014 0.7 25.2 0.6
C3 F:GOL2014 1.5 24.3 0.6
O F:HOH7707 1.7 15.1 0.4
C2 F:GOL2014 2.8 25.8 0.6
OG1 F:THR54 2.9 35.9 1.0
O2 F:GOL2014 3.3 26.2 0.6
NH2 F:ARG41 3.4 23.3 1.0
C1 F:GOL2014 3.5 27.1 0.6
O F:THR54 3.6 34.6 1.0
CD F:PRO50 3.6 35.5 1.0
CA F:LYS49 3.9 31.2 1.0
O1 F:GOL2014 3.9 26.9 0.6
C F:THR54 3.9 34.8 1.0
CB F:THR54 3.9 35.7 1.0
NH1 F:ARG41 4.0 22.6 1.0
O F:ASN51 4.0 40.0 1.0
N F:ASN51 4.1 38.9 1.0
O F:SER48 4.1 29.2 1.0
N F:PRO50 4.1 35.0 1.0
CZ F:ARG41 4.1 22.6 1.0
C F:LYS49 4.2 32.7 1.0
CB F:ASN51 4.3 40.4 1.0
N F:ALA55 4.4 33.5 1.0
CG F:PRO50 4.5 36.6 1.0
CB F:LYS49 4.5 30.6 1.0
CA F:THR54 4.5 35.4 1.0
O F:HOH7645 4.6 28.5 1.0
CA F:ASN51 4.6 39.9 1.0
CA F:ALA55 4.7 32.5 1.0
C F:ASN51 4.8 40.1 1.0
CG F:LYS49 4.8 30.2 1.0
N F:LYS49 4.9 29.8 1.0
CD1 F:TYR60 4.9 25.9 1.0
C F:SER48 4.9 29.3 1.0

Iodine binding site 10 out of 10 in 2af6

Go back to Iodine Binding Sites List in 2af6
Iodine binding site 10 out of 10 in the Crystal Structure of Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump)


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 Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtb Thyx) in the Presence of Co-Factor Fad and Substrate Analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (Brdump) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:I3003

b:64.9
occ:0.30
 O G:HOH6715 2.8 38.3 1.0
OG1 G:THR54 3.6 37.5 1.0
NH1 G:ARG41 3.9 24.7 1.0
CD G:PRO50 4.2 38.8 1.0
NH2 G:ARG41 4.5 25.1 1.0
O G:SER48 4.5 34.0 1.0
O G:HOH6709 4.6 21.8 1.0
CE1 G:TYR60 4.6 25.9 1.0
CZ G:ARG41 4.6 24.1 1.0
CB G:THR54 4.7 37.3 1.0
CG G:PRO50 4.7 39.5 1.0
OG G:SER46 4.8 27.4 1.0
CB G:ASN51 5.0 42.3 1.0
CD1 G:TYR60 5.0 25.0 1.0

Reference:

P.Sampathkumar, S.Turley, J.E.Ulmer, H.G.Rhie, C.H.Sibley, W.G.Hol. Structure of the Mycobacterium Tuberculosis Flavin Dependent Thymidylate Synthase (Mtbthyx) at 2.0A Resolution. J.Mol.Biol. V. 352 1091 2005.
ISSN: ISSN 0022-2836
PubMed: 16139296
DOI: 10.1016/J.JMB.2005.07.071
Page generated: Sun Aug 11 13:11:21 2024

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