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Iron in PDB 6ovt: Crystal Structure of Ilvd From Mycobacterium Tuberculosis

Enzymatic activity of Crystal Structure of Ilvd From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of Ilvd From Mycobacterium Tuberculosis:
4.2.1.9;

Protein crystallography data

The structure of Crystal Structure of Ilvd From Mycobacterium Tuberculosis, PDB code: 6ovt was solved by S.C.Almo, T.L.Grove, J.B.Bonanno, E.N.Baker, G.Bashiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.55 / 1.88
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 88.406, 88.406, 483.307, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 20.1

Other elements in 6ovt:

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

Magnesium (Mg) 12 atoms
Sodium (Na) 1 atom

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 6ovt

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Iron binding site 1 out of 8 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:21.7
occ:1.00
 FE1 A:FES602 0.0 21.7 1.0
S1 A:FES602 2.2 22.1 1.0
S2 A:FES602 2.2 24.3 1.0
SG A:CYS137 2.3 21.4 1.0
SG A:CYS64 2.4 23.2 1.0
FE2 A:FES602 2.7 23.8 1.0
CB A:CYS137 3.3 19.8 1.0
CB A:CYS64 3.4 21.2 1.0
CA A:CYS137 3.5 20.7 1.0
N A:ASP138 4.1 19.4 1.0
OG1 A:THR62 4.2 23.3 1.0
O A:HOH861 4.2 27.8 1.0
C A:CYS137 4.3 20.7 1.0
SG A:CYS214 4.4 22.6 1.0
N A:ASP96 4.6 19.3 1.0
N A:CYS137 4.7 19.9 1.0
CE C:MET36 4.7 27.1 1.0
CA A:CYS64 4.7 21.9 1.0
CG2 A:THR62 4.8 24.6 1.0
OG A:SER95 4.8 20.6 1.0
OD1 A:ASP138 4.8 22.6 1.0
CA A:SER95 4.9 19.4 1.0
O A:HOH867 4.9 19.0 1.0
CG A:ASP138 4.9 24.8 1.0

Iron binding site 2 out of 8 in 6ovt

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Iron binding site 2 out of 8 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:23.8
occ:1.00
 FE2 A:FES602 0.0 23.8 1.0
O A:HOH861 2.1 27.8 1.0
S1 A:FES602 2.2 22.1 1.0
S2 A:FES602 2.2 24.3 1.0
SG A:CYS214 2.3 22.6 1.0
FE1 A:FES602 2.7 21.7 1.0
CB A:CYS214 3.4 20.3 1.0
O A:HOH755 3.7 22.4 1.0
O A:HOH1022 3.8 41.3 1.0
N A:CYS214 4.0 20.1 1.0
OD1 A:ASP138 4.1 22.6 1.0
SG A:CYS64 4.2 23.2 1.0
OD2 A:ASP138 4.2 24.1 1.0
CA A:CYS214 4.3 20.1 1.0
CG A:ASP138 4.4 24.8 1.0
SG A:CYS137 4.5 21.4 1.0
CE C:MET36 4.7 27.1 1.0
N A:GLY97 4.8 25.1 1.0
O A:HOH867 4.8 19.0 1.0
CB A:ASP96 4.9 21.5 1.0
O A:HOH1005 4.9 23.4 1.0

Iron binding site 3 out of 8 in 6ovt

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Iron binding site 3 out of 8 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:28.3
occ:1.00
 FE1 B:FES602 0.0 28.3 1.0
S1 B:FES602 2.2 30.4 1.0
S2 B:FES602 2.2 28.2 1.0
SG B:CYS64 2.3 28.8 1.0
SG B:CYS137 2.4 28.7 1.0
FE2 B:FES602 2.7 32.0 1.0
CB B:CYS137 3.4 26.7 1.0
CB B:CYS64 3.4 27.0 1.0
CA B:CYS137 3.7 26.7 1.0
N B:ASP138 4.3 28.0 1.0
OG1 B:THR62 4.4 29.1 1.0
O B:HOH859 4.5 35.2 1.0
C B:CYS137 4.5 28.9 1.0
N B:ASP96 4.6 27.5 1.0
SG B:CYS214 4.6 32.0 1.0
OD1 B:ASP138 4.6 30.9 1.0
CE D:MET36 4.7 27.5 1.0
N B:CYS137 4.8 28.2 1.0
CA B:CYS64 4.8 24.7 1.0
O B:HOH803 4.8 24.2 1.0
N B:CYS214 4.8 26.5 1.0
CG B:ASP138 4.9 34.0 1.0
CA B:ALA213 4.9 23.9 1.0
OG B:SER95 4.9 24.4 1.0
N B:GLY97 5.0 30.0 1.0
CB B:ALA213 5.0 24.2 1.0
CB B:ASP96 5.0 30.0 1.0

Iron binding site 4 out of 8 in 6ovt

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Iron binding site 4 out of 8 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:32.0
occ:1.00
 FE2 B:FES602 0.0 32.0 1.0
S1 B:FES602 2.2 30.4 1.0
S2 B:FES602 2.2 28.2 1.0
SG B:CYS214 2.3 32.0 1.0
O B:HOH859 2.4 35.2 1.0
FE1 B:FES602 2.7 28.3 1.0
CB B:CYS214 3.2 27.2 1.0
N B:CYS214 3.8 26.5 1.0
OD1 B:ASP138 3.9 30.9 1.0
CA B:CYS214 4.1 27.4 1.0
SG B:CYS64 4.4 28.8 1.0
CG B:ASP138 4.5 34.0 1.0
OD2 B:ASP138 4.5 29.1 1.0
SG B:CYS137 4.6 28.7 1.0
CD1 B:ILE180 4.8 43.0 1.0
O B:HOH946 4.8 47.6 1.0
O B:HOH803 4.9 24.2 1.0
CE D:MET36 4.9 27.5 1.0
O B:HOH940 5.0 26.5 1.0
N B:GLY97 5.0 30.0 1.0
C B:ALA213 5.0 26.3 1.0

Iron binding site 5 out of 8 in 6ovt

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Iron binding site 5 out of 8 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe601

b:24.4
occ:1.00
 FE1 C:FES601 0.0 24.4 1.0
S2 C:FES601 2.2 29.7 1.0
S1 C:FES601 2.3 26.9 1.0
SG C:CYS64 2.3 23.7 1.0
SG C:CYS137 2.3 27.7 1.0
FE2 C:FES601 2.8 30.3 1.0
CB C:CYS137 3.3 28.0 1.0
CB C:CYS64 3.4 20.9 1.0
CA C:CYS137 3.7 28.6 1.0
N C:ASP138 4.3 29.5 1.0
OG1 C:THR62 4.4 25.6 1.0
OD1 C:ASP138 4.5 35.3 1.0
C C:CYS137 4.5 29.7 1.0
O C:HOH840 4.5 29.2 1.0
N C:ASP96 4.6 24.7 1.0
SG C:CYS214 4.7 30.1 1.0
CA C:CYS64 4.8 22.6 1.0
N C:CYS137 4.8 30.0 1.0
O C:HOH863 4.8 19.7 1.0
CE A:MET36 4.8 26.1 1.0
N C:CYS214 4.9 24.2 1.0
OG C:SER95 4.9 20.4 1.0
CG2 C:THR62 4.9 22.5 1.0
CG C:ASP138 4.9 33.8 1.0
N C:GLY97 5.0 25.1 1.0
CA C:ALA213 5.0 21.3 1.0

Iron binding site 6 out of 8 in 6ovt

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Iron binding site 6 out of 8 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe601

b:30.3
occ:1.00
 FE2 C:FES601 0.0 30.3 1.0
S2 C:FES601 2.2 29.7 1.0
S1 C:FES601 2.2 26.9 1.0
SG C:CYS214 2.4 30.1 1.0
O C:HOH840 2.4 29.2 1.0
FE1 C:FES601 2.8 24.4 1.0
CB C:CYS214 3.3 25.9 1.0
OD1 C:ASP138 3.8 35.3 1.0
N C:CYS214 3.9 24.2 1.0
CA C:CYS214 4.2 23.7 1.0
SG C:CYS64 4.4 23.7 1.0
CG C:ASP138 4.4 33.8 1.0
OD2 C:ASP138 4.6 34.6 1.0
SG C:CYS137 4.6 27.7 1.0
CD1 C:ILE180 4.6 41.1 1.0
O C:HOH977 4.7 46.0 1.0
O C:HOH863 4.8 19.7 1.0
N C:GLY97 4.9 25.1 1.0
CE A:MET36 4.9 26.1 1.0
O C:HOH984 5.0 27.6 1.0

Iron binding site 7 out of 8 in 6ovt

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Iron binding site 7 out of 8 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe603

b:23.6
occ:1.00
 FE1 D:FES603 0.0 23.6 1.0
S2 D:FES603 2.1 25.4 1.0
S1 D:FES603 2.3 26.0 1.0
SG D:CYS137 2.3 27.6 1.0
SG D:CYS64 2.4 20.9 1.0
FE2 D:FES603 2.7 28.0 1.0
CB D:CYS137 3.3 28.5 1.0
CB D:CYS64 3.3 21.7 1.0
CA D:CYS137 3.6 27.4 1.0
N D:ASP138 4.2 24.9 1.0
OG1 D:THR62 4.4 25.8 1.0
C D:CYS137 4.5 27.7 1.0
O D:HOH922 4.5 30.1 1.0
N D:ASP96 4.5 26.2 1.0
CE B:MET36 4.6 26.9 0.5
SG D:CYS214 4.6 29.2 1.0
OD1 D:ASP138 4.7 32.5 1.0
N D:CYS137 4.7 26.7 1.0
CA D:CYS64 4.7 18.8 1.0
CE B:MET36 4.8 19.1 0.5
N D:CYS214 4.9 25.2 1.0
O D:HOH875 4.9 19.5 1.0
CA D:ALA213 4.9 22.3 1.0
CB D:ALA213 4.9 25.0 1.0
OG D:SER95 5.0 25.3 1.0

Iron binding site 8 out of 8 in 6ovt

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Iron binding site 8 out of 8 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe603

b:28.0
occ:1.00
 FE2 D:FES603 0.0 28.0 1.0
S1 D:FES603 2.1 26.0 1.0
S2 D:FES603 2.2 25.4 1.0
O D:HOH922 2.3 30.1 1.0
SG D:CYS214 2.4 29.2 1.0
FE1 D:FES603 2.7 23.6 1.0
CB D:CYS214 3.3 27.0 1.0
O D:HOH708 3.7 42.9 1.0
N D:CYS214 3.9 25.2 1.0
OD1 D:ASP138 4.0 32.5 1.0
CA D:CYS214 4.2 25.3 1.0
SG D:CYS64 4.4 20.9 1.0
CG D:ASP138 4.5 35.9 1.0
CE B:MET36 4.5 26.9 0.5
SG D:CYS137 4.5 27.6 1.0
OD2 D:ASP138 4.6 37.3 1.0
O D:HOH997 4.9 21.9 1.0
O D:HOH1009 4.9 46.6 1.0
O D:HOH875 5.0 19.5 1.0

Reference:

G.Bashiri, T.L.Grove, S.S.Hegde, T.Lagautriere, G.J.Gerfen, S.C.Almo, C.J.Squire, J.S.Blanchard, E.N.Baker. The Active Site of Themycobacterium Tuberculosisbranched-Chain Amino Acid Biosynthesis Enzyme Dihydroxyacid Dehydratase Contains A 2FE-2S Cluster. J.Biol.Chem. V. 294 13158 2019.
ISSN: ESSN 1083-351X
PubMed: 31315931
DOI: 10.1074/JBC.RA119.009498
Page generated: Wed Aug 7 05:28:42 2024

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