Magnesium 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:

Iron (Fe) 8 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis (pdb code 6ovt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis, PDB code: 6ovt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6ovt

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Magnesium binding site 1 out of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:23.2
occ:1.00
 OQ2 A:KCX139 1.9 23.4 1.0
O A:HOH707 2.0 17.8 1.0
OD2 A:ASP138 2.1 24.1 1.0
OD2 A:ASP96 2.1 20.7 1.0
OE2 A:GLU465 2.2 19.6 1.0
O A:HOH737 2.2 23.4 1.0
CX A:KCX139 2.9 22.6 1.0
CG A:ASP138 3.1 24.8 1.0
CD A:GLU465 3.1 22.3 1.0
CG A:ASP96 3.2 19.6 1.0
OE1 A:GLU465 3.4 23.4 1.0
NZ A:KCX139 3.4 22.3 1.0
CB A:ASP138 3.6 23.4 1.0
CB A:ASP96 3.6 21.5 1.0
OG1 A:THR219 3.8 23.4 1.0
O A:HOH1005 3.8 23.4 1.0
ND2 A:ASN292 3.8 20.4 1.0
OQ1 A:KCX139 4.0 23.0 1.0
O A:HOH861 4.1 27.8 1.0
OD1 A:ASP138 4.1 22.6 1.0
CB A:THR219 4.1 21.0 1.0
OD1 A:ASP96 4.3 22.6 1.0
NH1 A:ARG489 4.5 23.5 1.0
CG A:GLU465 4.5 20.0 1.0
OG A:SER491 4.5 27.8 1.0
CA A:SER491 4.6 24.2 1.0
CG2 A:THR219 4.7 20.7 1.0
N A:GLY492 4.8 25.0 1.0
CE A:KCX139 4.8 21.0 1.0
CB A:SER491 4.9 24.7 1.0
CE A:MET105 5.0 23.6 1.0

Magnesium binding site 2 out of 12 in 6ovt

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Magnesium binding site 2 out of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:50.5
occ:1.00
 O A:HOH936 1.9 56.8 1.0
O A:HOH932 1.9 69.2 1.0
O A:HOH775 2.1 47.5 1.0
O A:HOH1014 2.2 43.5 1.0
O A:HOH965 2.2 30.2 1.0
OD1 A:ASP69 2.2 30.8 1.0
CG A:ASP69 3.4 30.9 1.0
O A:ASP69 3.9 22.3 1.0
O A:HOH1052 3.9 38.8 1.0
OE1 A:GLU88 4.1 26.3 1.0
O C:HOH947 4.1 30.0 1.0
OD2 A:ASP69 4.1 36.9 1.0
OE2 A:GLU88 4.2 23.6 1.0
O A:HOH1030 4.3 28.9 1.0
CA A:ASP69 4.4 22.0 1.0
C A:ASP69 4.4 19.0 1.0
OD1 A:ASN73 4.4 31.1 0.5
O C:HOH965 4.4 55.3 1.0
CB A:ASP69 4.5 25.9 1.0
CD A:GLU88 4.6 23.4 1.0
O A:HOH776 4.8 40.2 1.0
O C:HOH869 4.9 59.7 1.0
CG A:ASN73 5.0 24.5 0.5

Magnesium binding site 3 out of 12 in 6ovt

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Magnesium binding site 3 out of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:42.6
occ:1.00
 O A:HOH1072 2.0 45.4 1.0
O A:HOH1082 2.0 37.3 1.0
O A:HOH841 2.0 43.8 1.0
O A:HOH824 2.0 38.9 1.0
O A:HOH1058 2.2 47.3 1.0
O A:HOH713 2.2 28.5 1.0
O A:HOH843 4.1 41.0 1.0
OD2 A:ASP270 4.2 23.7 1.0
OD1 A:ASP270 4.2 25.6 1.0
OG1 A:THR267 4.3 27.2 1.0
O A:GLY265 4.4 28.2 1.0
CG A:ASP270 4.6 24.9 1.0
CG2 A:THR267 4.7 24.3 1.0

Magnesium binding site 4 out of 12 in 6ovt

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Magnesium binding site 4 out of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:36.5
occ:1.00
 OQ1 B:KCX139 2.0 33.3 1.0
OD2 B:ASP96 2.1 29.4 1.0
OD2 B:ASP138 2.1 29.1 1.0
OE2 B:GLU465 2.2 32.7 1.0
O B:HOH810 2.3 36.9 1.0
O B:HOH905 2.3 32.3 1.0
CX B:KCX139 3.0 35.4 1.0
CG B:ASP96 3.1 30.6 1.0
CG B:ASP138 3.1 34.0 1.0
CD B:GLU465 3.2 39.9 1.0
OE1 B:GLU465 3.4 35.8 1.0
NZ B:KCX139 3.4 34.5 1.0
CB B:ASP96 3.5 30.0 1.0
CB B:ASP138 3.6 30.4 1.0
OG1 B:THR219 3.8 39.6 1.0
O B:HOH769 4.1 27.6 1.0
OQ2 B:KCX139 4.2 32.4 1.0
OD1 B:ASP138 4.2 30.9 1.0
OD1 B:ASP96 4.3 29.4 1.0
ND2 B:ASN292 4.4 35.7 1.0
CB B:THR219 4.4 34.2 1.0
CG B:GLU465 4.6 38.4 1.0
O B:HOH946 4.6 47.6 1.0
O B:HOH859 4.6 35.2 1.0
CA B:ASP96 4.9 29.6 1.0
CE B:KCX139 4.9 32.4 1.0

Magnesium binding site 5 out of 12 in 6ovt

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Magnesium binding site 5 out of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:50.4
occ:1.00
 O B:HOH898 1.7 53.2 1.0
O B:HOH759 2.0 48.6 1.0
O B:HOH819 2.2 31.8 1.0
O B:HOH921 2.2 48.9 1.0
OD1 B:ASP69 2.3 37.6 1.0
O B:HOH755 2.4 51.5 1.0
CG B:ASP69 3.5 32.8 1.0
O B:ASP69 4.0 23.0 1.0
OD2 B:ASP69 4.0 41.0 1.0
O D:HOH972 4.1 31.9 1.0
OE1 B:GLU88 4.2 29.4 1.0
OE2 B:GLU88 4.2 26.2 1.0
C B:ASP69 4.6 23.1 1.0
CB B:ASP69 4.7 27.2 1.0
CD B:GLU88 4.7 25.9 1.0
CA B:ASP69 4.7 23.8 1.0
O B:HOH703 4.7 40.5 1.0
CB B:ASN73 4.9 29.5 1.0
O B:HOH926 4.9 35.4 1.0

Magnesium binding site 6 out of 12 in 6ovt

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Magnesium binding site 6 out of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:48.4
occ:1.00
 O B:HOH842 2.0 47.4 1.0
O B:HOH945 2.0 54.2 1.0
O B:HOH846 2.0 44.3 1.0
O B:HOH715 2.0 42.4 1.0
O B:HOH956 2.0 50.9 1.0
O B:HOH947 2.1 54.8 1.0
OD2 B:ASP270 4.0 37.4 1.0
OD1 B:ASP270 4.2 36.4 1.0
OG1 B:THR267 4.3 31.3 1.0
O B:GLY265 4.3 35.6 1.0
O B:HOH780 4.4 50.2 1.0
CG B:ASP270 4.6 37.6 1.0
CG2 B:THR267 4.6 34.7 1.0

Magnesium binding site 7 out of 12 in 6ovt

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Magnesium binding site 7 out of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:32.3
occ:1.00
 OQ2 C:KCX139 2.0 27.9 1.0
OD2 C:ASP138 2.1 34.6 1.0
O C:HOH926 2.1 30.1 1.0
O C:HOH829 2.2 34.2 1.0
OD2 C:ASP96 2.3 28.9 1.0
OE2 C:GLU465 2.3 39.4 1.0
CX C:KCX139 3.1 32.1 1.0
CG C:ASP138 3.2 33.8 1.0
CG C:ASP96 3.2 29.5 1.0
CD C:GLU465 3.3 40.2 1.0
NZ C:KCX139 3.4 30.7 1.0
CB C:ASP96 3.5 25.9 1.0
OE1 C:GLU465 3.5 38.1 1.0
CB C:ASP138 3.6 29.9 1.0
OG1 C:THR219 3.7 29.4 1.0
O C:HOH977 4.0 46.0 1.0
O C:HOH919 4.1 42.3 1.0
OQ1 C:KCX139 4.1 28.9 1.0
O C:HOH803 4.2 26.5 1.0
ND2 C:ASN292 4.2 27.7 1.0
O C:HOH840 4.3 29.2 1.0
OD1 C:ASP138 4.3 35.3 1.0
CB C:THR219 4.4 26.6 1.0
OD1 C:ASP96 4.4 28.9 1.0
CG C:GLU465 4.7 41.3 1.0
CE C:KCX139 4.9 24.6 1.0
CA C:ASP96 4.9 26.6 1.0

Magnesium binding site 8 out of 12 in 6ovt

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Magnesium binding site 8 out of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:41.6
occ:1.00
 O C:HOH874 2.0 51.7 1.0
O C:HOH961 2.0 49.0 1.0
O C:HOH869 2.1 59.7 1.0
O C:HOH847 2.1 29.1 1.0
O C:HOH851 2.2 44.6 1.0
OD1 C:ASP69 2.3 34.5 1.0
CG C:ASP69 3.5 32.9 1.0
O C:ASP69 4.0 20.6 1.0
OD2 C:ASP69 4.1 38.0 1.0
OE1 C:GLU88 4.1 27.9 1.0
O A:HOH1030 4.1 28.9 1.0
OE2 C:GLU88 4.2 28.3 1.0
O C:HOH701 4.5 48.0 1.0
CD C:GLU88 4.6 27.1 1.0
C C:ASP69 4.6 21.9 1.0
CB C:ASP69 4.7 25.0 1.0
CA C:ASP69 4.7 22.5 1.0
O C:HOH721 4.9 42.1 1.0
O C:HOH947 4.9 30.0 1.0
O A:HOH932 4.9 69.2 1.0

Magnesium binding site 9 out of 12 in 6ovt

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Magnesium binding site 9 out of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg605

b:39.2
occ:1.00
 O C:HOH993 2.0 38.8 1.0
O C:HOH986 2.0 44.5 1.0
O C:HOH886 2.0 34.8 1.0
O C:HOH723 2.1 35.8 1.0
O C:HOH802 2.1 39.4 1.0
O C:HOH1005 2.2 40.5 1.0
O C:HOH933 4.1 40.6 1.0
OD2 C:ASP270 4.1 25.1 1.0
OD1 C:ASP270 4.2 27.2 1.0
O C:GLY265 4.3 26.1 1.0
OG1 C:THR267 4.4 23.4 1.0
O C:HOH728 4.5 35.8 1.0
CG C:ASP270 4.6 25.9 1.0
O C:HOH1006 4.7 60.5 1.0
CG2 C:THR267 4.7 22.9 1.0

Magnesium binding site 10 out of 12 in 6ovt

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Magnesium binding site 10 out of 12 in the Crystal Structure of Ilvd From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Ilvd From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:40.0
occ:1.00
 OE2 D:GLU465 1.9 33.0 0.6
OQ1 D:KCX139 2.0 34.4 1.0
O D:HOH905 2.0 33.6 1.0
OD2 D:ASP138 2.2 37.3 1.0
O D:HOH906 2.3 38.2 1.0
OD2 D:ASP96 2.3 31.8 1.0
CD D:GLU465 2.9 39.5 0.6
OE1 D:GLU465 3.0 41.5 0.4
CX D:KCX139 3.1 33.5 1.0
OE1 D:GLU465 3.2 40.3 0.6
CG D:ASP96 3.4 28.8 1.0
CG D:ASP138 3.4 35.9 1.0
NZ D:KCX139 3.4 35.8 1.0
CB D:ASP96 3.7 29.5 1.0
OG1 D:THR219 3.9 30.5 1.0
CB D:ASP138 3.9 31.2 1.0
O D:HOH799 3.9 29.9 1.0
OQ2 D:KCX139 4.1 34.3 1.0
ND2 D:ASN292 4.2 32.0 1.0
CD D:GLU465 4.2 38.7 0.4
CG D:GLU465 4.3 38.0 0.6
OD1 D:ASP138 4.4 32.5 1.0
OD1 D:ASP96 4.5 31.6 1.0
CB D:THR219 4.5 28.6 1.0
O D:HOH1009 4.6 46.6 1.0
O D:HOH922 4.7 30.1 1.0
OE2 D:GLU465 4.8 42.0 0.4
CE D:KCX139 4.8 30.8 1.0
NH1 D:ARG489 4.9 31.8 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: Mon Dec 14 23:44:57 2020

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