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Magnesium in PDB 4ypo: Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+:
1.1.1.86;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+, PDB code: 4ypo was solved by Y.Lv, L.W.Guddat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.74 / 1.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.697, 54.797, 92.230, 90.00, 123.25, 90.00
R / Rfree (%) 15.5 / 16.3

Other elements in 4ypo:

The structure of Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ (pdb code 4ypo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+, PDB code: 4ypo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 4ypo

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Magnesium binding site 1 out of 13 in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:12.1
occ:1.00
O A:HOH572 2.0 12.8 1.0
O A:HOH734 2.1 15.2 1.0
O A:HOH757 2.1 12.6 1.0
OE2 A:GLU192 2.1 11.4 1.0
O B:HOH715 2.1 14.7 1.0
OD2 A:ASP188 2.1 11.7 1.0
CG A:ASP188 3.0 10.1 1.0
CD A:GLU192 3.1 10.7 1.0
OD1 A:ASP188 3.2 11.0 1.0
OE1 A:GLU192 3.5 11.7 1.0
O A:HOH573 3.9 11.0 1.0
HD12 A:LEU189 4.1 12.0 0.5
HB2 B:ALA252 4.1 14.2 1.0
O A:HOH873 4.1 24.5 1.0
O A:HOH840 4.3 38.5 1.0
O A:HOH731 4.3 15.2 1.0
CG A:GLU192 4.4 10.7 1.0
CB A:ASP188 4.4 9.3 1.0
O B:HOH544 4.5 11.7 1.0
OG B:SER249 4.5 16.0 1.0
HG3 A:GLU192 4.5 12.8 1.0
HB3 A:ASP188 4.5 11.2 1.0
O B:HOH801 4.6 19.9 1.0
CE1 A:HIS105 4.6 16.3 1.0
HG2 A:GLU192 4.6 12.8 1.0
HE1 A:HIS105 4.7 19.5 1.0
HD11 A:LEU189 4.7 12.0 0.5
MG A:MG410 4.7 10.6 1.0
HD23 A:LEU189 4.7 14.2 0.6
HB B:THR251 4.8 20.1 1.0
ND1 A:HIS105 4.8 15.5 1.0
CD1 A:LEU189 4.8 10.0 0.5
NE2 A:HIS105 4.8 16.9 1.0
HB2 A:ASP188 4.9 11.2 1.0
HG B:SER249 5.0 19.2 1.0

Magnesium binding site 2 out of 13 in 4ypo

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Magnesium binding site 2 out of 13 in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:13.0
occ:1.00
O A:HOH962 2.1 17.2 1.0
O A:HOH588 2.1 15.0 1.0
O A:HOH576 2.1 14.8 1.0
OE2 A:GLU56 4.1 17.1 1.0
OE1 A:GLU56 4.2 14.7 1.0
O A:HOH616 4.2 13.3 1.0
CD A:GLU56 4.6 14.7 1.0

Magnesium binding site 3 out of 13 in 4ypo

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Magnesium binding site 3 out of 13 in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+


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 Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:60.3
occ:1.00
O A:HOH888 2.1 92.8 1.0
O A:HOH973 2.1 60.8 1.0
O A:HOH642 2.3 27.2 1.0
O A:HOH699 2.4 56.7 1.0
O A:HOH872 2.5 41.7 1.0
O A:HOH559 2.5 21.6 1.0
O B:HOH604 3.9 35.0 1.0
OE1 A:GLU209 4.1 14.7 1.0
O B:HOH852 4.4 28.3 1.0
O A:HOH832 4.4 46.8 1.0
OE2 A:GLU202 4.4 20.5 1.0
HE2 A:LYS205 4.4 21.9 1.0
O A:HOH623 4.5 19.3 1.0
OE2 A:GLU209 4.5 15.5 1.0
O A:HOH879 4.6 25.9 1.0
HZ1 A:LYS205 4.6 23.6 1.0
CD A:GLU209 4.8 12.9 1.0
O A:HOH761 5.0 16.7 1.0

Magnesium binding site 4 out of 13 in 4ypo

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Magnesium binding site 4 out of 13 in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+


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 Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:30.4
occ:1.00
O A:HOH611 2.2 18.6 1.0
O A:HOH606 2.2 18.6 1.0
O A:HOH721 2.3 24.3 1.0
O A:HOH613 2.8 32.3 1.0
HZ2 A:LYS16 3.3 26.7 1.0
O A:TRP70 3.8 15.2 1.0
HD2 A:LYS16 3.8 21.1 1.0
HE3 A:LYS96 3.9 23.0 1.0
HZ3 A:LYS16 4.0 26.7 1.0
NZ A:LYS16 4.0 22.2 1.0
O A:HOH951 4.3 28.3 1.0
HA A:TRP70 4.5 17.3 1.0
OD1 A:ASP72 4.5 17.9 1.0
HZ1 A:LYS16 4.6 26.7 1.0
CD A:LYS16 4.6 17.6 1.0
O A:HOH549 4.7 25.1 1.0
C A:TRP70 4.7 14.4 1.0
HD3 A:LYS16 4.7 21.1 1.0
CE A:LYS96 4.8 19.1 1.0
O A:HOH801 4.9 44.5 1.0
CE A:LYS16 4.9 20.4 1.0
O A:LYS69 4.9 16.7 1.0
HD2 A:LYS96 5.0 22.2 1.0

Magnesium binding site 5 out of 13 in 4ypo

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Magnesium binding site 5 out of 13 in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+


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 Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:9.3
occ:1.00
OE1 A:GLU228 2.0 9.3 1.0
OD1 B:ASP188 2.0 9.9 1.0
OE1 A:GLU224 2.0 11.0 1.0
O B:HOH609 2.1 9.6 1.0
O A:HOH539 2.1 10.5 1.0
O A:HOH658 2.1 10.1 1.0
CD A:GLU228 3.0 10.4 1.0
CD A:GLU224 3.1 10.6 1.0
HA B:ASP188 3.2 9.3 1.0
CG B:ASP188 3.2 8.8 1.0
OE2 A:GLU228 3.3 12.2 1.0
HG3 B:GLU192 3.6 11.7 1.0
HA A:GLU224 3.7 10.1 1.0
OE2 A:GLU224 3.7 11.6 1.0
O B:HOH760 3.8 11.4 1.0
HD11 B:LEU196 3.8 12.5 1.0
CB B:ASP188 3.9 8.4 1.0
CA B:ASP188 3.9 7.8 1.0
HB2 B:ASP188 3.9 10.1 1.0
HD12 B:LEU196 3.9 12.5 1.0
O B:HOH555 4.0 13.5 1.0
HB3 A:GLU224 4.1 10.2 1.0
O B:ASP188 4.1 8.5 1.0
OD2 B:ASP188 4.1 10.2 1.0
OE2 B:GLU192 4.1 10.3 1.0
HZ1 B:LYS128 4.2 16.2 1.0
CG A:GLU224 4.3 9.6 1.0
O A:HOH883 4.3 29.6 1.0
CD1 B:LEU196 4.3 10.4 1.0
CG A:GLU228 4.4 9.2 1.0
C B:ASP188 4.4 8.4 1.0
CG B:GLU192 4.4 9.7 1.0
CB A:GLU224 4.5 8.5 1.0
HG3 A:GLU224 4.5 11.5 1.0
CA A:GLU224 4.5 8.4 1.0
HB3 A:GLU228 4.5 10.9 1.0
HB2 A:GLU228 4.5 10.9 1.0
HG2 B:GLU192 4.6 11.7 1.0
CD B:GLU192 4.6 9.6 1.0
O A:GLU224 4.6 8.7 1.0
HD13 B:LEU196 4.6 12.5 1.0
MG B:MG402 4.7 10.6 1.0
CB A:GLU228 4.7 9.1 1.0
HG3 A:GLU228 4.8 11.1 1.0
HB3 B:ASP188 4.8 10.1 1.0
HZ2 B:LYS128 4.9 16.2 1.0
NZ B:LYS128 4.9 13.5 1.0
HG2 A:GLU228 5.0 11.1 1.0

Magnesium binding site 6 out of 13 in 4ypo

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Magnesium binding site 6 out of 13 in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+


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 Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:20.6
occ:1.00
O A:HOH592 2.1 29.6 1.0
O A:HOH552 2.1 22.5 1.0
O A:HOH795 2.2 37.2 1.0
O B:HOH632 2.2 63.8 1.0
O A:HOH513 2.2 22.4 1.0
OD1 A:ASP250 2.4 27.9 1.0
CG A:ASP250 3.6 25.1 1.0
O A:HOH652 3.9 28.1 1.0
O A:TYR246 4.0 18.0 1.0
OE2 A:GLU253 4.0 15.5 1.0
O A:VAL248 4.0 16.2 1.0
HA A:TYR246 4.1 20.2 1.0
OD2 A:ASP250 4.2 29.6 1.0
HH11 B:ARG303 4.2 21.1 1.0
O B:HOH842 4.2 31.3 1.0
HH12 B:ARG303 4.3 21.1 1.0
HA A:ASP250 4.3 22.6 1.0
NH1 B:ARG303 4.4 17.6 1.0
H A:ASP250 4.4 20.9 1.0
N A:ASP250 4.5 17.4 1.0
O A:TYR245 4.6 14.1 1.0
O A:HOH749 4.6 22.6 1.0
CA A:ASP250 4.8 18.8 1.0
C A:TYR246 4.8 16.1 1.0
CB A:ASP250 4.8 23.4 1.0
O A:HOH634 4.8 46.6 1.0
O A:HOH769 4.8 43.8 1.0
O A:HOH727 4.8 20.0 1.0
HA A:SER249 4.9 16.8 1.0
CA A:TYR246 4.9 16.9 1.0
C A:SER249 4.9 15.7 1.0

Magnesium binding site 7 out of 13 in 4ypo

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Magnesium binding site 7 out of 13 in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+


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 Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:46.0
occ:1.00
O A:HOH511 2.0 27.3 1.0
O A:HOH515 2.2 26.5 1.0
O A:HOH582 2.2 19.4 1.0
O A:HOH737 2.5 45.8 1.0
OD1 A:ASP62 3.0 25.7 1.0
HH12 A:ARG51 3.4 23.6 1.0
HA A:ASP62 3.7 16.4 1.0
OE2 A:GLU66 4.1 17.4 1.0
CG A:ASP62 4.2 23.1 1.0
HH22 A:ARG51 4.2 22.5 1.0
NH1 A:ARG51 4.3 19.7 1.0
O A:VAL61 4.3 16.5 0.6
OE1 A:GLU66 4.3 16.9 1.0
O A:VAL61 4.5 15.2 0.4
O A:HOH620 4.5 40.8 1.0
CA A:ASP62 4.6 13.6 1.0
CD A:GLU66 4.7 15.1 1.0
OE1 A:GLN46 4.7 0.5 1.0
HH11 A:ARG51 4.7 23.6 1.0
H A:THR63 4.9 14.7 1.0
CB A:ASP62 4.9 16.3 1.0
NH2 A:ARG51 4.9 18.7 1.0
HG23 A:THR63 4.9 18.0 1.0

Magnesium binding site 8 out of 13 in 4ypo

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Magnesium binding site 8 out of 13 in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+


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 Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:10.6
occ:1.00
OD1 A:ASP188 2.0 11.0 1.0
OE1 B:GLU228 2.0 10.4 1.0
OE1 B:GLU224 2.0 12.3 1.0
O A:HOH573 2.1 11.0 1.0
O B:HOH544 2.1 11.7 1.0
O B:HOH687 2.2 11.2 1.0
CD B:GLU228 3.0 11.0 1.0
CD B:GLU224 3.1 11.8 1.0
CG A:ASP188 3.2 10.1 1.0
HA A:ASP188 3.2 10.9 1.0
OE2 B:GLU228 3.3 13.1 1.0
HA B:GLU224 3.6 11.2 1.0
HG3 A:GLU192 3.6 12.8 1.0
OE2 B:GLU224 3.7 13.4 1.0
O A:HOH757 3.7 12.6 1.0
HD11 A:LEU196 3.8 13.4 1.0
HD12 A:LEU196 3.9 13.4 1.0
CB A:ASP188 3.9 9.3 1.0
CA A:ASP188 3.9 9.1 1.0
HB2 A:ASP188 3.9 11.2 1.0
O A:HOH543 4.0 14.5 1.0
HZ1 A:LYS128 4.1 17.3 1.0
OE2 A:GLU192 4.1 11.4 1.0
O A:ASP188 4.1 9.9 1.0
OD2 A:ASP188 4.1 11.7 1.0
HB3 B:GLU224 4.1 12.0 1.0
CG B:GLU224 4.3 10.6 1.0
CD1 A:LEU196 4.3 11.2 1.0
CG B:GLU228 4.4 10.0 1.0
CG A:GLU192 4.4 10.7 1.0
C A:ASP188 4.4 8.8 1.0
CA B:GLU224 4.5 9.3 1.0
O B:HOH924 4.5 40.2 1.0
HG3 B:GLU224 4.5 12.7 1.0
CB B:GLU224 4.5 10.0 1.0
HG2 A:GLU192 4.6 12.8 1.0
HB2 B:GLU228 4.6 11.1 1.0
HB3 B:GLU228 4.6 11.1 1.0
CD A:GLU192 4.6 10.7 1.0
HD13 A:LEU196 4.6 13.4 1.0
O B:GLU224 4.7 10.2 1.0
MG A:MG401 4.7 12.1 1.0
CB B:GLU228 4.8 9.2 1.0
HZ2 A:LYS128 4.8 17.3 1.0
HG3 B:GLU228 4.8 12.0 1.0
NZ A:LYS128 4.8 14.4 1.0
HB3 A:ASP188 4.8 11.2 1.0
HG2 B:GLU228 5.0 12.0 1.0

Magnesium binding site 9 out of 13 in 4ypo

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Magnesium binding site 9 out of 13 in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+


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 Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:26.9
occ:1.00
O B:HOH678 2.0 20.0 1.0
O B:HOH850 2.1 35.1 1.0
HA B:PRO154 3.8 15.4 1.0
O B:HOH948 3.9 44.8 1.0
O B:PRO154 4.2 12.4 1.0
O B:ASP153 4.2 12.3 1.0
CA B:PRO154 4.7 12.8 1.0
C B:PRO154 4.8 12.4 1.0

Magnesium binding site 10 out of 13 in 4ypo

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Magnesium binding site 10 out of 13 in the Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+


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 Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase in Complex with MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:10.6
occ:1.00
O B:HOH760 2.1 11.4 1.0
O B:HOH576 2.1 11.7 1.0
O B:HOH742 2.1 14.2 1.0
OE2 B:GLU192 2.1 10.3 1.0
OD2 B:ASP188 2.1 10.2 1.0
O B:HOH747 2.1 13.3 1.0
CG B:ASP188 3.0 8.8 1.0
CD B:GLU192 3.1 9.6 1.0
OD1 B:ASP188 3.2 9.9 1.0
OE1 B:GLU192 3.4 10.3 1.0
O B:HOH507 3.5 44.6 1.0
O B:HOH525 3.8 36.6 1.0
O B:HOH609 3.9 9.6 1.0
HG A:SER249 3.9 18.1 1.0
O B:HOH862 4.0 22.9 1.0
HD12 B:LEU189 4.1 11.5 0.5
HB2 A:ALA252 4.1 12.4 1.0
O B:HOH846 4.2 34.7 1.0
O B:HOH733 4.3 13.1 1.0
CG B:GLU192 4.4 9.7 1.0
CB B:ASP188 4.4 8.4 1.0
O A:HOH539 4.4 10.5 1.0
HG3 B:GLU192 4.5 11.7 1.0
O A:HOH770 4.5 19.3 1.0
HB3 B:ASP188 4.5 10.1 1.0
OG A:SER249 4.6 15.1 1.0
CE1 B:HIS105 4.6 12.9 1.0
HG2 B:GLU192 4.6 11.7 1.0
HD23 B:LEU189 4.7 13.0 0.5
HE1 B:HIS105 4.7 15.5 1.0
MG A:MG406 4.7 9.3 1.0
HD11 B:LEU189 4.7 11.5 0.5
ND1 B:HIS105 4.7 12.0 1.0
O B:HOH841 4.8 35.3 1.0
CD1 B:LEU189 4.8 9.6 0.5
HB2 B:ASP188 4.9 10.1 1.0
NE2 B:HIS105 4.9 13.9 1.0
HB A:THR251 5.0 22.4 1.0
OD2 B:ASP80 5.0 48.7 1.0

Reference:

Y.Lv, A.Kandale, S.J.Wun, R.P.Mcgeary, S.J.Williams, B.Kobe, V.Sieber, M.A.Schembri, G.Schenk, L.W.Guddat. Crystal Structure of Mycobacterium Tuberculosis Ketol-Acid Reductoisomerase at 1.0 Angstrom Resolution - A Potential Target For Anti-Tuberculosis Drug Discovery. Febs J. V. 283 1184 2016.
ISSN: ISSN 1742-464X
PubMed: 26876563
DOI: 10.1111/FEBS.13672
Page generated: Mon Dec 14 19:55:20 2020

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