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Magnesium in PDB 6jx2: Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum

Enzymatic activity of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum

All present enzymatic activity of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum:
1.1.1.86;

Protein crystallography data

The structure of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum, PDB code: 6jx2 was solved by D.Lee, J.Hong, K.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.91 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.949, 90.179, 157.817, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 26.7

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum (pdb code 6jx2). 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 Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum, PDB code: 6jx2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 6jx2

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Magnesium binding site 1 out of 13 in the Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:46.8
occ:1.00
 OE2 A:GLU196 2.3 43.1 1.0
OD2 A:ASP192 2.4 38.7 1.0
CG A:ASP192 3.3 34.5 1.0
CD A:GLU196 3.4 42.6 1.0
OD1 A:ASP192 3.5 43.7 1.0
OE1 A:GLU196 3.9 44.5 1.0
OG B:SER253 4.2 36.5 1.0
MG B:MG401 4.6 50.1 1.0
CG A:GLU196 4.6 38.9 1.0
CB A:ASP192 4.7 33.1 1.0
CE1 A:HIS109 5.0 38.7 1.0
ND1 A:HIS109 5.0 37.7 1.0

Magnesium binding site 2 out of 13 in 6jx2

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Magnesium binding site 2 out of 13 in the Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:50.5
occ:1.00
 OE1 A:GLU232 2.3 54.5 1.0
OD1 B:ASP192 2.4 35.9 1.0
OE1 A:GLU228 2.8 47.2 1.0
OE2 B:GLU196 2.9 43.4 1.0
CD A:GLU232 3.4 50.3 1.0
CG B:ASP192 3.5 33.1 1.0
CG B:GLU196 3.6 38.4 1.0
CD B:GLU196 3.6 38.5 1.0
OE2 A:GLU232 3.9 55.1 1.0
CD2 B:LEU200 3.9 43.3 1.0
CD A:GLU228 3.9 47.4 1.0
OD2 B:ASP192 4.1 35.9 1.0
MG B:MG402 4.2 45.9 1.0
OE2 A:GLU228 4.3 58.6 1.0
O B:ASP192 4.5 34.3 1.0
CG A:GLU232 4.6 44.8 1.0
OE1 B:GLU196 4.7 40.2 1.0
CB B:ASP192 4.7 32.5 1.0
CB A:GLU232 4.8 42.0 1.0
CA B:ASP192 4.9 34.7 1.0

Magnesium binding site 3 out of 13 in 6jx2

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Magnesium binding site 3 out of 13 in the Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:59.7
occ:1.00
 OD1 A:ASN100 2.0 48.4 1.0
OD2 A:ASP103 2.6 45.8 1.0
O A:ALA75 2.9 40.1 1.0
O A:ASN98 3.0 44.4 1.0
CG A:ASN100 3.2 43.8 1.0
CG A:ASP103 3.3 39.4 1.0
OD1 A:ASP103 3.3 45.4 1.0
O A:ALA73 3.7 43.2 1.0
ND2 A:ASN100 3.9 50.0 1.0
O A:ALA72 4.0 37.1 1.0
C A:ALA75 4.1 35.7 1.0
C A:ASN98 4.3 41.3 1.0
CB A:ASN100 4.3 43.2 1.0
C A:ALA73 4.6 37.6 1.0
N A:ASN100 4.6 48.2 1.0
CB A:ASP103 4.7 37.5 1.0
N A:ALA75 4.8 33.2 1.0
CA A:ALA73 4.9 38.0 1.0
N A:ASP76 5.0 35.1 1.0

Magnesium binding site 4 out of 13 in 6jx2

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Magnesium binding site 4 out of 13 in the Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:59.3
occ:1.00
 OD1 A:ASP254 2.4 42.0 1.0
O A:TYR250 3.5 40.9 1.0
CG A:ASP254 3.7 44.7 1.0
O A:VAL252 3.8 39.3 1.0
OE1 A:GLU257 4.0 43.9 1.0
OD2 A:ASP254 4.2 45.6 1.0
O A:ASN249 4.3 39.5 1.0
C A:TYR250 4.3 47.0 1.0
CA A:TYR250 4.6 50.8 1.0
NH2 B:ARG307 4.8 44.5 1.0
N A:ASP254 4.8 40.7 1.0
CB A:ASP254 4.9 41.2 1.0
CA A:ASP254 5.0 41.0 1.0

Magnesium binding site 5 out of 13 in 6jx2

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Magnesium binding site 5 out of 13 in the Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:50.1
occ:1.00
 OD1 A:ASP192 1.9 43.7 1.0
OE1 B:GLU228 2.1 49.8 1.0
OE1 B:GLU232 2.2 65.1 1.0
CG A:ASP192 3.1 34.5 1.0
CD B:GLU232 3.1 59.1 1.0
CD B:GLU228 3.3 45.5 1.0
OE2 B:GLU232 3.4 68.0 1.0
OE2 A:GLU196 3.8 43.1 1.0
CA A:ASP192 3.9 31.4 1.0
CB A:ASP192 4.0 33.1 1.0
OD2 A:ASP192 4.0 38.7 1.0
OE2 B:GLU228 4.0 54.7 1.0
O A:ASP192 4.1 33.0 1.0
CG A:GLU196 4.3 38.9 1.0
CD1 A:LEU200 4.4 39.4 1.0
C A:ASP192 4.4 29.9 1.0
CG B:GLU228 4.4 42.0 1.0
CB B:GLU228 4.5 39.3 1.0
CD A:GLU196 4.5 42.6 1.0
CG B:GLU232 4.5 51.8 1.0
CA B:GLU228 4.6 38.5 1.0
MG A:MG401 4.6 46.8 1.0
O B:GLU228 4.9 37.9 1.0
CB B:GLU232 4.9 44.0 1.0

Magnesium binding site 6 out of 13 in 6jx2

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Magnesium binding site 6 out of 13 in the Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:45.9
occ:1.00
 OE2 B:GLU196 2.3 43.4 1.0
OD2 B:ASP192 2.3 35.9 1.0
CD B:GLU196 3.2 38.5 1.0
CG B:ASP192 3.3 33.1 1.0
OE1 B:GLU196 3.4 40.2 1.0
OD1 B:ASP192 3.6 35.9 1.0
MG A:MG402 4.2 50.5 1.0
OG A:SER253 4.3 31.7 1.0
NE2 B:HIS109 4.6 51.0 1.0
CG B:GLU196 4.6 38.4 1.0
CB B:ASP192 4.7 32.5 1.0
CD2 B:HIS109 4.7 49.9 1.0
CE1 B:HIS109 4.8 55.3 1.0
CB A:ALA256 5.0 35.4 1.0

Magnesium binding site 7 out of 13 in 6jx2

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Magnesium binding site 7 out of 13 in the Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:56.8
occ:1.00
 OD1 B:ASP116 2.6 63.1 1.0
CG B:ASP116 3.8 56.5 1.0
O B:ILE113 4.0 36.4 1.0
OD2 B:ASP155 4.2 43.2 1.0
CD B:LYS119 4.2 67.3 1.0
OD2 B:ASP116 4.4 68.4 1.0
O B:ILE118 4.4 50.0 1.0
OE1 B:GLN156 4.7 47.0 1.0
CG B:LYS119 4.8 59.9 1.0
CA B:LYS119 4.8 50.0 1.0
CG2 B:ILE113 4.9 29.5 1.0
CB B:ASP116 4.9 54.8 1.0
CA B:ASP116 5.0 51.0 1.0

Magnesium binding site 8 out of 13 in 6jx2

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Magnesium binding site 8 out of 13 in the Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:56.3
occ:1.00
 OD1 B:ASP254 2.1 45.5 1.0
CG B:ASP254 3.3 43.1 1.0
OD2 B:ASP254 3.8 41.9 1.0
O B:TYR250 4.1 44.7 1.0
O B:VAL252 4.2 30.1 1.0
OE1 B:GLU257 4.2 33.2 1.0
N B:ASP254 4.6 36.7 1.0
CB B:ASP254 4.6 38.3 1.0
O A:HOH533 4.7 38.1 1.0
CA B:ASP254 4.7 37.2 1.0
O B:ASN249 4.8 46.3 1.0
C B:TYR250 4.9 37.8 1.0
NH2 A:ARG307 4.9 35.5 1.0

Magnesium binding site 9 out of 13 in 6jx2

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Magnesium binding site 9 out of 13 in the Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:47.2
occ:1.00
 OD1 B:ASN100 1.8 64.7 1.0
O B:ALA75 2.2 48.0 1.0
OD1 B:ASP103 2.6 47.6 1.0
CG B:ASN100 2.8 58.4 1.0
OD2 B:ASP103 2.9 48.8 1.0
CG B:ASP103 3.1 46.2 1.0
ND2 B:ASN100 3.2 63.8 1.0
C B:ALA75 3.3 45.4 1.0
O B:ALA73 3.6 46.0 1.0
O B:ALA72 4.0 47.8 1.0
CB B:ASN100 4.1 55.9 1.0
N B:ALA75 4.2 51.9 1.0
N B:ASP76 4.2 44.8 1.0
OD1 B:ASP76 4.3 51.7 1.0
CA B:ALA75 4.3 47.1 1.0
CA B:ASP76 4.4 40.7 1.0
N B:ASN100 4.4 66.5 1.0
C B:ALA73 4.5 47.9 1.0
CB B:ASP103 4.7 46.4 1.0
C B:TRP74 4.7 48.1 1.0
CA B:ASN100 4.9 59.7 1.0
O B:TRP74 4.9 52.0 1.0
O B:ASN98 5.0 63.3 1.0

Magnesium binding site 10 out of 13 in 6jx2

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Magnesium binding site 10 out of 13 in the Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Strcuture of Ketol-Acid Reductoisomerase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:55.8
occ:1.00
 OE2 C:GLU196 2.2 53.5 1.0
OD2 C:ASP192 2.4 56.1 1.0
CD C:GLU196 3.3 52.9 1.0
CG C:ASP192 3.3 52.2 1.0
OD1 C:ASP192 3.5 58.8 1.0
OE1 C:GLU196 3.7 53.7 1.0
OG D:SER253 4.1 47.5 1.0
O2D C:NAP403 4.1 74.0 1.0
C6N C:NAP403 4.5 69.4 1.0
C5N C:NAP403 4.5 71.0 1.0
CG C:GLU196 4.6 50.6 1.0
CE1 C:HIS109 4.6 60.6 1.0
N1N C:NAP403 4.6 72.5 1.0
MG D:MG401 4.7 63.1 1.0
C4N C:NAP403 4.7 75.5 1.0
ND1 C:HIS109 4.7 61.5 1.0
C2N C:NAP403 4.7 76.1 1.0
CB C:ASP192 4.8 51.3 1.0
C3N C:NAP403 4.8 77.6 1.0
NE2 C:HIS109 4.8 59.4 1.0
CB D:SER253 4.9 48.6 1.0
CG C:HIS109 4.9 60.4 1.0
CB D:ALA256 4.9 59.2 1.0
CD2 C:HIS109 5.0 59.5 1.0

Reference:

D.Lee, J.Hong, K.J.Kim. Crystal Structure and Biochemical Characterization of Ketol-Acid Reductoisomerase Fromcorynebacterium Glutamicum. J.Agric.Food Chem. V. 67 8527 2019.
ISSN: ESSN 1520-5118
PubMed: 31298526
DOI: 10.1021/ACS.JAFC.9B03262
Page generated: Tue Oct 1 06:20:12 2024

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