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Magnesium in PDB 4kqx: Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor

Enzymatic activity of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor

All present enzymatic activity of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor:
1.1.1.86;

Protein crystallography data

The structure of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor, PDB code: 4kqx was solved by S.Brinkmann-Chen, T.Flock, J.K.B.Cahn, C.D.Snow, E.M.Brustad, J.A.Mcintosh, P.Meinhold, L.Zhang, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.83 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.985, 105.346, 122.357, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 25.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor (pdb code 4kqx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor, PDB code: 4kqx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 4kqx

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Magnesium binding site 1 out of 10 in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:9.1
occ:1.00
 OE1 A:GLU266 2.7 15.1 1.0
O A:ASN258 2.7 15.8 1.0
O A:ILE261 2.8 13.6 1.0
OD1 A:ASN263 2.9 15.2 1.0
C A:SER262 3.5 12.7 1.0
O A:SER262 3.6 13.5 1.0
N A:ASN263 3.6 13.2 1.0
C A:ILE261 3.7 13.6 1.0
O A:HOH578 3.7 28.8 1.0
CA A:ASN263 3.8 13.5 1.0
CD A:GLU266 3.8 14.0 1.0
O A:TYR259 3.8 17.5 1.0
C A:ASN258 3.9 17.4 1.0
CB A:GLU266 3.9 12.6 1.0
CG A:ASN263 4.0 15.5 1.0
CA A:TYR259 4.2 17.2 1.0
NH2 B:ARG316 4.2 15.1 1.0
C A:TYR259 4.2 16.4 1.0
CG1 A:ILE261 4.2 11.1 1.0
CA A:SER262 4.2 12.5 1.0
MG A:MG404 4.3 11.7 1.0
N A:SER262 4.3 12.2 1.0
CG A:GLU266 4.5 13.5 1.0
N A:TYR259 4.5 15.1 1.0
CB A:ASN263 4.5 14.4 1.0
CA A:ILE261 4.7 12.8 1.0
OE2 A:GLU266 4.8 13.7 1.0
N A:ILE261 4.8 13.0 1.0

Magnesium binding site 2 out of 10 in 4kqx

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Magnesium binding site 2 out of 10 in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:11.7
occ:1.00
 O A:ILE261 2.5 13.6 1.0
O A:TYR259 2.7 17.5 1.0
O A:HOH595 2.9 33.1 1.0
O1N B:NAD402 2.9 17.8 1.0
O A:SER260 2.9 13.1 1.0
O1A B:NAD402 3.0 20.4 1.0
O2A B:NAD402 3.4 20.5 1.0
C A:SER260 3.4 13.6 1.0
C A:ILE261 3.4 13.6 1.0
PA B:NAD402 3.5 21.0 1.0
CB B:SER37 3.7 15.1 1.0
C A:TYR259 3.8 16.4 1.0
PN B:NAD402 3.9 21.3 1.0
O3 B:NAD402 4.1 20.3 1.0
CA A:SER260 4.1 15.7 1.0
N A:ILE261 4.1 13.0 1.0
N A:SER262 4.2 12.2 1.0
CA A:SER262 4.2 12.5 1.0
O7N B:NAD402 4.3 21.8 1.0
MG A:MG403 4.3 9.1 1.0
CA A:ILE261 4.3 12.8 1.0
N A:SER260 4.4 16.4 1.0
N B:SER37 4.4 14.4 1.0
O B:HOH560 4.5 20.1 1.0
O2N B:NAD402 4.5 16.1 1.0
CA B:SER37 4.7 15.8 1.0
OG B:SER37 4.8 16.7 1.0
C A:SER262 5.0 12.7 1.0

Magnesium binding site 3 out of 10 in 4kqx

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Magnesium binding site 3 out of 10 in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:20.6
occ:1.00
 O3 B:HIO401 1.9 19.4 1.0
O B:HOH634 1.9 15.8 1.0
OD1 A:ASP201 2.1 15.8 1.0
O B:HOH628 2.1 10.9 1.0
O2 B:HIO401 2.1 18.5 1.0
O A:HOH602 2.2 11.2 1.0
N3 B:HIO401 2.7 18.1 1.0
C2 B:HIO401 2.8 18.5 1.0
CG A:ASP201 3.0 15.8 1.0
OD2 A:ASP201 3.5 14.8 1.0
MG A:MG406 3.6 12.3 1.0
NZ A:LYS141 3.9 13.4 1.0
C4 B:HIO401 4.0 19.3 1.0
OE1 B:GLU241 4.0 16.4 1.0
OE1 B:GLU237 4.1 16.7 1.0
OE2 B:GLU241 4.2 19.8 1.0
O A:HOH611 4.2 20.3 1.0
CB A:ASP201 4.2 17.2 1.0
OE2 B:GLU237 4.2 18.0 1.0
C1 B:HIO401 4.2 16.3 1.0
OE1 A:GLU205 4.3 13.6 1.0
O B:HOH633 4.4 16.9 1.0
O A:PRO140 4.5 14.8 1.0
CD B:GLU241 4.5 16.7 1.0
CE A:LYS141 4.5 12.0 1.0
C5N A:NAD401 4.6 21.9 1.0
CA A:ASP201 4.6 13.8 1.0
CD B:GLU237 4.6 17.2 1.0
O12 B:HIO401 4.7 16.8 1.0
C42 B:HIO401 4.7 20.1 1.0
O A:ASP201 4.7 16.2 1.0
C4N A:NAD401 4.9 23.0 1.0
CD A:LYS141 4.9 11.9 1.0
CA A:LYS141 5.0 14.1 1.0
C A:ASP201 5.0 15.7 1.0

Magnesium binding site 4 out of 10 in 4kqx

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Magnesium binding site 4 out of 10 in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:12.3
occ:1.00
 O B:HOH633 1.9 16.9 1.0
OD2 A:ASP201 2.0 14.8 1.0
O2 B:HIO401 2.1 18.5 1.0
O12 B:HIO401 2.2 16.8 1.0
O A:HOH605 2.2 10.7 1.0
OE1 A:GLU205 2.4 13.6 1.0
C2 B:HIO401 2.8 18.5 1.0
C1 B:HIO401 2.9 16.3 1.0
CG A:ASP201 3.0 15.8 1.0
OD1 A:ASP201 3.3 15.8 1.0
CD A:GLU205 3.5 13.5 1.0
MG A:MG405 3.6 20.6 1.0
O B:HOH628 3.8 10.9 1.0
OE2 A:GLU205 3.9 12.4 1.0
N3 B:HIO401 4.0 18.1 1.0
O11 B:HIO401 4.1 13.9 1.0
CE1 A:HIS118 4.2 18.8 1.0
NE2 A:HIS118 4.3 17.0 1.0
O A:HOH611 4.3 20.3 1.0
OG B:SER262 4.3 13.1 1.0
CB A:ASP201 4.3 17.2 1.0
ND1 A:HIS118 4.3 15.2 1.0
CD2 A:HIS118 4.4 17.9 1.0
O3 B:HIO401 4.5 19.4 1.0
O2D A:NAD401 4.5 20.2 1.0
O A:HOH602 4.5 11.2 1.0
CG A:HIS118 4.5 17.4 1.0
O A:ASP201 4.7 16.2 1.0
C6N A:NAD401 4.7 23.3 1.0
CG A:GLU205 4.8 12.9 1.0
C5N A:NAD401 4.8 21.9 1.0
C A:ASP201 4.8 15.7 1.0
CB B:ALA265 4.8 13.0 1.0
N1N A:NAD401 5.0 23.8 1.0

Magnesium binding site 5 out of 10 in 4kqx

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Magnesium binding site 5 out of 10 in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:9.2
occ:1.00
 O B:ILE261 2.5 14.2 1.0
O B:ASN258 2.8 15.7 1.0
OE1 B:GLU266 2.8 12.9 1.0
OD1 B:ASN263 3.2 13.3 1.0
O B:HOH639 3.2 19.9 1.0
O B:SER262 3.4 12.1 1.0
C B:SER262 3.5 11.8 1.0
N B:ASN263 3.6 11.2 1.0
C B:ILE261 3.6 14.2 1.0
CB B:GLU266 3.8 12.5 1.0
O A:HOH537 3.8 18.9 1.0
CD B:GLU266 3.8 11.7 1.0
O B:TYR259 3.9 19.4 1.0
CA B:ASN263 3.9 13.2 1.0
C B:ASN258 3.9 15.5 1.0
CG1 B:ILE261 4.1 13.4 1.0
O A:HOH529 4.2 28.2 1.0
CG B:ASN263 4.2 13.8 1.0
CA B:SER262 4.2 12.6 1.0
N B:SER262 4.3 14.0 1.0
CG B:GLU266 4.3 13.0 1.0
C B:TYR259 4.3 19.4 1.0
CA B:TYR259 4.4 18.8 1.0
MG B:MG406 4.5 9.0 1.0
NH2 A:ARG316 4.6 13.2 1.0
O B:HOH538 4.7 22.9 1.0
CA B:ILE261 4.7 14.7 1.0
N B:ILE261 4.7 14.5 1.0
N B:TYR259 4.7 18.7 1.0
CB B:ASN263 4.7 12.2 1.0
OE2 B:GLU266 4.7 14.9 1.0
CA B:ASN258 5.0 14.1 1.0

Magnesium binding site 6 out of 10 in 4kqx

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Magnesium binding site 6 out of 10 in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:8.6
occ:1.00
 O B:GLU82 2.5 20.2 1.0
OD1 B:ASN112 2.7 16.8 1.0
O B:ALA81 2.7 19.8 1.0
O B:ALA84 2.7 17.0 1.0
O B:HIS107 2.9 17.2 1.0
O B:HOH649 3.0 22.5 1.0
C B:GLU82 3.4 21.1 1.0
CG B:ASN112 3.6 15.2 1.0
C B:ALA81 3.8 19.1 1.0
C B:ALA84 3.9 18.6 1.0
ND2 B:ASN112 3.9 15.7 1.0
CA B:GLU82 3.9 21.2 1.0
CD1 B:ILE87 4.0 17.5 1.0
N B:ALA84 4.0 18.7 1.0
C B:HIS107 4.0 19.5 1.0
CG B:LYS109 4.1 26.7 1.0
N B:GLU82 4.3 20.5 1.0
N B:GLU83 4.5 21.0 1.0
C B:GLU83 4.5 21.1 1.0
CA B:ALA84 4.5 17.8 1.0
N B:LYS109 4.6 18.9 1.0
CA B:LEU108 4.6 18.1 1.0
O B:HOH570 4.7 23.4 1.0
N B:LEU108 4.7 16.7 1.0
CB B:LYS109 4.9 23.1 1.0
CB B:ASN112 4.9 15.8 1.0
CA B:GLU83 5.0 21.3 1.0
CB B:HIS107 5.0 19.2 1.0

Magnesium binding site 7 out of 10 in 4kqx

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Magnesium binding site 7 out of 10 in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:9.0
occ:1.00
 O B:HOH639 1.8 19.9 1.0
O1N A:NAD401 2.8 22.9 1.0
O B:ILE261 2.9 14.2 1.0
O1A A:NAD401 3.0 18.8 1.0
O B:TYR259 3.0 19.4 1.0
O B:SER260 3.0 17.0 1.0
C B:SER260 3.4 17.5 1.0
C B:ILE261 3.4 14.2 1.0
PA A:NAD401 3.5 17.5 1.0
O2A A:NAD401 3.6 19.2 1.0
CB A:SER37 3.6 20.6 1.0
PN A:NAD401 3.8 18.1 1.0
N B:ILE261 4.0 14.5 1.0
C B:TYR259 4.1 19.4 1.0
O3 A:NAD401 4.1 20.0 1.0
O7N A:NAD401 4.1 23.8 1.0
N B:SER262 4.1 14.0 1.0
CA B:SER260 4.1 16.5 1.0
CA B:SER262 4.2 12.6 1.0
CA B:ILE261 4.2 14.7 1.0
N A:SER37 4.3 16.8 1.0
O A:HOH527 4.4 17.1 1.0
O2N A:NAD401 4.5 17.0 1.0
MG B:MG404 4.5 9.2 1.0
N B:SER260 4.5 20.5 1.0
OG A:SER37 4.6 17.4 1.0
CA A:SER37 4.6 17.2 1.0
C B:SER262 5.0 11.8 1.0

Magnesium binding site 8 out of 10 in 4kqx

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Magnesium binding site 8 out of 10 in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:15.4
occ:1.00
 OD1 B:ASP201 2.0 13.7 1.0
O2 A:HIO402 2.1 18.1 1.0
O A:HOH504 2.2 11.3 1.0
O B:HOH516 2.2 14.8 1.0
O A:HOH502 2.3 10.0 1.0
O3 A:HIO402 2.3 23.6 1.0
C2 A:HIO402 2.9 17.8 1.0
N3 A:HIO402 2.9 16.5 1.0
CG B:ASP201 3.0 13.3 1.0
OD2 B:ASP201 3.4 12.5 1.0
MG B:MG409 3.8 17.0 1.0
OE1 A:GLU237 3.9 14.4 1.0
OE2 A:GLU241 4.0 13.2 1.0
OE1 B:GLU205 4.0 12.7 1.0
NZ B:LYS141 4.0 12.2 1.0
OE1 A:GLU241 4.1 13.1 1.0
OE2 A:GLU237 4.1 15.8 1.0
O B:HOH526 4.1 19.1 1.0
CB B:ASP201 4.2 13.1 1.0
C4 A:HIO402 4.3 16.9 1.0
C1 A:HIO402 4.4 15.7 1.0
O B:HOH514 4.4 12.3 1.0
CD A:GLU241 4.5 11.4 1.0
O B:ASP201 4.5 12.2 1.0
CD A:GLU237 4.5 14.5 1.0
C5N B:NAD402 4.5 21.3 1.0
O B:PRO140 4.5 12.4 1.0
CA B:ASP201 4.5 13.5 1.0
CE B:LYS141 4.5 14.3 1.0
C41 A:HIO402 4.6 16.4 1.0
C4N B:NAD402 4.8 20.4 1.0
O11 A:HIO402 4.8 14.1 1.0
CA B:LYS141 4.9 13.6 1.0
C B:ASP201 4.9 12.9 1.0
C42 A:HIO402 5.0 18.0 1.0

Magnesium binding site 9 out of 10 in 4kqx

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Magnesium binding site 9 out of 10 in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:23.8
occ:1.00
 O2N B:NAD402 2.6 16.1 1.0
N B:GLY39 2.8 14.6 1.0
O B:LEU90 2.8 16.2 1.0
N B:GLY36 3.0 19.9 1.0
CA B:GLY36 3.2 16.7 1.0
C B:GLY36 3.3 16.7 1.0
N B:SER37 3.4 14.4 1.0
CA B:GLY39 3.5 17.8 1.0
N B:GLN38 3.6 15.0 1.0
O3 B:NAD402 3.6 20.3 1.0
CB B:LEU90 3.7 13.7 1.0
PN B:NAD402 3.7 21.3 1.0
O1A B:NAD402 3.7 20.4 1.0
O5B B:NAD402 3.8 19.9 1.0
C B:LEU90 3.8 14.4 1.0
C B:GLN38 3.8 14.9 1.0
O B:GLY36 3.8 15.1 1.0
CA B:GLN38 4.0 14.7 1.0
CB B:GLN38 4.1 17.0 1.0
PA B:NAD402 4.1 21.0 1.0
C B:TYR35 4.2 17.4 1.0
C B:SER37 4.2 17.0 1.0
C5D B:NAD402 4.3 17.5 1.0
CA B:LEU90 4.3 14.8 1.0
CA B:SER37 4.3 15.8 1.0
O5D B:NAD402 4.5 18.9 1.0
C4B B:NAD402 4.5 21.2 1.0
N B:TYR35 4.6 16.7 1.0
C5B B:NAD402 4.6 22.6 1.0
CA B:TYR35 4.7 17.5 1.0
C B:GLY39 4.7 14.7 1.0
C B:GLY34 4.8 17.2 1.0
CG B:LEU90 4.8 14.7 1.0
N B:VAL91 4.9 13.0 1.0
O B:GLY34 4.9 19.0 1.0
N B:HIS40 4.9 16.2 1.0
O B:GLN38 5.0 12.8 1.0

Magnesium binding site 10 out of 10 in 4kqx

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Magnesium binding site 10 out of 10 in the Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Mutant Slackia Exigua Kari Ddv in Complex with Nad and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg409

b:17.0
occ:1.00
 O B:HOH632 1.9 9.5 1.0
OD2 B:ASP201 2.0 12.5 1.0
O2 A:HIO402 2.1 18.1 1.0
OE1 B:GLU205 2.2 12.7 1.0
O B:HOH514 2.2 12.3 1.0
O11 A:HIO402 2.3 14.1 1.0
C2 A:HIO402 2.8 17.8 1.0
C1 A:HIO402 3.0 15.7 1.0
CD B:GLU205 3.0 9.8 1.0
CG B:ASP201 3.1 13.3 1.0
OE2 B:GLU205 3.1 11.3 1.0
OD1 B:ASP201 3.5 13.7 1.0
MG B:MG407 3.8 15.4 1.0
O A:HOH502 4.0 10.0 1.0
N3 A:HIO402 4.1 16.5 1.0
O12 A:HIO402 4.2 16.4 1.0
CE1 B:HIS118 4.2 12.3 1.0
NE2 B:HIS118 4.2 12.5 1.0
OG A:SER262 4.3 12.9 1.0
O B:HOH526 4.3 19.1 1.0
ND1 B:HIS118 4.4 13.5 1.0
CD2 B:HIS118 4.4 12.6 1.0
O B:ASP201 4.4 12.2 1.0
CB B:ASP201 4.4 13.1 1.0
CG B:GLU205 4.4 11.4 1.0
O2D B:NAD402 4.5 14.6 1.0
CB A:ALA265 4.5 12.7 1.0
CG B:HIS118 4.6 13.2 1.0
O B:HOH516 4.6 14.8 1.0
C B:ASP201 4.7 12.9 1.0
O3 A:HIO402 4.8 23.6 1.0
CB B:GLU205 4.8 10.6 1.0
C6N B:NAD402 4.9 20.4 1.0
C5N B:NAD402 5.0 21.3 1.0

Reference:

S.Brinkmann-Chen, T.Flock, J.K.Cahn, C.D.Snow, E.M.Brustad, J.A.Mcintosh, P.Meinhold, L.Zhang, F.H.Arnold. General Approach to Reversing Ketol-Acid Reductoisomerase Cofactor Dependence From Nadph to Nadh. Proc.Natl.Acad.Sci.Usa V. 110 10946 2013.
ISSN: ISSN 0027-8424
PubMed: 23776225
DOI: 10.1073/PNAS.1306073110
Page generated: Sat Aug 17 03:55:54 2024

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