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Magnesium in PDB 4xdy: Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean

Enzymatic activity of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean

All present enzymatic activity of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean:
1.1.1.86;

Protein crystallography data

The structure of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean, PDB code: 4xdy was solved by J.K.B.Cahn, S.Brinkmann-Chen, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 102.57 / 1.54
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.695, 141.748, 148.598, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean (pdb code 4xdy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean, PDB code: 4xdy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4xdy

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Magnesium binding site 1 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:13.9
occ:1.00
 O2 A:HIO406 2.0 17.6 1.0
OE1 A:GLU199 2.0 16.4 1.0
O11 A:HIO406 2.0 17.2 1.0
OD2 A:ASP195 2.1 17.3 1.0
O A:HOH528 2.1 19.1 1.0
O A:HOH647 2.2 15.4 1.0
C2 A:HIO406 2.7 18.7 1.0
C1 A:HIO406 2.8 16.8 1.0
CD A:GLU199 3.1 17.4 1.0
CG A:ASP195 3.1 16.8 1.0
OE2 A:GLU199 3.4 17.7 1.0
OD1 A:ASP195 3.5 20.0 1.0
MG A:MG402 3.6 17.1 1.0
N3 A:HIO406 3.9 20.7 1.0
O B:HOH539 3.9 19.2 1.0
O12 A:HIO406 4.1 19.2 1.0
O A:HOH534 4.2 17.7 1.0
OG B:SER256 4.2 17.0 1.0
NE2 A:HIS112 4.3 21.9 1.0
CE1 A:HIS112 4.3 22.2 1.0
CB A:ASP195 4.4 19.2 1.0
CG A:GLU199 4.5 17.2 1.0
O A:HOH527 4.5 20.2 1.0
O2D A:NAI403 4.5 19.2 1.0
ND1 A:HIS112 4.5 18.0 1.0
CD2 A:HIS112 4.5 22.3 1.0
O A:ASP195 4.6 17.4 1.0
O3 A:HIO406 4.6 25.5 1.0
CB B:ALA259 4.7 17.5 1.0
CG A:HIS112 4.7 19.7 1.0
C A:ASP195 4.8 17.1 1.0
CB A:GLU199 4.8 17.5 1.0
C4 A:HIO406 5.0 23.3 1.0

Magnesium binding site 2 out of 6 in 4xdy

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Magnesium binding site 2 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.1
occ:1.00
 OD1 A:ASP195 2.0 20.0 1.0
O3 A:HIO406 2.0 25.5 1.0
O2 A:HIO406 2.0 17.6 1.0
O B:HOH539 2.1 19.2 1.0
O B:HOH540 2.2 18.7 1.0
O A:HOH527 2.2 20.2 1.0
N3 A:HIO406 2.7 20.7 1.0
C2 A:HIO406 2.7 18.7 1.0
CG A:ASP195 3.0 16.8 1.0
OD2 A:ASP195 3.5 17.3 1.0
MG A:MG401 3.6 13.9 1.0
OE1 A:GLU199 4.0 16.4 1.0
OE1 B:GLU235 4.0 20.4 1.0
NZ A:LYS135 4.0 20.0 1.0
C4 A:HIO406 4.1 23.3 1.0
OE2 B:GLU235 4.1 22.2 1.0
OE2 B:GLU231 4.1 20.8 1.0
C1 A:HIO406 4.2 16.8 1.0
OE1 B:GLU231 4.2 19.4 1.0
O A:HOH534 4.2 17.7 1.0
CB A:ASP195 4.3 19.2 1.0
O A:HOH647 4.4 15.4 1.0
C41 A:HIO406 4.4 24.1 1.0
CD B:GLU235 4.5 22.4 1.0
CE A:LYS135 4.6 21.5 1.0
O11 A:HIO406 4.6 17.2 1.0
O A:ASP195 4.6 17.4 1.0
CA A:ASP195 4.6 18.4 1.0
CD B:GLU231 4.6 18.5 1.0
O A:PRO134 4.7 19.7 1.0
C5N A:NAI403 4.8 24.2 1.0
C42 A:HIO406 4.8 23.7 1.0
C4N A:NAI403 4.9 24.1 1.0
C A:ASP195 5.0 17.1 1.0

Magnesium binding site 3 out of 6 in 4xdy

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Magnesium binding site 3 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:34.2
occ:1.00
 O A:HOH623 1.9 35.0 1.0
O A:HOH665 2.1 32.9 1.0
O A:HOH533 2.1 23.8 1.0
OD1 A:ASN257 2.1 20.5 1.0
O A:HOH630 2.1 34.7 1.0
CG A:ASN257 3.3 18.7 1.0
ND2 A:ASN257 3.9 18.6 1.0
OE1 A:GLU260 4.0 24.5 1.0
NH2 B:ARG310 4.1 27.1 1.0
O A:GLU253 4.1 19.1 1.0
O A:ILE255 4.2 16.5 1.0
N A:ASN257 4.3 16.2 1.0
O B:HOH553 4.4 18.6 1.0
O A:ALA252 4.4 20.6 1.0
CB A:ASN257 4.4 16.9 1.0
CA A:ASN257 4.5 15.1 1.0
O1A B:NAI404 4.5 20.5 1.0
O B:HOH640 4.6 33.2 1.0
C A:SER256 4.8 16.2 1.0
C A:GLU253 4.8 20.4 1.0
O B:HOH557 4.8 17.8 1.0
O B:HOH570 4.9 29.1 1.0
O A:HOH565 5.0 26.2 1.0
CA A:GLU253 5.0 20.6 1.0

Magnesium binding site 4 out of 6 in 4xdy

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Magnesium binding site 4 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:14.2
occ:1.00
 OD2 B:ASP195 2.0 16.9 1.0
O11 B:HIO401 2.1 15.4 1.0
OE1 B:GLU199 2.1 15.1 1.0
O2 B:HIO401 2.1 15.6 1.0
O B:HOH536 2.2 17.1 1.0
O B:HOH537 2.2 17.4 1.0
C2 B:HIO401 2.8 17.1 1.0
C1 B:HIO401 2.8 16.3 1.0
CD B:GLU199 3.1 17.2 1.0
CG B:ASP195 3.1 14.8 1.0
OE2 B:GLU199 3.4 17.5 1.0
OD1 B:ASP195 3.5 15.0 1.0
MG B:MG403 3.7 15.3 1.0
O A:HOH525 3.9 17.9 1.0
N3 B:HIO401 4.0 19.4 1.0
O12 B:HIO401 4.0 15.8 1.0
O B:HOH544 4.2 19.4 1.0
NE2 B:HIS112 4.2 18.6 1.0
CE1 B:HIS112 4.3 18.2 1.0
OG A:SER256 4.3 15.8 1.0
O B:HOH682 4.3 45.4 1.0
CB B:ASP195 4.4 14.8 1.0
O2D B:NAI404 4.4 17.9 1.0
O B:HOH538 4.5 17.6 1.0
ND1 B:HIS112 4.5 18.1 1.0
CG B:GLU199 4.5 16.2 1.0
CD2 B:HIS112 4.5 18.5 1.0
O B:ASP195 4.5 15.0 1.0
O3 B:HIO401 4.5 21.6 1.0
CB A:ALA259 4.6 16.9 1.0
CG B:HIS112 4.6 17.0 1.0
C B:ASP195 4.7 15.4 1.0
CB B:GLU199 4.9 16.9 1.0

Magnesium binding site 5 out of 6 in 4xdy

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Magnesium binding site 5 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:15.3
occ:1.00
 OD1 B:ASP195 2.0 15.0 1.0
O3 B:HIO401 2.0 21.6 1.0
O2 B:HIO401 2.0 15.6 1.0
O A:HOH526 2.0 16.3 1.0
O B:HOH538 2.1 17.6 1.0
O A:HOH525 2.2 17.9 1.0
C2 B:HIO401 2.8 17.1 1.0
N3 B:HIO401 2.9 19.4 1.0
CG B:ASP195 3.0 14.8 1.0
OD2 B:ASP195 3.4 16.9 1.0
MG B:MG402 3.7 14.2 1.0
NZ B:LYS135 3.9 18.9 1.0
O B:HOH682 3.9 45.4 1.0
OE1 A:GLU235 4.0 17.7 1.0
OE1 B:GLU199 4.1 15.1 1.0
OE2 A:GLU235 4.1 18.1 1.0
OE2 A:GLU231 4.2 17.1 1.0
O B:HOH544 4.2 19.4 1.0
OE1 A:GLU231 4.2 17.4 1.0
C4 B:HIO401 4.2 19.2 1.0
CB B:ASP195 4.3 14.8 1.0
C1 B:HIO401 4.3 16.3 1.0
O B:HOH537 4.5 17.4 1.0
CD A:GLU235 4.5 17.0 1.0
CE B:LYS135 4.5 18.7 1.0
O B:PRO134 4.6 17.9 1.0
CA B:ASP195 4.6 14.9 1.0
O B:ASP195 4.6 15.0 1.0
O11 B:HIO401 4.6 15.4 1.0
CD A:GLU231 4.7 16.4 1.0
C41 B:HIO401 4.7 21.0 1.0
C5N B:NAI404 4.7 20.3 1.0
C4N B:NAI404 4.9 19.8 1.0
C42 B:HIO401 4.9 19.9 1.0
C B:ASP195 5.0 15.4 1.0
CA B:LYS135 5.0 15.6 1.0

Magnesium binding site 6 out of 6 in 4xdy

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Magnesium binding site 6 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:34.3
occ:1.00
 O A:HOH625 1.9 35.6 1.0
O B:HOH694 2.0 37.2 1.0
OD1 B:ASN257 2.1 20.7 1.0
O B:HOH649 2.1 31.3 1.0
O B:HOH551 2.1 26.0 1.0
CG B:ASN257 3.2 20.4 1.0
ND2 B:ASN257 3.8 22.9 1.0
O B:GLU253 4.0 20.5 1.0
OE1 B:GLU260 4.1 23.0 1.0
O B:ILE255 4.1 17.8 1.0
NH2 A:ARG310 4.3 31.2 1.0
N B:ASN257 4.3 19.0 1.0
O A:HOH531 4.3 23.3 1.0
O B:ALA252 4.4 19.1 1.0
O1A A:NAI403 4.4 23.4 1.0
CB B:ASN257 4.5 20.8 1.0
CA B:ASN257 4.5 18.3 1.0
C B:GLU253 4.8 20.2 1.0
C B:SER256 4.8 18.0 1.0
O A:HOH544 4.8 19.8 1.0
O A:HOH557 4.9 27.9 1.0
CA B:GLU253 5.0 22.6 1.0

Reference:

J.K.Cahn, S.Brinkmann-Chen, T.Spatzal, J.A.Wiig, A.R.Buller, O.Einsle, Y.Hu, M.W.Ribbe, F.H.Arnold. Cofactor Specificity Motifs and the Induced Fit Mechanism in Class I Ketol-Acid Reductoisomerases. Biochem.J. 2015.
ISSN: ESSN 1470-8728
PubMed: 25849365
DOI: 10.1042/BJ20150183
Page generated: Tue Aug 20 15:27:23 2024

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