Magnesium in PDB 4xdz: Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans

All present enzymatic activity of Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans:
1.1.1.86;

The structure of Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans, PDB code: 4xdz 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)	68.42 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.579, 90.753, 69.525, 90.00, 100.25, 90.00
R / Rfree (%)	15.7 / 19

The binding sites of Magnesium atom in the Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans (pdb code 4xdz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans, PDB code: 4xdz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:6.7 occ:1.00 OD2 A:ASP191 2.0 7.8 1.0 O12 A:40E404 2.1 7.8 1.0 O A:HOH597 2.1 6.9 1.0 O A:HOH598 2.1 7.0 1.0 OE1 A:GLU195 2.1 6.7 1.0 O2 A:40E404 2.1 8.1 1.0 C2 A:40E404 2.7 7.7 1.0 C1 A:40E404 2.8 9.4 1.0 CG A:ASP191 3.0 7.8 1.0 CD A:GLU195 3.1 6.2 1.0 OE2 A:GLU195 3.4 7.5 1.0 OD1 A:ASP191 3.4 8.9 1.0 MG A:MG403 3.7 8.9 1.0 O B:HOH676 3.9 13.0 1.0 N3 A:40E404 3.9 10.0 1.0 O11 A:40E404 4.1 8.2 1.0 O A:HOH596 4.2 7.8 1.0 OG B:SER252 4.3 6.5 1.0 CE1 A:HIS108 4.3 9.0 1.0 CB A:ASP191 4.3 6.9 1.0 NE2 A:HIS108 4.4 7.9 1.0 ND1 A:HIS108 4.4 8.6 1.0 O A:HOH595 4.5 10.5 1.0 O2D A:NDP401 4.5 7.0 1.0 CG A:GLU195 4.5 7.5 1.0 O A:ASP191 4.5 6.2 1.0 CD2 A:HIS108 4.6 7.3 1.0 CG A:HIS108 4.6 7.3 1.0 C A:ASP191 4.7 5.4 1.0 CB B:ALA255 4.7 6.8 1.0 CB A:GLU195 4.9 8.6 1.0 C4N A:NDP401 5.0 7.3 1.0

Magnesium binding site 2 out of 4 in the Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:8.9 occ:1.00 O B:HOH598 2.0 12.4 1.0 OD1 A:ASP191 2.0 8.9 1.0 O2 A:40E404 2.1 8.1 1.0 O A:HOH595 2.1 10.5 1.0 O B:HOH747 2.1 19.3 1.0 O B:HOH676 2.2 13.0 1.0 C2 A:40E404 2.9 7.7 1.0 CG A:ASP191 3.1 7.8 1.0 N3 A:40E404 3.1 10.0 1.0 OD2 A:ASP191 3.5 7.8 1.0 MG A:MG402 3.7 6.7 1.0 OE1 B:GLU231 3.9 11.2 1.0 NZ A:LYS131 3.9 12.2 1.0 OE1 B:GLU227 4.1 14.4 1.0 OE2 B:GLU231 4.1 11.6 1.0 O A:HOH596 4.2 7.8 1.0 OE2 B:GLU227 4.2 12.5 1.0 OE1 A:GLU195 4.2 6.7 1.0 CB A:ASP191 4.2 6.9 1.0 C1 A:40E404 4.3 9.4 1.0 O A:HOH597 4.3 6.9 1.0 C4 A:40E404 4.4 9.8 1.0 O A:PRO130 4.4 7.3 1.0 CD B:GLU231 4.5 11.2 1.0 CE A:LYS131 4.5 11.3 1.0 CD B:GLU227 4.6 15.2 1.0 C5N A:NDP401 4.6 8.1 1.0 C4N A:NDP401 4.6 7.3 1.0 CA A:ASP191 4.6 6.7 1.0 O12 A:40E404 4.7 7.8 1.0 O A:ASP191 4.7 6.2 1.0 C41 A:40E404 4.9 12.2 1.0 CD A:LYS131 5.0 10.0 1.0 CA A:LYS131 5.0 8.2 1.0

Magnesium binding site 3 out of 4 in the Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:8.8 occ:1.00 O A:HOH599 2.0 12.3 1.0 OD1 B:ASP191 2.0 9.0 1.0 O2 B:40E404 2.0 7.8 1.0 O B:HOH602 2.1 10.6 1.0 O A:HOH740 2.2 19.0 1.0 O A:HOH673 2.3 13.2 1.0 C2 B:40E404 2.9 7.3 1.0 N3 B:40E404 3.1 10.3 1.0 CG B:ASP191 3.1 7.0 1.0 OD2 B:ASP191 3.5 8.4 1.0 MG B:MG403 3.7 6.7 1.0 OE1 A:GLU231 3.9 11.6 1.0 NZ B:LYS131 4.0 12.2 1.0 OE2 A:GLU231 4.1 10.4 1.0 OE1 A:GLU227 4.1 14.3 1.0 O B:HOH601 4.2 8.3 1.0 OE2 A:GLU227 4.2 13.3 1.0 OE1 B:GLU195 4.2 6.6 1.0 CB B:ASP191 4.3 7.0 1.0 C1 B:40E404 4.3 9.6 1.0 O B:HOH600 4.4 6.4 1.0 C4 B:40E404 4.4 10.5 1.0 O B:PRO130 4.4 7.5 1.0 CD A:GLU231 4.4 10.0 1.0 CE B:LYS131 4.5 11.4 1.0 C5N B:NDP401 4.5 8.9 1.0 CD A:GLU227 4.6 14.2 1.0 C4N B:NDP401 4.6 6.7 1.0 O11 B:40E404 4.7 7.5 1.0 CA B:ASP191 4.7 6.5 1.0 O B:ASP191 4.8 5.9 1.0 C41 B:40E404 4.9 10.9 1.0 CD B:LYS131 5.0 9.6 1.0 CA B:LYS131 5.0 7.3 1.0

Magnesium binding site 4 out of 4 in the Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Holo Structure of Ketol-Acid Reductoisomerase From Ignisphaera Aggregans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:6.7 occ:1.00 OD2 B:ASP191 2.0 8.4 1.0 O B:HOH599 2.0 7.7 1.0 O11 B:40E404 2.1 7.5 1.0 O B:HOH600 2.1 6.4 1.0 OE1 B:GLU195 2.1 6.6 1.0 O2 B:40E404 2.2 7.8 1.0 C2 B:40E404 2.7 7.3 1.0 C1 B:40E404 2.9 9.6 1.0 CG B:ASP191 3.0 7.0 1.0 CD B:GLU195 3.1 6.3 1.0 OE2 B:GLU195 3.4 7.2 1.0 OD1 B:ASP191 3.4 9.0 1.0 MG B:MG402 3.7 8.8 1.0 N3 B:40E404 3.9 10.3 1.0 O A:HOH673 4.0 13.2 1.0 O12 B:40E404 4.1 8.0 1.0 O B:HOH601 4.2 8.3 1.0 OG A:SER252 4.3 7.2 1.0 CE1 B:HIS108 4.3 6.7 1.0 NE2 B:HIS108 4.4 7.0 1.0 ND1 B:HIS108 4.4 6.8 1.0 CB B:ASP191 4.4 7.0 1.0 O2D B:NDP401 4.5 6.8 1.0 CG B:GLU195 4.5 7.7 1.0 O B:HOH602 4.5 10.6 1.0 O B:ASP191 4.5 5.9 1.0 CD2 B:HIS108 4.6 7.9 1.0 CG B:HIS108 4.6 6.6 1.0 C B:ASP191 4.7 5.5 1.0 CB A:ALA255 4.7 6.7 1.0 CB B:GLU195 4.9 7.2 1.0

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