Magnesium in PDB 6sy1: Crystal Structure of A Dehydrogenase

All present enzymatic activity of Crystal Structure of A Dehydrogenase:
1.2.4.2;

The structure of Crystal Structure of A Dehydrogenase, PDB code: 6sy1 was solved by G.A.Bezerra, W.Foster, L.Shrestha, I.A.Pena, J.Coker, S.Kolker, B.B.Nicola, F.Von Delft, A.Edwards, C.Arrowsmith, C.Bountra, W.W.Yue, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.01 / 1.87
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.550, 81.220, 86.900, 63.43, 76.96, 72.06
R / Rfree (%)	19 / 23

The binding sites of Magnesium atom in the Crystal Structure of A Dehydrogenase (pdb code 6sy1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Dehydrogenase, PDB code: 6sy1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of A Dehydrogenase


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 A Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:18.1 occ:1.00 O1B A:TPP1001 2.0 16.3 1.0 OD1 A:ASP333 2.0 21.5 1.0 O1A A:TPP1001 2.0 18.4 1.0 OD1 A:ASN366 2.1 18.5 1.0 O A:HOH1133 2.1 25.2 1.0 O A:LEU368 2.2 18.7 1.0 CG A:ASP333 3.1 18.4 1.0 CG A:ASN366 3.1 18.7 1.0 PB A:TPP1001 3.1 20.4 1.0 PA A:TPP1001 3.2 19.2 1.0 O3A A:TPP1001 3.3 17.0 1.0 C A:LEU368 3.3 21.6 1.0 ND2 A:ASN366 3.4 18.5 1.0 OD2 A:ASP333 3.5 21.4 1.0 O3B A:TPP1001 3.7 21.6 1.0 N A:ASP333 3.9 16.6 1.0 O7 A:TPP1001 4.0 15.3 1.0 N A:LEU368 4.1 20.6 1.0 N A:GLY369 4.2 19.1 1.0 CA A:GLY369 4.2 19.6 1.0 O A:HOH1308 4.2 23.1 1.0 CB A:ASP333 4.3 18.5 1.0 N A:ASN366 4.3 20.1 1.0 CA A:LEU368 4.4 22.9 1.0 N A:ALA334 4.4 15.3 1.0 O A:VAL364 4.4 20.0 1.0 O2B A:TPP1001 4.4 16.4 1.0 CB A:ASN366 4.4 20.1 1.0 O2A A:TPP1001 4.4 19.1 1.0 CA A:ASP333 4.6 20.1 1.0 N A:GLN367 4.6 20.3 1.0 CA A:ASN366 4.7 20.5 1.0 C A:ASN366 4.7 21.0 1.0 C A:GLY332 4.8 18.6 1.0 CA A:GLY332 4.8 17.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of A Dehydrogenase


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 A Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:22.2 occ:1.00 O B:HOH1378 2.0 20.3 1.0 O A:HOH1378 2.1 20.3 1.0 OE1 A:GLU641 2.1 19.2 1.0 OE1 B:GLU641 2.1 17.3 1.0 O B:HOH1237 2.2 20.3 1.0 O B:HOH1171 2.3 20.3 1.0 CD A:GLU641 3.1 19.2 1.0 CD B:GLU641 3.1 16.8 1.0 OE2 A:GLU641 3.5 18.2 1.0 OE2 B:GLU641 3.5 18.6 1.0 O A:HOH1310 4.3 15.8 1.0 O B:HOH1454 4.3 18.9 1.0 O B:GLY671 4.3 17.3 1.0 O A:GLY671 4.3 16.2 1.0 CG A:GLU641 4.4 16.6 1.0 CG B:GLU641 4.4 17.8 1.0 OE2 A:GLU344 4.5 19.6 1.0 OE2 B:GLU344 4.5 17.9 1.0 CB A:GLU641 4.5 16.9 1.0 CB B:GLU641 4.6 16.2 1.0 O B:HOH1458 4.6 17.5 1.0 O A:HOH1447 4.8 13.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of A Dehydrogenase


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 A Dehydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:18.3 occ:1.00 O1A B:TPP1001 2.0 18.1 1.0 OD1 B:ASP333 2.1 19.9 1.0 OD1 B:ASN366 2.1 21.1 1.0 O2B B:TPP1001 2.1 20.3 1.0 O B:LEU368 2.1 20.6 1.0 O B:HOH1228 2.2 25.2 1.0 CG B:ASN366 3.1 22.0 1.0 PA B:TPP1001 3.1 22.2 1.0 CG B:ASP333 3.2 21.5 1.0 O3A B:TPP1001 3.2 21.3 1.0 PB B:TPP1001 3.2 20.7 1.0 C B:LEU368 3.3 21.0 1.0 ND2 B:ASN366 3.4 20.5 1.0 OD2 B:ASP333 3.7 19.6 1.0 O1B B:TPP1001 3.7 21.7 1.0 O7 B:TPP1001 3.9 18.8 1.0 N B:ASP333 4.0 17.3 1.0 N B:LEU368 4.1 20.5 1.0 N B:GLY369 4.2 21.4 1.0 CA B:GLY369 4.2 21.1 1.0 O B:HOH1225 4.3 19.2 1.0 CA B:LEU368 4.3 21.8 1.0 N B:ASN366 4.4 20.3 1.0 O2A B:TPP1001 4.4 17.3 1.0 N B:ALA334 4.4 18.8 1.0 CB B:ASP333 4.4 21.5 1.0 O B:VAL364 4.4 21.8 1.0 CB B:ASN366 4.4 19.7 1.0 O3B B:TPP1001 4.5 18.9 1.0 CA B:ASP333 4.7 20.6 1.0 N B:GLN367 4.7 19.9 1.0 CA B:ASN366 4.7 19.1 1.0 C B:ASN366 4.8 19.8 1.0 C B:GLY332 4.8 18.3 1.0 CA B:GLY332 4.8 18.5 1.0 CB B:ALA334 5.0 18.9 1.0

G.A.Bezerra, W.Foster, L.Shrestha, I.A.Pena, J.Coker, S.Kolker, A.Edwards, C.Arrowsmith, C.Bountra, W.Y.Wyatt. Crystal Structure of Dehydrogenase E1 and Transketolase Domain-Containing Protein 1 (DHTKD1) To Be Published.