Magnesium in PDB 7yqa: Crystal Structure of D-Threonine Aldolase From Chlamydomonas Reinhardtii

All present enzymatic activity of Crystal Structure of D-Threonine Aldolase From Chlamydomonas Reinhardtii:
4.1.2.42;

The structure of Crystal Structure of D-Threonine Aldolase From Chlamydomonas Reinhardtii, PDB code: 7yqa was solved by Y.Hirato, M.Goto, T.Mizobuchi, H.Muramatsu, M.Tanigawa, K.Nishimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.46 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	64.792, 74.096, 89.939, 77.07, 69.34, 71.93
R / Rfree (%)	21.7 / 24.9

The binding sites of Magnesium atom in the Crystal Structure of D-Threonine Aldolase From Chlamydomonas Reinhardtii (pdb code 7yqa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of D-Threonine Aldolase From Chlamydomonas Reinhardtii, PDB code: 7yqa:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of D-Threonine Aldolase From Chlamydomonas Reinhardtii


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 D-Threonine Aldolase From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:22.6 occ:1.00 O A:HOH719 2.1 24.6 1.0 O B:HOH675 2.1 14.2 1.0 OD1 A:ASP386 2.2 21.7 1.0 O A:HOH664 2.2 18.7 1.0 NE2 A:HIS384 2.3 18.9 1.0 O A:HOH691 2.5 26.3 1.0 CG A:ASP386 3.0 20.7 1.0 CD2 A:HIS384 3.2 18.4 1.0 OD2 A:ASP386 3.3 21.3 1.0 CE1 A:HIS384 3.4 18.7 1.0 OG A:SER275 4.1 22.1 1.0 CB A:ASP386 4.1 20.1 1.0 O A:HOH692 4.2 21.8 1.0 CG A:HIS384 4.4 18.9 1.0 ND1 A:HIS384 4.4 18.6 1.0 OD2 B:ASP353 4.6 23.0 1.0 OD1 B:ASP353 4.6 23.2 1.0 OP3 A:LLP80 4.6 21.1 1.0 N A:ASP386 4.7 19.1 1.0 OP1 A:LLP80 4.8 21.6 1.0 CD A:PRO387 4.9 17.6 1.0 SG A:CYS385 4.9 22.2 1.0 CG B:ASP353 5.0 22.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of D-Threonine Aldolase From Chlamydomonas Reinhardtii


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 D-Threonine Aldolase From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg500 b:19.3 occ:1.00 O B:HOH702 2.1 19.3 1.0 O B:HOH637 2.1 20.5 1.0 O A:HOH714 2.2 16.8 1.0 OD1 B:ASP386 2.2 21.4 1.0 NE2 B:HIS384 2.2 19.2 1.0 CG B:ASP386 2.9 20.7 1.0 CD2 B:HIS384 3.2 19.6 1.0 OD2 B:ASP386 3.2 21.1 1.0 CE1 B:HIS384 3.3 19.6 1.0 OG B:SER275 4.0 16.1 1.0 CB B:ASP386 4.1 20.1 1.0 O B:HOH690 4.2 22.9 1.0 OD2 A:ASP353 4.3 21.3 1.0 CG B:HIS384 4.3 20.2 1.0 ND1 B:HIS384 4.3 20.2 1.0 OP3 B:LLP80 4.5 22.7 1.0 O B:HOH647 4.5 20.8 1.0 N B:ASP386 4.7 19.4 1.0 CE B:LLP80 4.8 24.3 1.0 OP1 B:LLP80 4.8 23.6 1.0 SG B:CYS385 4.9 21.3 1.0 CD B:PRO387 4.9 17.7 1.0 CG A:ASP353 5.0 20.4 1.0 OD1 A:ASP353 5.0 21.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of D-Threonine Aldolase From Chlamydomonas Reinhardtii


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 D-Threonine Aldolase From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg500 b:19.9 occ:1.00 O C:HOH681 1.7 22.5 1.0 O D:HOH711 2.0 18.7 1.0 OD1 C:ASP386 2.2 22.3 1.0 O C:HOH655 2.3 22.2 1.0 O C:HOH705 2.3 16.4 1.0 NE2 C:HIS384 2.7 23.4 1.0 CG C:ASP386 2.8 21.0 1.0 OD2 C:ASP386 3.1 20.7 1.0 CD2 C:HIS384 3.5 22.4 1.0 CE1 C:HIS384 3.8 23.1 1.0 CB C:ASP386 4.0 20.7 1.0 OG C:SER275 4.1 18.5 1.0 OD2 D:ASP353 4.2 18.6 1.0 CE C:LLP80 4.3 23.1 1.0 OP3 C:LLP80 4.3 22.1 1.0 O C:HOH644 4.4 16.5 1.0 N C:ASP386 4.6 20.3 1.0 OD1 D:ASP353 4.6 18.4 1.0 CG C:HIS384 4.7 22.9 1.0 CG D:ASP353 4.8 18.8 1.0 O C:HOH629 4.8 33.4 1.0 ND1 C:HIS384 4.8 22.8 1.0 OP1 C:LLP80 4.8 21.5 1.0 CA C:ASP386 4.9 19.6 1.0 SG C:CYS385 5.0 23.4 1.0 C4' C:LLP80 5.0 25.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of D-Threonine Aldolase From Chlamydomonas Reinhardtii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of D-Threonine Aldolase From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg500 b:22.8 occ:1.00 O C:HOH703 2.0 11.6 1.0 O D:HOH688 2.1 14.9 1.0 NE2 D:HIS384 2.1 19.3 1.0 O D:HOH698 2.2 21.9 1.0 OD1 D:ASP386 2.3 20.6 1.0 CG D:ASP386 3.0 20.3 1.0 CE1 D:HIS384 3.1 19.2 1.0 CD2 D:HIS384 3.1 18.9 1.0 OD2 D:ASP386 3.3 21.1 1.0 CB D:ASP386 4.0 19.8 1.0 OG D:SER275 4.2 21.1 1.0 ND1 D:HIS384 4.2 19.1 1.0 O D:HOH625 4.3 21.4 1.0 CG D:HIS384 4.3 19.5 1.0 OD2 C:ASP353 4.5 23.1 1.0 OD1 C:ASP353 4.6 22.8 1.0 OP3 D:LLP80 4.7 22.7 1.0 N D:ASP386 4.8 18.9 1.0 OP1 D:LLP80 4.8 24.4 1.0 CE D:LLP80 4.9 22.0 1.0 CG C:ASP353 4.9 22.2 1.0 CD D:PRO387 5.0 18.1 1.0

Y.Hirato, M.Goto, T.Mizobuchi, H.Muramatsu, M.Tanigawa, K.Nishimura. Structure of Pyridoxal 5'-Phosphate-Bound D-Threonine Aldolase From Chlamydomonas Reinhardtii. Acta Crystallogr.,Sect.F V. 79 31 2023.
ISSN: ESSN 2053-230X
PubMed: 36748339
DOI: 10.1107/S2053230X23000304