Manganese in PDB 4v15: Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans

All present enzymatic activity of Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans:
4.1.2.42;

The structure of Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans, PDB code: 4v15 was solved by M.K.Uhl, G.Oberdorfer, G.Steinkellner, L.Riegler, M.Schuermann, K.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.759 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.267, 84.278, 72.852, 90.00, 111.90, 90.00
R / Rfree (%)	14.84 / 17.67

The structure of Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans (pdb code 4v15). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans, PDB code: 4v15:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1382 b:18.4 occ:1.00 O A:HOH2482 1.8 18.2 1.0 O A:HOH2481 1.9 26.3 1.0 O A:HOH2120 2.2 19.1 1.0 NE2 A:HIS347 2.2 13.7 1.0 OD1 A:ASP349 2.3 18.1 1.0 O A:HOH2387 2.3 20.0 1.0 CD2 A:HIS347 3.1 12.6 1.0 CG A:ASP349 3.2 19.1 1.0 CE1 A:HIS347 3.2 13.1 1.0 OD2 A:ASP349 3.5 18.9 1.0 O A:HOH2314 3.9 43.5 1.0 O A:HOH2313 4.1 27.5 1.0 OD1 B:ASP321 4.2 40.3 1.0 OG A:SER252 4.2 15.8 1.0 O2P A:PLP1380 4.2 13.7 0.6 CG A:HIS347 4.3 12.5 1.0 O A:HOH2315 4.3 19.7 1.0 ND1 A:HIS347 4.3 15.5 1.0 CB A:ASP349 4.4 9.5 1.0 O1P A:PLP1381 4.6 10.8 0.4 O B:HOH2399 4.7 41.6 1.0 CG B:ASP321 4.7 39.4 1.0 O2P A:PLP1381 4.7 12.2 0.4 N A:ASP349 4.7 10.4 1.0 OD2 B:ASP321 4.8 45.4 1.0 O4A A:PLP1381 4.8 28.9 0.4 NZ A:LYS59 4.8 23.5 0.4 CD A:PRO350 4.9 10.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1382 b:15.7 occ:1.00 O B:HOH2415 2.0 19.0 1.0 O A:HOH2460 2.0 20.1 1.0 O B:HOH2111 2.1 15.4 1.0 NE2 B:HIS347 2.2 13.9 1.0 OD1 B:ASP349 2.3 15.9 1.0 O B:HOH2337 2.3 16.2 1.0 CD2 B:HIS347 3.1 14.2 1.0 CG B:ASP349 3.2 16.0 1.0 CE1 B:HIS347 3.3 12.2 1.0 OD2 B:ASP349 3.5 16.0 1.0 O B:HOH2414 4.0 39.3 1.0 O B:HOH2272 4.0 28.1 1.0 OG B:SER252 4.2 13.0 1.0 O2P B:PLP1380 4.2 12.9 0.5 OD1 A:ASP321 4.3 40.1 1.0 NZ B:LYS59 4.3 21.7 0.5 CG B:HIS347 4.3 12.7 1.0 ND1 B:HIS347 4.3 13.3 1.0 O B:HOH2279 4.4 14.8 1.0 CB B:ASP349 4.4 11.3 1.0 O1P B:PLP1381 4.5 12.2 0.5 O A:HOH2457 4.6 39.5 1.0 O3P B:PLP1381 4.7 13.3 0.5 N B:ASP349 4.7 10.4 1.0 CG A:ASP321 4.8 38.1 1.0 OD2 A:ASP321 4.8 39.5 1.0 NZ B:LYS59 4.9 25.6 0.5 CD B:PRO350 4.9 10.7 1.0

M.K.Uhl, G.Oberdorfer, G.Steinkellner, L.Riegler, M.Schuermann, K.Gruber. The Crystal Structure of D-Threonine Aldolase From Alcaligenes Xylosoxidans Provides Insight Into A Metal Ion Assisted Plp-Dependent Mechanism To Be Published.