Manganese in PDB 5hn4: Crystal Structure of Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis Complexed with Mn and Homoisocitrate

The structure of Crystal Structure of Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis Complexed with Mn and Homoisocitrate, PDB code: 5hn4 was solved by T.Shimizu, T.Tomita, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	143.23 / 2.64
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.669, 113.669, 143.226, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22

The binding sites of Manganese atom in the Crystal Structure of Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis Complexed with Mn and Homoisocitrate (pdb code 5hn4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis Complexed with Mn and Homoisocitrate, PDB code: 5hn4:

Manganese binding site 1 out of 1 in the Crystal Structure of Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis Complexed with Mn and Homoisocitrate


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 Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis Complexed with Mn and Homoisocitrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:53.9 occ:1.00 OD1 A:ASP218 2.0 45.9 1.0 OAF A:48Y401 2.1 45.2 1.0 O A:HOH504 2.2 43.7 1.0 OAD A:48Y401 2.3 48.8 1.0 O A:HOH511 2.4 54.4 1.0 CAK A:48Y401 2.9 44.5 1.0 CG A:ASP218 3.0 42.7 1.0 CAM A:48Y401 3.1 44.7 1.0 OD2 A:ASP218 3.4 39.5 1.0 OD1 A:ASP222 3.9 52.3 1.0 O A:ASP218 4.1 53.2 1.0 CAL A:48Y401 4.1 52.8 1.0 OAB A:48Y401 4.1 43.1 1.0 NH1 A:ARG96 4.2 57.1 1.0 CAN A:48Y401 4.2 48.0 1.0 CB A:ASP218 4.3 43.5 1.0 NH2 A:ARG111 4.3 50.9 1.0 OAC A:48Y401 4.4 54.4 1.0 OAG A:48Y401 4.4 50.5 1.0 CG A:ASP222 4.4 52.5 1.0 C2 A:IMD403 4.6 79.0 1.0 CA A:ASP218 4.6 46.3 1.0 OD2 A:ASP222 4.6 56.6 1.0 C A:ASP218 4.6 47.2 1.0 N1 A:IMD403 4.8 73.1 1.0 CAI A:48Y401 5.0 54.3 1.0

T.Shimizu, L.Yin, A.Yoshida, Y.Yokooji, S.I.Hachisuka, T.Sato, T.Tomita, H.Nishida, H.Atomi, T.Kuzuyama, M.Nishiyama. Structure and Function of An Ancestral-Type Beta-Decarboxylating Dehydrogenase From Thermococcus Kodakarensis Biochem. J. V. 474 105 2017.
ISSN: ESSN 1470-8728
PubMed: 27831491
DOI: 10.1042/BCJ20160699