Magnesium in PDB 6ze6: Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Nitrocatechol

The structure of Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Nitrocatechol, PDB code: 6ze6 was solved by L.Svecova, T.Skalova, P.Kolenko, T.Koval, L.H.Oestergaard, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.06 / 1.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.565, 109.746, 116.071, 90, 90, 90
R / Rfree (%)	11.3 / 14.7

The structure of Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Nitrocatechol also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Nitrocatechol (pdb code 6ze6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Nitrocatechol, PDB code: 6ze6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Nitrocatechol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Nitrocatechol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg711 b:53.8 occ:1.00 O A:HOH1512 2.1 26.6 0.7 O A:HOH966 2.1 37.8 1.0 O A:HOH1001 2.6 20.4 1.0 OD1 A:ASN182 2.6 12.9 1.0 O A:HOH1556 3.0 32.9 1.0 CG A:ASN182 3.6 10.3 1.0 O A:HOH1468 4.0 36.8 1.0 O A:HOH1386 4.1 24.4 1.0 CB A:ASN182 4.2 10.4 1.0 O A:HOH975 4.3 24.2 1.0 CA A:ASN182 4.4 9.9 1.0 O6 A:NAG703 4.4 19.1 0.5 O5 A:NAG703 4.4 11.7 0.5 O A:HOH1620 4.5 27.1 0.5 O A:HOH1752 4.6 46.1 1.0 ND2 A:ASN182 4.7 11.2 1.0 C1 A:NAG703 4.7 10.9 0.5 O5 A:NAG703 4.9 13.9 0.5 C5 A:NAG703 5.0 12.3 0.5 O A:ALA179 5.0 11.4 1.0 O A:HOH1275 5.0 21.1 0.6

Magnesium binding site 2 out of 3 in the Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Nitrocatechol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Nitrocatechol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg712 b:13.4 occ:1.00 O A:HOH1746 2.0 16.0 1.0 O A:HOH1494 2.0 12.7 1.0 O B:HOH1138 2.1 14.0 1.0 O A:HOH1152 2.1 14.0 1.0 O B:HOH1277 2.1 13.8 1.0 O A:HOH1280 2.1 13.9 1.0 O A:HOH1286 4.1 13.0 1.0 O B:HOH1267 4.1 12.4 1.0 O B:HOH1686 4.2 29.0 1.0 O A:HOH1717 4.2 28.7 1.0 O A:PRO172 4.3 9.9 1.0 O B:PRO172 4.3 9.6 1.0 O B:HOH1558 4.4 26.8 1.0 O A:HOH1607 4.4 28.6 1.0 O B:PRO173 4.4 10.4 1.0 O A:PRO173 4.5 10.9 1.0 CG A:PRO172 4.7 13.3 0.5 CG B:PRO172 4.7 12.8 0.5 CA B:SER174 4.9 10.1 0.7 C B:PRO173 5.0 9.7 1.0 CA A:SER174 5.0 10.9 0.3 CD A:PRO175 5.0 12.5 0.5 C A:PRO173 5.0 9.9 1.0 CA A:SER174 5.0 10.4 0.7

Magnesium binding site 3 out of 3 in the Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Nitrocatechol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fad-Dependent Oxidoreductase From Chaetomium Thermophilum in Complex with Fragment 4-Nitrocatechol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg710 b:29.1 occ:0.50 O B:HOH1017 2.2 32.4 1.0 O B:HOH1498 2.2 28.8 1.0 O B:HOH980 2.4 21.5 1.0 OD1 B:ASN182 2.6 11.6 1.0 O B:HOH1511 3.0 30.9 1.0 O B:HOH1592 3.6 39.9 1.0 CG B:ASN182 3.7 9.9 1.0 O B:HOH1711 4.0 42.4 1.0 O B:HOH1388 4.1 23.3 1.0 CB B:ASN182 4.3 9.7 1.0 O6 B:NAG703 4.3 12.6 0.5 CA B:ASN182 4.4 9.1 1.0 O B:HOH1095 4.5 16.3 1.0 O B:HOH1414 4.5 30.0 1.0 O5 B:NAG703 4.6 11.2 1.0 O B:HOH1211 4.6 31.3 1.0 ND2 B:ASN182 4.7 9.1 1.0 O B:ALA179 4.8 11.1 1.0 C1 B:NAG703 4.9 10.1 1.0

L.Svecova, L.H.Ostergaard, T.Skalova, K.M.Schnorr, T.Koval', P.Kolenko, J.Stransky, D.Sedlak, J.Duskova, M.Trundova, J.Hasek, J.Dohnalek. Crystallographic Fragment Screening-Based Study of A Novel Fad-Dependent Oxidoreductase From Chaetomium Thermophilum Acta Crystallogr.,Sect.D 2021.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798321003533