Magnesium in PDB 6ze7: Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol

The structure of Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol, PDB code: 6ze7 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)	47.23 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.611, 109.674, 115.634, 90, 90, 90
R / Rfree (%)	15.5 / 18.2

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

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol (pdb code 6ze7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol, PDB code: 6ze7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg713 b:23.5 occ:0.50 O A:HOH1083 1.9 23.4 1.0 O A:HOH965 1.9 16.5 1.0 O A:HOH1385 2.1 22.7 0.5 O A:HOH909 2.2 33.6 1.0 O A:HOH1398 2.2 25.8 0.5 O A:HOH1398 3.7 25.4 0.5 O A:HOH1139 3.8 30.9 0.5 OD1 A:ASN213 4.0 14.3 1.0 O A:HOH1450 4.1 43.0 1.0 O6 A:NAG703 4.2 18.3 0.5 OD1 A:ASN216 4.3 14.4 1.0 CB A:ASN216 4.3 12.1 1.0 O A:HOH1372 4.4 13.4 0.3 O A:ASN213 4.4 11.9 1.0 CB A:ASN213 4.5 12.4 1.0 CG A:ASN213 4.5 12.3 1.0 CA A:ASN213 4.6 11.1 1.0 O A:HOH1192 4.7 21.1 0.7 CG A:ASN216 4.8 11.9 1.0 OE2 A:GLU217 4.9 30.5 1.0

Magnesium binding site 2 out of 5 in the Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg714 b:34.9 occ:1.00 O A:HOH1168 2.1 34.8 1.0 O A:HOH1203 2.2 25.8 1.0 O A:HOH1043 2.3 23.9 1.0 OD1 A:ASN182 2.4 12.3 1.0 O A:HOH842 3.1 39.7 1.0 CG A:ASN182 3.4 11.0 1.0 CB A:ASN182 4.1 10.8 1.0 O A:HOH1248 4.1 20.4 1.0 O2 A:FMT709 4.2 31.9 1.0 CA A:ASN182 4.2 10.2 1.0 O6 A:NAG703 4.3 13.0 0.5 O5 A:NAG703 4.4 12.7 1.0 ND2 A:ASN182 4.4 12.0 1.0 O A:HOH1157 4.5 19.9 1.0 O A:HOH1262 4.6 17.2 0.5 C1 A:NAG703 4.6 12.2 1.0 O A:ALA179 4.7 10.6 1.0 C5 A:NAG703 5.0 14.2 1.0 O A:HOH1419 5.0 44.1 1.0

Magnesium binding site 3 out of 5 in the Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg715 b:12.8 occ:1.00 O A:HOH1014 2.0 13.3 1.0 O B:HOH1389 2.1 12.1 1.0 O A:HOH1104 2.1 12.0 1.0 O A:HOH1531 2.1 12.5 1.0 O B:HOH1080 2.1 11.9 1.0 O B:HOH1031 2.2 13.1 1.0 O A:HOH1149 4.1 11.7 1.0 O B:HOH1531 4.1 21.0 1.0 O B:HOH1240 4.1 11.9 1.0 O A:HOH1514 4.2 21.6 1.0 O A:PRO172 4.2 10.1 1.0 O B:PRO172 4.3 10.0 1.0 O A:PRO173 4.3 9.7 1.0 O A:HOH1472 4.4 23.1 1.0 O B:PRO173 4.5 10.4 1.0 O B:HOH1479 4.5 24.9 1.0 C A:PRO173 4.9 10.1 1.0 CA A:SER174 4.9 11.0 0.5 O B:HOH1388 5.0 44.5 1.0 CA A:SER174 5.0 11.2 0.5 C A:PRO172 5.0 9.5 1.0 CD A:PRO175 5.0 12.1 1.0

Magnesium binding site 4 out of 5 in the Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg714 b:44.0 occ:1.00 O B:HOH943 2.1 20.4 1.0 O B:HOH1548 2.2 37.0 1.0 O B:HOH1449 2.3 31.2 1.0 O B:HOH936 4.0 15.9 1.0 O6 B:NAG703 4.1 22.1 1.0 OD1 B:ASN216 4.2 15.1 1.0 O B:HOH1215 4.3 18.4 1.0 C6 B:NAG703 4.4 16.6 1.0 O B:HOH1498 4.4 33.8 1.0

Magnesium binding site 5 out of 5 in the Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Chaetomium Thermophilum Fad-Dependent Oxidoreductase in Complex with 4-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg715 b:37.9 occ:1.00 O B:HOH1122 2.1 36.9 1.0 O B:HOH1410 2.3 27.5 1.0 OD1 B:ASN182 2.4 12.9 1.0 O B:HOH1058 2.4 24.1 1.0 O B:HOH1451 3.1 34.1 1.0 CG B:ASN182 3.4 11.9 1.0 CB B:ASN182 4.1 10.4 1.0 CA B:ASN182 4.2 11.1 1.0 O B:HOH1237 4.2 22.6 1.0 O B:HOH1360 4.3 30.3 1.0 O B:HOH1215 4.3 18.4 1.0 O6 B:NAG703 4.3 22.1 1.0 O B:HOH1221 4.4 29.8 1.0 O5 B:NAG703 4.4 13.4 1.0 ND2 B:ASN182 4.5 12.9 1.0 O B:ALA179 4.7 12.7 1.0 C1 B:NAG703 4.7 13.7 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