Magnesium in PDB 8h41: Crystal Structure of A Decarboxylase From Trichosporon Moniliiforme in Complex with O-Nitrophenol

All present enzymatic activity of Crystal Structure of A Decarboxylase From Trichosporon Moniliiforme in Complex with O-Nitrophenol:
4.1.1.91;

The structure of Crystal Structure of A Decarboxylase From Trichosporon Moniliiforme in Complex with O-Nitrophenol, PDB code: 8h41 was solved by J.Gao, Y.P.Zhao, Q.Li, W.D.Liu, X.Sheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.93 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.916, 92.31, 128.66, 90, 90, 90
R / Rfree (%)	16.6 / 19.4

The binding sites of Magnesium atom in the Crystal Structure of A Decarboxylase From Trichosporon Moniliiforme in Complex with O-Nitrophenol (pdb code 8h41). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of A Decarboxylase From Trichosporon Moniliiforme in Complex with O-Nitrophenol, PDB code: 8h41:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A Decarboxylase From Trichosporon Moniliiforme in Complex with O-Nitrophenol


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 A Decarboxylase From Trichosporon Moniliiforme in Complex with O-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:16.1 occ:1.00 OE2 A:GLU8 2.0 15.8 1.0 O3 A:OPO401 2.1 19.9 1.0 OD1 A:ASP298 2.1 21.2 1.0 OH A:OPO401 2.2 17.1 1.0 NE2 A:HIS169 2.2 17.4 1.0 O A:HOH719 2.3 25.0 1.0 N1 A:OPO401 3.0 28.0 1.0 CG A:ASP298 3.0 21.6 1.0 CE1 A:HIS169 3.0 12.9 1.0 C2 A:OPO401 3.1 20.0 1.0 CD A:GLU8 3.2 15.1 1.0 OD2 A:ASP298 3.3 21.3 1.0 CD2 A:HIS169 3.3 16.3 1.0 C1 A:OPO401 3.4 20.5 1.0 CG A:GLU8 3.7 16.1 1.0 O A:HOH542 4.0 16.0 1.0 O2 A:OPO401 4.1 19.6 1.0 NE2 A:HIS224 4.1 17.9 1.0 O A:HOH686 4.2 13.8 1.0 OE1 A:GLU8 4.2 15.0 1.0 ND1 A:HIS169 4.2 12.3 1.0 O A:GLU8 4.3 18.3 1.0 C3 A:OPO401 4.3 19.9 1.0 CB A:ASP298 4.4 17.9 1.0 CG A:HIS169 4.4 13.5 1.0 CE1 A:HIS224 4.4 16.7 1.0 CA A:ASP298 4.7 13.3 1.0 CB A:GLU8 4.7 14.7 1.0 C6 A:OPO401 4.8 19.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Decarboxylase From Trichosporon Moniliiforme in Complex with O-Nitrophenol


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 A Decarboxylase From Trichosporon Moniliiforme in Complex with O-Nitrophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:14.8 occ:1.00 OE2 B:GLU8 2.1 12.5 1.0 O3 B:OPO401 2.1 20.2 1.0 OD1 B:ASP298 2.1 22.4 1.0 OH B:OPO401 2.2 15.6 1.0 O B:HOH686 2.2 25.0 1.0 NE2 B:HIS169 2.2 10.2 1.0 CG B:ASP298 2.9 23.1 1.0 N1 B:OPO401 3.1 22.5 1.0 C2 B:OPO401 3.1 14.4 1.0 CD B:GLU8 3.2 14.7 1.0 CE1 B:HIS169 3.2 10.2 1.0 OD2 B:ASP298 3.2 21.7 1.0 CD2 B:HIS169 3.2 16.7 1.0 C1 B:OPO401 3.5 18.3 1.0 CG B:GLU8 3.6 14.1 1.0 O B:HOH743 4.1 13.5 1.0 O2 B:OPO401 4.1 19.0 1.0 O B:HOH643 4.1 12.7 1.0 NE2 B:HIS224 4.2 12.7 1.0 OE1 B:GLU8 4.2 14.3 1.0 O B:GLU8 4.2 14.0 1.0 CB B:ASP298 4.3 14.5 1.0 ND1 B:HIS169 4.3 11.1 1.0 C3 B:OPO401 4.4 17.9 1.0 CE1 B:HIS224 4.4 13.4 1.0 CG B:HIS169 4.4 9.2 1.0 CA B:ASP298 4.7 16.5 1.0 CB B:GLU8 4.7 11.8 1.0 C6 B:OPO401 4.8 18.3 1.0

F.Chen, Y.Zhao, C.Zhang, W.Wang, J.Gao, Q.Li, H.Qin, Y.Dai, W.Liu, F.Liu, H.Su, X.Sheng. A Combined Computational-Experimental Study on the Substrate Binding and Reaction Mechanism of Salicylic Acid Decarboxylase Catalysts V. 12 2022.
ISSN: ESSN 2073-4344
DOI: 10.3390/CATAL12121577