Magnesium in PDB 6i3d: Crystal Structure of Human Soluble Catechol O-Methyltransferase in Complex with 3,5-Dinitrocatechol and Sinefungin

All present enzymatic activity of Crystal Structure of Human Soluble Catechol O-Methyltransferase in Complex with 3,5-Dinitrocatechol and Sinefungin:
2.1.1.6;

The structure of Crystal Structure of Human Soluble Catechol O-Methyltransferase in Complex with 3,5-Dinitrocatechol and Sinefungin, PDB code: 6i3d was solved by C.W.Levy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.02 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.961, 75.797, 64.345, 90.00, 94.62, 90.00
R / Rfree (%)	11.9 / 14.6

The binding sites of Magnesium atom in the Crystal Structure of Human Soluble Catechol O-Methyltransferase in Complex with 3,5-Dinitrocatechol and Sinefungin (pdb code 6i3d). 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 Human Soluble Catechol O-Methyltransferase in Complex with 3,5-Dinitrocatechol and Sinefungin, PDB code: 6i3d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Soluble Catechol O-Methyltransferase in Complex with 3,5-Dinitrocatechol and Sinefungin


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 Human Soluble Catechol O-Methyltransferase in Complex with 3,5-Dinitrocatechol and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:8.6 occ:1.00 O A:HOH427 2.1 9.1 1.0 OD2 A:ASP169 2.1 7.7 1.0 OD1 A:ASP141 2.1 7.4 1.0 O1 A:DNC301 2.1 9.7 1.0 OD1 A:ASN170 2.1 9.7 1.0 O2 A:DNC301 2.1 9.7 1.0 C1 A:DNC301 2.9 9.5 1.0 C2 A:DNC301 2.9 10.7 1.0 CG A:ASP141 3.1 7.1 1.0 CG A:ASN170 3.1 8.4 1.0 CG A:ASP169 3.1 8.4 1.0 OD2 A:ASP141 3.3 8.4 1.0 ND2 A:ASN170 3.4 9.6 1.0 CB A:ASP169 3.7 7.4 1.0 NZ A:LYS144 3.8 9.3 1.0 NE A:SFG303 4.1 9.0 1.0 OE2 A:GLU199 4.1 10.4 1.0 OD1 A:ASP169 4.2 8.9 1.0 C6 A:DNC301 4.2 10.7 1.0 O A:MET40 4.3 10.9 0.7 O A:MET40 4.3 8.7 0.3 C3 A:DNC301 4.3 12.1 1.0 CB A:ASN170 4.4 8.6 1.0 CB A:ASP141 4.5 7.2 1.0 O A:ASP141 4.6 9.2 1.0 OE1 A:GLU199 4.6 9.5 1.0 NZ A:LYS46 4.7 10.6 1.0 CE A:LYS144 4.7 9.4 1.0 O3 A:DNC301 4.8 14.9 1.0 CD A:GLU199 4.8 9.1 1.0 CA A:ASP141 4.9 6.6 1.0 CA A:ASP169 4.9 7.3 1.0 C A:ASP169 4.9 8.0 1.0 CA A:VAL42 5.0 8.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Soluble Catechol O-Methyltransferase in Complex with 3,5-Dinitrocatechol and Sinefungin


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 Human Soluble Catechol O-Methyltransferase in Complex with 3,5-Dinitrocatechol and Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:13.3 occ:1.00 OD1 B:ASP141 2.1 13.2 1.0 O B:HOH419 2.1 13.8 1.0 OD2 B:ASP169 2.1 13.0 1.0 OD1 B:ASN170 2.1 13.6 1.0 O1 B:DNC301 2.1 14.9 1.0 O2 B:DNC301 2.1 15.3 1.0 C1 B:DNC301 2.9 15.5 1.0 C2 B:DNC301 2.9 16.2 1.0 CG B:ASP141 3.0 11.2 1.0 CG B:ASN170 3.1 13.0 1.0 CG B:ASP169 3.1 12.3 1.0 OD2 B:ASP141 3.3 13.1 1.0 ND2 B:ASN170 3.4 14.5 1.0 CB B:ASP169 3.7 11.5 1.0 NZ B:LYS144 3.8 13.3 1.0 NE B:SFG303 4.1 13.3 1.0 OE2 B:GLU199 4.1 15.9 1.0 OD1 B:ASP169 4.2 12.9 1.0 C6 B:DNC301 4.2 16.4 1.0 O B:MET40 4.3 14.9 0.7 O B:MET40 4.3 15.1 0.3 C3 B:DNC301 4.3 17.8 1.0 CB B:ASP141 4.4 11.3 1.0 CB B:ASN170 4.4 13.2 1.0 O B:ASP141 4.6 12.6 1.0 OE1 B:GLU199 4.6 17.0 1.0 NZ B:LYS46 4.7 15.1 1.0 CE B:LYS144 4.7 13.6 1.0 O4 B:DNC301 4.8 22.7 1.0 CD B:GLU199 4.8 16.5 1.0 CA B:ASP141 4.9 10.6 1.0 C B:ASP169 4.9 10.8 1.0 CA B:VAL42 5.0 13.3 1.0 CA B:ASP169 5.0 10.2 1.0 N B:ASN170 5.0 11.3 1.0

S.Czarnota, L.O.Johannissen, N.J.Baxter, F.Rummel, A.L.Wilson, M.J.Cliff, C.W.Levy, N.S.Scrutton, J.P.Waltho, S.Hay. Equatorial Active Site Compaction and Electrostatic Reorganization in Catechol-O-Methyltransferase. Acs Catalysis V. 9 4394 2019.
ISSN: ESSN 2155-5435
PubMed: 31080692
DOI: 10.1021/ACSCATAL.9B00174