Magnesium in PDB 7kjf: Wild-Type Epi-Isozizaene Synthase: Complex with 3 MG2+ and Neridronate

All present enzymatic activity of Wild-Type Epi-Isozizaene Synthase: Complex with 3 MG2+ and Neridronate:
4.2.3.37;

The structure of Wild-Type Epi-Isozizaene Synthase: Complex with 3 MG2+ and Neridronate, PDB code: 7kjf was solved by T.A.Ronnebaum, S.M.Gardner, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.16 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.530, 46.760, 74.820, 90.00, 98.34, 90.00
R / Rfree (%)	19.4 / 23.9

The binding sites of Magnesium atom in the Wild-Type Epi-Isozizaene Synthase: Complex with 3 MG2+ and Neridronate (pdb code 7kjf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Wild-Type Epi-Isozizaene Synthase: Complex with 3 MG2+ and Neridronate, PDB code: 7kjf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Wild-Type Epi-Isozizaene Synthase: Complex with 3 MG2+ and Neridronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Wild-Type Epi-Isozizaene Synthase: Complex with 3 MG2+ and Neridronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:10.1 occ:1.00 OAN A:NRD405 2.0 26.0 0.1 OAK A:NRD405 2.1 4.4 0.9 OAN A:NRD405 2.1 7.6 0.9 O A:HOH526 2.1 12.2 1.0 OD2 A:ASP99 2.1 10.2 1.0 O A:HOH566 2.2 12.7 1.0 O A:HOH621 2.2 11.0 1.0 OAK A:NRD405 2.3 51.7 0.1 CG A:ASP99 3.1 8.8 1.0 PAM A:NRD405 3.2 77.7 0.1 MG A:MG402 3.2 9.4 1.0 PAM A:NRD405 3.2 7.0 0.9 PAI A:NRD405 3.3 7.2 0.9 OD1 A:ASP99 3.4 10.3 1.0 PAI A:NRD405 3.5 66.0 0.1 CAG A:NRD405 3.6 7.7 0.9 CAG A:NRD405 3.6 4.1 0.1 OAO A:NRD405 3.7 7.7 0.1 CAF A:NRD405 3.7 9.8 0.1 CAF A:NRD405 3.8 9.1 0.9 OAO A:NRD405 3.8 10.4 0.9 NZ A:LYS247 3.9 17.9 1.0 O A:HOH591 3.9 15.8 1.0 NH2 A:ARG338 4.0 8.3 1.0 OAL A:NRD405 4.0 9.0 0.9 OE1 A:GLU253 4.1 15.3 1.0 O A:HOH550 4.2 11.4 1.0 OE2 A:GLU248 4.3 12.4 1.0 OAL A:NRD405 4.3 5.0 0.1 O A:HOH595 4.3 12.8 1.0 OAP A:NRD405 4.4 43.9 0.1 OAJ A:NRD405 4.5 13.2 0.9 CB A:ASP99 4.5 9.7 1.0 O A:HOH561 4.5 13.9 1.0 OAP A:NRD405 4.5 7.3 0.9 O A:HOH537 4.6 14.9 1.0 OAJ A:NRD405 4.6 1.5 0.1 O A:HOH542 4.7 11.4 1.0 MG A:MG403 4.8 9.0 1.0 O A:HOH562 4.8 13.4 1.0 CAE A:NRD405 4.9 63.5 0.9 CE A:LYS247 4.9 18.7 1.0 O A:HOH507 4.9 10.0 1.0 CAE A:NRD405 5.0 49.5 0.1 OAH A:NRD405 5.0 10.9 0.9

Magnesium binding site 2 out of 3 in the Wild-Type Epi-Isozizaene Synthase: Complex with 3 MG2+ and Neridronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Wild-Type Epi-Isozizaene Synthase: Complex with 3 MG2+ and Neridronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:9.4 occ:1.00 O A:HOH542 2.0 11.4 1.0 O A:HOH507 2.0 10.0 1.0 O A:HOH550 2.0 11.4 1.0 OD1 A:ASP99 2.1 10.3 1.0 OAN A:NRD405 2.1 7.6 0.9 OAN A:NRD405 2.1 26.0 0.1 O A:HOH566 2.2 12.7 1.0 CG A:ASP99 3.1 8.8 1.0 MG A:MG401 3.2 10.1 1.0 PAM A:NRD405 3.3 7.0 0.9 PAM A:NRD405 3.4 77.7 0.1 OD2 A:ASP99 3.4 10.2 1.0 OAP A:NRD405 3.5 43.9 0.1 OAP A:NRD405 3.5 7.3 0.9 OH A:TYR172 3.7 14.2 1.0 O A:HOH595 3.9 12.8 1.0 OE1 A:GLU175 4.0 16.4 1.0 CZ A:TYR172 4.1 12.8 1.0 O A:HOH612 4.2 22.5 1.0 O A:HOH561 4.2 13.9 1.0 OE2 A:GLU175 4.2 11.9 1.0 OAO A:NRD405 4.3 10.4 0.9 O A:HOH526 4.3 12.2 1.0 OAO A:NRD405 4.3 7.7 0.1 CE2 A:TYR172 4.3 12.5 1.0 OE1 A:GLU253 4.4 15.3 1.0 CB A:ASP99 4.4 9.7 1.0 CAF A:NRD405 4.5 9.8 0.1 CD A:GLU175 4.5 10.9 1.0 CAF A:NRD405 4.6 9.1 0.9 CAG A:NRD405 4.7 4.1 0.1 CAG A:NRD405 4.7 7.7 0.9 CAE A:NRD405 4.7 63.5 0.9 OAK A:NRD405 4.8 4.4 0.9 CAE A:NRD405 4.8 49.5 0.1 O A:HOH621 4.9 11.0 1.0 ND1 A:HIS102 4.9 12.0 1.0 CE1 A:TYR172 5.0 13.2 1.0

Magnesium binding site 3 out of 3 in the Wild-Type Epi-Isozizaene Synthase: Complex with 3 MG2+ and Neridronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Wild-Type Epi-Isozizaene Synthase: Complex with 3 MG2+ and Neridronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:9.0 occ:1.00 OAO A:NRD405 2.0 7.7 0.1 OAL A:NRD405 2.0 9.0 0.9 OE2 A:GLU248 2.0 12.4 1.0 O A:HOH572 2.1 9.8 1.0 OAL A:NRD405 2.1 5.0 0.1 OD1 A:ASN240 2.1 9.8 1.0 OAO A:NRD405 2.1 10.4 0.9 OG A:SER244 2.3 8.4 1.0 CD A:GLU248 3.1 11.5 1.0 CG A:ASN240 3.1 7.7 1.0 PAI A:NRD405 3.3 7.2 0.9 CB A:SER244 3.3 10.2 1.0 PAI A:NRD405 3.3 66.0 0.1 PAM A:NRD405 3.3 77.7 0.1 PAM A:NRD405 3.4 7.0 0.9 ND2 A:ASN240 3.4 7.7 1.0 OE1 A:GLU248 3.5 11.7 1.0 CAG A:NRD405 3.7 7.7 0.9 CAG A:NRD405 3.8 4.1 0.1 O A:HOH561 3.8 13.9 1.0 OAH A:NRD405 3.8 10.9 0.9 NH2 A:ARG194 3.8 9.0 1.0 OAK A:NRD405 3.9 51.7 0.1 O A:HOH526 3.9 12.2 1.0 OAK A:NRD405 4.0 4.4 0.9 OAH A:NRD405 4.0 35.6 0.1 O A:ASN240 4.1 9.3 1.0 OAN A:NRD405 4.2 26.0 0.1 OAN A:NRD405 4.2 7.6 0.9 CG A:GLU248 4.3 11.3 1.0 OAP A:NRD405 4.3 43.9 0.1 C A:ASN240 4.4 8.2 1.0 OD1 A:ASP241 4.4 9.4 1.0 OAP A:NRD405 4.4 7.3 0.9 CB A:ASN240 4.5 8.0 1.0 OAJ A:NRD405 4.5 13.2 0.9 OAJ A:NRD405 4.5 1.5 0.1 CA A:SER244 4.7 10.8 1.0 N A:ASP241 4.7 9.6 1.0 MG A:MG401 4.8 10.1 1.0 CA A:ASP241 4.8 10.7 1.0 CZ A:ARG194 4.9 7.8 1.0

T.A.Ronnebaum, S.M.Gardner, D.W.Christianson. An Aromatic Cluster in the Active Site of Epi -Isozizaene Synthase Is An Electrostatic Toggle For Divergent Terpene Cyclization Pathways. Biochemistry 2020.
ISSN: ISSN 0006-2960
PubMed: 33270439
DOI: 10.1021/ACS.BIOCHEM.0C00876