Atomistry » Magnesium » PDB 7khe-7ko3 » 7kjf
Atomistry »
  Magnesium »
    PDB 7khe-7ko3 »
      7kjf »

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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 7kjf

Go back to Magnesium Binding Sites List in 7kjf
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 7kjf

Go back to Magnesium Binding Sites List in 7kjf
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 7kjf

Go back to Magnesium Binding Sites List in 7kjf
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

Reference:

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
Page generated: Wed Oct 2 22:20:38 2024

Last articles

Ni in 4ZXH
Ni in 4ZP1
Ni in 4ZMV
Ni in 4ZJO
Ni in 4ZJQ
Ni in 4ZJL
Ni in 4ZMW
Ni in 4ZIW
Ni in 4ZIV
Ni in 4ZFA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy