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Magnesium in PDB 6w26: Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole

Protein crystallography data

The structure of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole, PDB code: 6w26 was solved by C.J.Herbst-Gervasoni, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.82 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.860, 87.201, 163.730, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.4

Other elements in 6w26:

The structure of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole (pdb code 6w26). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole, PDB code: 6w26:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6w26

Go back to Magnesium Binding Sites List in 6w26
Magnesium binding site 1 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg402

b:16.6
occ:1.00
 O I:HOH528 2.1 8.7 1.0
O6 I:POP406 2.1 10.6 1.0
O3 I:POP406 2.2 14.1 1.0
OD2 I:ASP94 2.2 18.6 1.0
O I:HOH568 2.2 10.3 1.0
OE2 I:GLU98 2.3 8.9 1.0
P2 I:POP406 3.1 10.0 1.0
CG I:ASP94 3.1 19.7 1.0
O I:POP406 3.2 15.3 1.0
P1 I:POP406 3.2 14.0 1.0
CD I:GLU98 3.2 16.5 1.0
MG I:MG403 3.2 10.2 1.0
OD1 I:ASP94 3.4 12.4 1.0
OE1 I:GLU98 3.4 8.3 1.0
O4 I:POP406 3.5 7.8 1.0
NH1 I:ARG216 3.7 13.6 1.0
NH2 I:ARG300 4.0 13.1 1.0
O2 I:POP406 4.0 8.9 1.0
O I:HOH557 4.1 9.6 1.0
O I:HOH551 4.2 7.9 1.0
O1 I:POP406 4.4 8.7 1.0
OE1 I:GLU217 4.4 10.7 1.0
O5 I:POP406 4.4 12.8 1.0
CB I:ASP94 4.5 19.2 1.0
CG I:GLU98 4.6 14.9 1.0
O I:HOH525 4.6 8.3 1.0
CZ I:ARG216 4.6 16.7 1.0
NH2 I:ARG216 4.7 17.5 1.0
MG I:MG404 4.7 12.1 1.0
OG I:SER95 4.8 15.1 1.0
C I:ASP94 4.9 17.6 1.0
O I:ASP94 5.0 21.9 1.0

Magnesium binding site 2 out of 6 in 6w26

Go back to Magnesium Binding Sites List in 6w26
Magnesium binding site 2 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg403

b:10.2
occ:1.00
 O I:HOH557 2.0 9.6 1.0
OD1 I:ASP94 2.1 12.4 1.0
OE2 I:GLU98 2.1 8.9 1.0
O6 I:POP406 2.1 10.6 1.0
O I:HOH516 2.1 8.1 1.0
O I:HOH525 2.2 8.3 1.0
CD I:GLU98 3.1 16.5 1.0
CG I:ASP94 3.1 19.7 1.0
MG I:MG402 3.2 16.6 1.0
OD2 I:ASP94 3.4 18.6 1.0
P2 I:POP406 3.5 10.0 1.0
O I:HOH571 3.7 14.2 1.0
CG I:GLU98 3.7 14.9 1.0
OD1 I:ASP168 3.8 13.1 1.0
O5 I:POP406 3.9 12.8 1.0
OD2 I:ASP168 3.9 9.3 1.0
OE1 I:GLU98 4.0 8.3 1.0
O I:HOH551 4.0 7.9 1.0
CG I:ASP168 4.2 11.3 1.0
O4 I:POP406 4.3 7.8 1.0
CB I:ASP94 4.4 19.2 1.0
O I:ASP94 4.5 21.9 1.0
O I:HOH528 4.5 8.7 1.0
NH1 I:ARG165 4.5 8.7 1.0
O I:POP406 4.5 15.3 1.0
O I:ASP168 4.5 12.2 1.0
O I:HOH568 4.9 10.3 1.0
CD1 I:ILE227 4.9 14.3 1.0
C I:ASP94 4.9 17.6 1.0
CA I:ASP94 5.0 16.9 1.0

Magnesium binding site 3 out of 6 in 6w26

Go back to Magnesium Binding Sites List in 6w26
Magnesium binding site 3 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg404

b:12.1
occ:1.00
 OE1 I:GLU217 2.0 10.7 1.0
O2 I:POP406 2.1 8.9 1.0
ND2 I:ASN209 2.1 10.4 1.0
O I:HOH531 2.1 6.8 1.0
O4 I:POP406 2.1 7.8 1.0
OG I:SER213 2.2 9.2 1.0
CD I:GLU217 3.1 13.6 1.0
CB I:SER213 3.1 11.5 1.0
CG I:ASN209 3.2 12.5 1.0
P1 I:POP406 3.3 14.0 1.0
P2 I:POP406 3.4 10.0 1.0
OD1 I:ASN209 3.5 9.2 1.0
OE2 I:GLU217 3.6 13.9 1.0
NH2 I:ARG165 3.6 18.2 1.0
O I:POP406 3.7 15.3 1.0
O I:HOH551 3.9 7.9 1.0
O3 I:POP406 3.9 14.1 1.0
O I:ASN209 4.0 10.7 1.0
O I:HOH528 4.0 8.7 1.0
O5 I:POP406 4.3 12.8 1.0
C I:ASN209 4.3 11.4 1.0
CG I:GLU217 4.4 15.6 1.0
O6 I:POP406 4.4 10.6 1.0
CB I:ASN209 4.4 8.7 1.0
O1 I:POP406 4.5 8.7 1.0
CA I:SER213 4.5 8.9 1.0
NH1 I:ARG216 4.6 13.6 1.0
OD2 I:ASP210 4.7 11.2 1.0
MG I:MG402 4.7 16.6 1.0
N I:ASP210 4.7 8.4 1.0
OH I:TYR301 4.8 11.4 1.0
O I:SER213 4.8 14.9 1.0
C I:SER213 4.8 13.9 1.0
CZ I:ARG165 4.9 12.6 1.0
CA I:ASP210 4.9 9.0 1.0
ND2 I:ASN228 5.0 8.3 1.0
CA I:ASN209 5.0 10.6 1.0
CZ I:TYR301 5.0 8.5 1.0

Magnesium binding site 4 out of 6 in 6w26

Go back to Magnesium Binding Sites List in 6w26
Magnesium binding site 4 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:19.0
occ:1.00
 O A:HOH503 2.0 17.2 1.0
OD1 A:ASP94 2.0 19.6 1.0
O2 A:POP405 2.0 22.8 1.0
O A:HOH514 2.1 19.1 1.0
O A:HOH534 2.1 17.5 1.0
OE2 A:GLU98 2.2 22.6 1.0
MG A:MG403 2.9 24.4 1.0
CG A:ASP94 3.0 26.0 1.0
CD A:GLU98 3.2 31.0 1.0
P1 A:POP405 3.3 21.6 1.0
OD2 A:ASP94 3.3 17.3 1.0
O1 A:POP405 3.4 17.5 1.0
CG A:GLU98 3.8 23.3 1.0
OD1 A:ASP168 3.9 18.2 1.0
O A:HOH523 4.0 17.9 1.0
O A:HOH553 4.0 26.8 1.0
O A:HOH526 4.1 16.3 1.0
O3 A:POP405 4.1 22.0 1.0
OE1 A:GLU98 4.1 20.6 1.0
OD2 A:ASP168 4.2 17.4 1.0
NH1 A:ARG165 4.3 16.5 1.0
CB A:ASP94 4.4 21.9 1.0
O A:POP405 4.4 19.2 1.0
CG A:ASP168 4.4 25.1 1.0
O A:ASP94 4.6 19.9 1.0
O A:ASP168 4.6 16.7 1.0
O5 A:POP405 4.6 25.1 1.0
O A:HOH550 4.9 24.6 1.0
C A:ASP94 4.9 22.4 1.0
CD1 A:ILE227 5.0 23.8 1.0

Magnesium binding site 5 out of 6 in 6w26

Go back to Magnesium Binding Sites List in 6w26
Magnesium binding site 5 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.4
occ:1.00
 OE2 A:GLU217 2.0 23.0 1.0
O A:HOH530 2.1 14.3 1.0
ND2 A:ASN209 2.1 12.3 1.0
O6 A:POP405 2.1 13.2 1.0
O3 A:POP405 2.1 22.0 1.0
OG A:SER213 2.2 9.5 1.0
CD A:GLU217 3.0 19.2 1.0
CG A:ASN209 3.1 15.5 1.0
CB A:SER213 3.2 18.1 1.0
P2 A:POP405 3.3 19.8 1.0
P1 A:POP405 3.3 21.6 1.0
OE1 A:GLU217 3.4 21.3 1.0
O A:POP405 3.5 19.2 1.0
NH2 A:ARG165 3.5 24.7 1.0
OD1 A:ASN209 3.5 22.0 1.0
O A:HOH523 3.7 17.9 1.0
O A:HOH526 3.8 16.3 1.0
O5 A:POP405 3.9 25.1 1.0
O A:ASN209 4.0 19.1 1.0
O2 A:POP405 4.2 22.8 1.0
C A:ASN209 4.2 16.2 1.0
CG A:GLU217 4.3 21.9 1.0
OD2 A:ASP210 4.4 23.0 1.0
CB A:ASN209 4.4 21.5 1.0
O1 A:POP405 4.4 17.5 1.0
O4 A:POP405 4.5 12.4 1.0
N A:ASP210 4.5 9.4 1.0
CA A:SER213 4.5 25.1 1.0
CA A:ASP210 4.7 16.6 1.0
CZ A:ARG165 4.7 22.1 1.0
ND2 A:ASN228 4.8 18.0 1.0
C A:SER213 4.9 21.7 1.0
MG A:MG403 4.9 24.4 1.0
O A:SER213 4.9 24.0 1.0
O A:ILE227 4.9 22.6 1.0
CA A:ASN209 4.9 18.7 1.0
OH A:TYR301 4.9 20.2 1.0

Magnesium binding site 6 out of 6 in 6w26

Go back to Magnesium Binding Sites List in 6w26
Magnesium binding site 6 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:24.4
occ:1.00
 O2 A:POP405 2.0 22.8 1.0
OE2 A:GLU98 2.0 22.6 1.0
O5 A:POP405 2.1 25.1 1.0
OD2 A:ASP94 2.1 17.3 1.0
O A:HOH526 2.1 16.3 1.0
O A:HOH550 2.3 24.6 1.0
MG A:MG401 2.9 19.0 1.0
CG A:ASP94 3.0 26.0 1.0
CD A:GLU98 3.0 31.0 1.0
OD1 A:ASP94 3.2 19.6 1.0
P1 A:POP405 3.2 21.6 1.0
P2 A:POP405 3.3 19.8 1.0
OE1 A:GLU98 3.3 20.6 1.0
O A:POP405 3.5 19.2 1.0
NH2 A:ARG216 3.7 19.8 0.5
O3 A:POP405 3.8 22.0 1.0
NH2 A:ARG300 3.9 21.9 1.0
O A:HOH523 4.2 17.9 1.0
O6 A:POP405 4.2 13.2 1.0
O A:HOH503 4.3 17.2 1.0
O4 A:POP405 4.3 12.4 1.0
CG A:GLU98 4.4 23.3 1.0
O1 A:POP405 4.4 17.5 1.0
OE2 A:GLU217 4.4 23.0 1.0
CB A:ASP94 4.4 21.9 1.0
O A:HOH514 4.4 19.1 1.0
O A:HOH556 4.6 27.2 1.0
C A:ASP94 4.8 22.4 1.0
O A:HOH534 4.8 17.5 1.0
O A:ASP94 4.8 19.9 1.0
CZ A:ARG216 4.8 19.3 0.5
MG A:MG402 4.9 17.4 1.0
N A:SER95 4.9 19.4 1.0
OG A:SER95 5.0 31.5 1.0

Reference:

C.J.Herbst-Gervasoni, D.W.Christianson. Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Imidazole To Be Published.
Page generated: Tue Oct 1 22:54:53 2024

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