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Magnesium in PDB 6vyd: Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation

Protein crystallography data

The structure of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation, PDB code: 6vyd 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) 46.17 / 1.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.599, 87.260, 163.209, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.4

Other elements in 6vyd:

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

Chlorine (Cl) 3 atoms
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 Benzyltriethylammonium Cation (pdb code 6vyd). 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 Benzyltriethylammonium Cation, PDB code: 6vyd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6vyd

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Magnesium binding site 1 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation


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 Benzyltriethylammonium Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:14.2
occ:1.00
 O2 A:POP406 2.0 12.9 1.0
O5 A:POP406 2.0 12.8 1.0
O A:HOH557 2.1 14.7 1.0
OD2 A:ASP94 2.1 15.7 1.0
OE2 A:GLU98 2.1 14.8 1.0
O A:HOH565 2.2 16.2 1.0
CG A:ASP94 3.1 16.3 1.0
CD A:GLU98 3.1 14.6 1.0
MG A:MG402 3.1 14.6 1.0
P1 A:POP406 3.2 12.6 1.0
P2 A:POP406 3.3 13.4 1.0
OD1 A:ASP94 3.4 15.5 1.0
O A:POP406 3.4 12.6 1.0
OE1 A:GLU98 3.5 16.3 1.0
O1 A:POP406 3.7 14.4 1.0
NH2 A:ARG300 3.9 15.6 1.0
NH1 A:ARG216 3.9 17.4 1.0
O6 A:POP406 4.1 15.3 1.0
O A:HOH570 4.2 14.5 1.0
OE1 A:GLU217 4.3 14.9 1.0
O4 A:POP406 4.4 13.6 1.0
CG A:GLU98 4.4 14.8 1.0
O A:HOH581 4.4 14.1 1.0
NH2 A:ARG216 4.4 18.3 1.0
CB A:ASP94 4.4 15.6 1.0
O3 A:POP406 4.5 13.7 1.0
O A:HOH729 4.5 20.7 1.0
OG A:SER95 4.6 15.9 1.0
O A:HOH567 4.6 14.9 1.0
CZ A:ARG216 4.6 19.0 1.0
MG A:MG403 4.7 13.7 1.0
O A:HOH721 4.8 20.4 1.0
C A:ASP94 4.9 13.7 1.0
O A:ASP94 4.9 15.3 1.0
N A:SER95 4.9 15.8 1.0

Magnesium binding site 2 out of 6 in 6vyd

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Magnesium binding site 2 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation


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 Benzyltriethylammonium Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:14.6
occ:1.00
 O A:HOH570 2.0 14.5 1.0
O A:HOH567 2.1 14.9 1.0
OD1 A:ASP94 2.1 15.5 1.0
OE2 A:GLU98 2.1 14.8 1.0
O A:HOH562 2.1 15.8 1.0
O2 A:POP406 2.1 12.9 1.0
CD A:GLU98 3.1 14.6 1.0
CG A:ASP94 3.1 16.3 1.0
MG A:MG401 3.1 14.2 1.0
P1 A:POP406 3.3 12.6 1.0
OD2 A:ASP94 3.4 15.7 1.0
CG A:GLU98 3.6 14.8 1.0
O3 A:POP406 3.6 13.7 1.0
O A:HOH624 3.8 19.7 1.0
OD1 A:ASP168 4.0 14.8 1.0
OE1 A:GLU98 4.1 16.3 1.0
OD2 A:ASP168 4.1 15.1 1.0
O A:HOH581 4.1 14.1 1.0
O1 A:POP406 4.2 14.4 1.0
O A:HOH557 4.3 14.7 1.0
CG A:ASP168 4.4 13.5 1.0
NH1 A:ARG165 4.4 13.4 1.0
CB A:ASP94 4.4 15.6 1.0
O A:POP406 4.5 12.6 1.0
O A:ASP168 4.5 16.6 1.0
O A:ASP94 4.6 15.3 1.0
O5 A:POP406 4.8 12.8 1.0
O A:HOH565 4.9 16.2 1.0
C A:ASP94 5.0 13.7 1.0

Magnesium binding site 3 out of 6 in 6vyd

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Magnesium binding site 3 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation


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 Benzyltriethylammonium Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:13.7
occ:1.00
 O1 A:POP406 2.0 14.4 1.0
O6 A:POP406 2.1 15.3 1.0
OE1 A:GLU217 2.1 14.9 1.0
OD1 A:ASN209 2.1 13.1 1.0
O A:HOH591 2.1 13.0 1.0
OG A:SER213 2.3 14.2 1.0
CG A:ASN209 3.1 13.4 1.0
CD A:GLU217 3.1 15.5 1.0
P2 A:POP406 3.2 13.4 1.0
CB A:SER213 3.3 13.2 1.0
P1 A:POP406 3.3 12.6 1.0
O A:POP406 3.4 12.6 1.0
ND2 A:ASN209 3.5 13.2 1.0
OE2 A:GLU217 3.6 14.5 1.0
O A:HOH581 3.8 14.1 1.0
NH2 A:ARG165 3.8 13.5 1.0
O5 A:POP406 3.9 12.8 1.0
O A:HOH557 3.9 14.7 1.0
O A:ASN209 4.1 13.7 1.0
O2 A:POP406 4.2 12.9 1.0
O3 A:POP406 4.3 13.7 1.0
CG A:GLU217 4.3 16.0 1.0
C A:ASN209 4.4 11.4 1.0
CB A:ASN209 4.4 13.0 1.0
O4 A:POP406 4.5 13.6 1.0
NH1 A:ARG216 4.5 17.4 1.0
CA A:SER213 4.6 12.8 1.0
OD2 A:ASP210 4.7 15.1 1.0
N A:ASP210 4.7 12.7 1.0
MG A:MG401 4.7 14.2 1.0
CA A:ASP210 4.8 12.1 1.0
CZ A:ARG165 4.8 12.5 1.0
ND2 A:ASN228 5.0 16.8 1.0
C A:SER213 5.0 13.5 1.0
OH A:TYR301 5.0 15.1 1.0

Magnesium binding site 4 out of 6 in 6vyd

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Magnesium binding site 4 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation


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 Benzyltriethylammonium Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:27.4
occ:1.00
 OD2 B:ASP94 2.0 23.6 1.0
O3 B:POP408 2.0 24.5 1.0
O B:HOH566 2.1 20.3 1.0
O5 B:POP408 2.1 21.9 1.0
O B:HOH574 2.1 21.4 1.0
OE2 B:GLU98 2.2 23.4 1.0
CG B:ASP94 3.0 24.7 1.0
CD B:GLU98 3.2 29.0 1.0
MG B:MG402 3.2 22.7 1.0
P2 B:POP408 3.2 22.3 1.0
P1 B:POP408 3.3 23.1 1.0
OD1 B:ASP94 3.4 24.0 1.0
O B:POP408 3.4 21.1 1.0
OE1 B:GLU98 3.4 30.8 1.0
O6 B:POP408 3.7 21.8 1.0
NH1 B:ARG300 4.0 23.5 1.0
NH2 B:ARG216 4.0 34.2 1.0
O2 B:POP408 4.1 23.8 1.0
OE2 B:GLU217 4.3 27.1 1.0
NH1 B:ARG216 4.4 36.8 1.0
CB B:ASP94 4.4 24.9 1.0
O B:HOH540 4.4 20.5 1.0
O1 B:POP408 4.4 23.4 1.0
O B:HOH669 4.5 33.9 1.0
CG B:GLU98 4.5 30.6 1.0
O4 B:POP408 4.5 24.1 1.0
O B:HOH558 4.5 22.3 1.0
CZ B:ARG216 4.6 36.5 1.0
O B:HOH538 4.6 19.5 1.0
OG B:SER95 4.7 32.2 1.0
MG B:MG403 4.8 25.7 1.0
C B:ASP94 4.9 27.2 1.0
N B:SER95 4.9 27.1 1.0
O B:ASP94 5.0 28.1 1.0

Magnesium binding site 5 out of 6 in 6vyd

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Magnesium binding site 5 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation


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 Benzyltriethylammonium Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:22.7
occ:1.00
 O B:HOH583 2.1 24.0 1.0
OD1 B:ASP94 2.1 24.0 1.0
O B:HOH540 2.1 20.5 1.0
O B:HOH538 2.1 19.5 1.0
O5 B:POP408 2.1 21.9 1.0
OE2 B:GLU98 2.1 23.4 1.0
CG B:ASP94 3.1 24.7 1.0
CD B:GLU98 3.1 29.0 1.0
MG B:MG401 3.2 27.4 1.0
P2 B:POP408 3.3 22.3 1.0
OD2 B:ASP94 3.4 23.6 1.0
O4 B:POP408 3.6 24.1 1.0
CG B:GLU98 3.6 30.6 1.0
O B:HOH648 3.8 29.8 1.0
OD2 B:ASP168 4.0 23.6 1.0
OE1 B:GLU98 4.1 30.8 1.0
OD1 B:ASP168 4.1 24.6 1.0
O B:HOH558 4.1 22.3 1.0
O6 B:POP408 4.1 21.8 1.0
O B:HOH566 4.3 20.3 1.0
CG B:ASP168 4.4 23.5 1.0
NH1 B:ARG165 4.4 21.7 1.0
CB B:ASP94 4.4 24.9 1.0
O B:POP408 4.5 21.1 1.0
O B:HOH502 4.5 39.8 1.0
O B:ASP168 4.5 24.2 1.0
O B:ASP94 4.6 28.1 1.0
O B:HOH574 4.8 21.4 1.0
O3 B:POP408 4.8 24.5 1.0
C B:ASP94 5.0 27.2 1.0
CA B:ASP94 5.0 24.8 1.0

Magnesium binding site 6 out of 6 in 6vyd

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Magnesium binding site 6 out of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation


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 Benzyltriethylammonium Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:25.7
occ:1.00
 OE2 B:GLU217 2.0 27.1 1.0
O6 B:POP408 2.1 21.8 1.0
OD1 B:ASN209 2.1 20.7 1.0
O2 B:POP408 2.2 23.8 1.0
O B:HOH541 2.2 21.9 1.0
OG B:SER213 2.2 23.7 1.0
CD B:GLU217 3.0 26.4 1.0
CG B:ASN209 3.1 21.6 1.0
CB B:SER213 3.3 24.8 1.0
P1 B:POP408 3.4 23.1 1.0
P2 B:POP408 3.4 22.3 1.0
OE1 B:GLU217 3.5 24.4 1.0
O B:POP408 3.6 21.1 1.0
ND2 B:ASN209 3.6 22.3 1.0
NH2 B:ARG165 3.7 23.8 1.0
O B:HOH558 3.9 22.3 1.0
O B:HOH566 4.0 20.3 1.0
O B:ASN209 4.0 21.2 1.0
O3 B:POP408 4.1 24.5 1.0
O5 B:POP408 4.3 21.9 1.0
CG B:GLU217 4.3 26.5 1.0
C B:ASN209 4.3 19.9 1.0
O4 B:POP408 4.4 24.1 1.0
CB B:ASN209 4.5 20.2 1.0
OD1 B:ASP210 4.5 22.5 1.0
O1 B:POP408 4.6 23.4 1.0
N B:ASP210 4.6 22.4 1.0
NH2 B:ARG216 4.6 34.2 1.0
CA B:SER213 4.7 25.5 1.0
CA B:ASP210 4.7 22.6 1.0
CZ B:ARG165 4.8 21.3 1.0
MG B:MG401 4.8 27.4 1.0
ND2 B:ASN228 4.9 25.6 1.0
C B:SER213 5.0 29.3 1.0
O B:ILE227 5.0 27.3 1.0

Reference:

C.J.Herbst-Gervasoni, D.W.Christianson. Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation To Be Published.
Page generated: Tue Oct 1 22:16:51 2024

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