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Magnesium in PDB 5gul: Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190

Protein crystallography data

The structure of Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190, PDB code: 5gul was solved by T.Tomita, M.Kobayashi, M.Nishiyama, T.Kuzuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.04 / 1.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.851, 61.661, 82.242, 74.00, 84.54, 86.04
R / Rfree (%) 21.6 / 27.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190 (pdb code 5gul). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190, PDB code: 5gul:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5gul

Go back to Magnesium Binding Sites List in 5gul
Magnesium binding site 1 out of 4 in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190


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 Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:30.1
occ:1.00
O2 A:POP301 2.0 25.5 1.0
O2 A:POP302 2.0 26.1 1.0
O4 A:POP302 2.1 33.4 1.0
O A:HOH421 2.1 30.5 1.0
OD1 A:ASP9 2.2 27.7 1.0
O A:HOH401 2.4 26.1 1.0
P1 A:POP302 3.1 26.2 1.0
P2 A:POP302 3.2 29.4 1.0
CG A:ASP9 3.2 29.3 1.0
O6 A:POP302 3.4 30.2 1.0
P1 A:POP301 3.4 29.1 1.0
O A:POP302 3.5 26.1 1.0
OD2 A:ASP9 3.6 29.8 1.0
O3 A:POP302 3.7 25.5 1.0
O3 A:TRS304 3.8 28.3 1.0
O5 A:POP301 3.8 30.3 1.0
O3 A:POP301 3.9 30.9 1.0
NH2 A:ARG60 4.0 29.2 1.0
O B:HOH425 4.0 26.9 1.0
NH2 A:ARG13 4.1 28.6 1.0
O A:POP301 4.2 27.2 1.0
C3 A:TRS304 4.4 26.9 1.0
NE B:ARG211 4.4 34.4 1.0
N A:GLY10 4.4 27.3 1.0
NH2 B:ARG211 4.4 35.3 1.0
O1 A:POP302 4.5 26.6 1.0
O1 A:POP301 4.5 32.4 1.0
CB A:ASP9 4.5 29.7 1.0
P2 A:POP301 4.5 27.7 1.0
O5 A:POP302 4.6 31.0 1.0
O4 A:POP301 4.9 25.4 1.0
CZ B:ARG211 4.9 36.8 1.0
NH2 A:ARG163 4.9 27.6 1.0
CA A:ASP9 4.9 28.8 1.0
CA A:GLY10 5.0 27.4 1.0

Magnesium binding site 2 out of 4 in 5gul

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Magnesium binding site 2 out of 4 in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190


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 Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:28.6
occ:1.00
O4 B:POP302 2.0 27.8 1.0
O5 B:POP301 2.0 30.0 1.0
OD1 B:ASP9 2.1 30.5 1.0
O2 B:POP302 2.1 34.3 1.0
O B:HOH406 2.1 28.5 1.0
O B:HOH419 2.2 27.4 1.0
CG B:ASP9 3.1 28.4 1.0
P2 B:POP302 3.2 30.6 1.0
P1 B:POP302 3.2 31.7 1.0
P2 B:POP301 3.4 28.8 1.0
OD2 B:ASP9 3.4 30.2 1.0
O1 B:POP302 3.6 26.5 1.0
O B:POP302 3.6 32.6 1.0
O3 B:TRS304 3.7 28.0 1.0
O5 B:POP302 3.8 27.9 1.0
O6 B:POP301 3.8 28.3 1.0
NH2 B:ARG60 3.8 26.2 1.0
O B:HOH408 3.9 28.8 1.0
O2 B:POP301 4.0 29.1 1.0
O B:POP301 4.1 30.6 1.0
NH2 B:ARG13 4.1 30.5 1.0
N B:GLY10 4.4 27.5 1.0
O4 B:POP301 4.4 29.2 1.0
C3 B:TRS304 4.4 28.3 1.0
CB B:ASP9 4.4 28.5 1.0
O6 B:POP302 4.5 26.7 1.0
O3 B:POP302 4.5 30.5 1.0
P1 B:POP301 4.5 28.3 1.0
NE A:ARG211 4.6 32.2 1.0
NH2 A:ARG211 4.6 32.9 1.0
NH2 B:ARG163 4.8 35.0 1.0
CA B:ASP9 4.9 28.8 1.0
O1 B:POP301 4.9 27.2 1.0

Magnesium binding site 3 out of 4 in 5gul

Go back to Magnesium Binding Sites List in 5gul
Magnesium binding site 3 out of 4 in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:32.5
occ:1.00
O C:HOH402 1.9 34.0 1.0
O6 C:POP301 2.1 30.2 1.0
O2 C:POP301 2.1 32.8 1.0
O4 C:POP302 2.1 29.8 1.0
OD1 C:ASP9 2.2 33.1 1.0
O C:HOH416 2.3 35.1 1.0
CG C:ASP9 3.1 29.7 1.0
P1 C:POP301 3.2 35.5 1.0
P2 C:POP301 3.3 31.9 1.0
P2 C:POP302 3.5 30.1 1.0
OD2 C:ASP9 3.5 33.1 1.0
O3 C:POP301 3.6 36.4 1.0
O C:POP301 3.6 32.1 1.0
O5 C:POP301 3.8 29.2 1.0
O5 C:POP302 3.8 31.7 1.0
O1 C:POP302 3.8 35.6 1.0
O1 C:TRS304 3.8 32.1 1.0
O C:HOH405 4.0 27.8 1.0
NH2 C:ARG60 4.1 33.1 1.0
O C:POP302 4.2 32.8 1.0
NH2 C:ARG13 4.3 36.2 1.0
N C:GLY10 4.3 35.2 1.0
C1 C:TRS304 4.4 32.2 1.0
NE D:ARG211 4.4 35.6 1.0
NH2 D:ARG211 4.5 31.4 1.0
CB C:ASP9 4.5 32.7 1.0
O1 C:POP301 4.5 39.1 1.0
O6 C:POP302 4.5 31.8 1.0
O4 C:POP301 4.6 27.4 1.0
P1 C:POP302 4.6 32.3 1.0
O3 C:POP302 4.8 29.4 1.0
CA C:ASP9 4.9 34.2 1.0
CZ D:ARG211 4.9 34.7 1.0
NH2 C:ARG163 4.9 31.4 1.0
CA C:GLY10 5.0 33.8 1.0

Magnesium binding site 4 out of 4 in 5gul

Go back to Magnesium Binding Sites List in 5gul
Magnesium binding site 4 out of 4 in the Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tris/PPIX2/MG2+ Bound Form of Cyclolavandulyl Diphosphate Synthase (Clds) From Streptomyces Sp. CL190 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:42.9
occ:1.00
O C:HOH413 2.0 46.2 1.0
O6 D:POP302 2.0 44.7 1.0
O6 D:POP301 2.1 43.1 1.0
O D:HOH407 2.2 41.7 1.0
OD1 D:ASP9 2.2 37.2 1.0
O1 D:POP301 2.3 51.7 1.0
O2 D:POP301 3.0 41.0 1.0
P1 D:POP301 3.1 50.8 1.0
CG D:ASP9 3.3 43.6 1.0
P2 D:POP301 3.4 43.7 1.0
P2 D:POP302 3.5 43.9 1.0
O D:POP301 3.6 44.6 1.0
NH2 D:ARG60 3.7 44.1 1.0
OD2 D:ASP9 3.7 46.5 1.0
O3 D:POP302 3.7 50.4 1.0
O1 D:TRS304 4.0 39.9 1.0
O4 D:POP302 4.0 35.6 1.0
NE C:ARG211 4.0 43.2 1.0
O D:POP302 4.2 44.3 1.0
O4 D:POP301 4.2 36.2 1.0
NH2 D:ARG13 4.2 58.8 1.0
NH2 C:ARG211 4.4 41.3 1.0
O5 D:POP301 4.5 47.1 1.0
O3 D:POP301 4.5 61.5 1.0
O5 D:POP302 4.5 42.6 1.0
P1 D:POP302 4.6 41.8 1.0
C1 D:TRS304 4.6 43.0 1.0
CB D:ASP9 4.7 41.7 1.0
CZ C:ARG211 4.7 47.8 1.0
O2 D:POP302 4.8 40.5 1.0
N D:GLY10 4.9 51.4 1.0
CZ D:ARG60 4.9 43.6 1.0
CD C:ARG211 4.9 43.4 1.0

Reference:

T.Tomita, M.Kobayashi, Y.Karita, Y.Yasuno, T.Shinada, M.Nishiyama, T.Kuzuyama. Structure and Mechanism of the Monoterpene Cyclolavandulyl Diphosphate Synthase That Catalyzes Consecutive Condensation and Cyclization. Angew. Chem. Int. Ed. Engl. V. 56 14913 2017.
ISSN: ESSN 1521-3773
PubMed: 28922556
DOI: 10.1002/ANIE.201708474
Page generated: Sun Sep 29 15:26:27 2024

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