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Magnesium in PDB 7y88: Class I Diterpene Synthase (Cys-Ggpp-MG2+) From Streptomyces Cattleya

Protein crystallography data

The structure of Class I Diterpene Synthase (Cys-Ggpp-MG2+) From Streptomyces Cattleya, PDB code: 7y88 was solved by B.Xing, M.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.75 / 1.87
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 100.56, 113.137, 138.052, 90, 90, 90
R / Rfree (%) 18.1 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Class I Diterpene Synthase (Cys-Ggpp-MG2+) From Streptomyces Cattleya (pdb code 7y88). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Class I Diterpene Synthase (Cys-Ggpp-MG2+) From Streptomyces Cattleya, PDB code: 7y88:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7y88

Go back to Magnesium Binding Sites List in 7y88
Magnesium binding site 1 out of 2 in the Class I Diterpene Synthase (Cys-Ggpp-MG2+) From Streptomyces Cattleya


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Class I Diterpene Synthase (Cys-Ggpp-MG2+) From Streptomyces Cattleya within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:23.6
occ:1.00
OD1 A:ASP232 2.2 17.2 1.0
O2A A:GRG401 2.3 28.0 1.0
OG A:SER236 2.5 20.2 1.0
O2B A:GRG401 2.5 38.8 1.0
O A:HOH552 2.5 23.4 1.0
O3B A:GRG401 2.7 31.6 1.0
PB A:GRG401 3.0 35.5 1.0
CG A:ASP232 3.3 21.9 1.0
CB A:SER236 3.4 20.3 1.0
PA A:GRG401 3.4 34.8 1.0
O3A A:GRG401 3.6 37.2 1.0
OD2 A:ASP232 3.6 20.6 1.0
O A:HOH513 3.7 30.5 1.0
NH2 A:ARG186 3.7 16.1 1.0
O A:ASP232 3.9 15.4 1.0
O1 A:GRG401 4.0 35.1 1.0
O A:HOH601 4.1 35.7 1.0
C A:ASP232 4.3 16.8 1.0
OD1 A:ASP233 4.4 15.7 1.0
O1B A:GRG401 4.4 37.5 1.0
CB A:ASP232 4.6 15.2 1.0
N A:ASP233 4.6 15.8 1.0
O1A A:GRG401 4.6 41.6 1.0
CA A:ASP233 4.7 16.1 1.0
CA A:SER236 4.8 20.0 1.0
CZ A:ARG186 4.9 18.2 1.0

Magnesium binding site 2 out of 2 in 7y88

Go back to Magnesium Binding Sites List in 7y88
Magnesium binding site 2 out of 2 in the Class I Diterpene Synthase (Cys-Ggpp-MG2+) From Streptomyces Cattleya


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Class I Diterpene Synthase (Cys-Ggpp-MG2+) From Streptomyces Cattleya within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:53.0
occ:1.00
OD2 A:ASP89 2.6 43.3 1.0
O3A A:GRG401 2.7 37.2 1.0
NH2 A:ARG324 3.5 31.3 1.0
CG A:ASP89 3.5 42.1 1.0
O1B A:GRG401 3.5 37.5 1.0
PB A:GRG401 3.6 35.5 1.0
OD1 A:ASP89 3.7 48.2 1.0
O1A A:GRG401 3.7 41.6 1.0
PA A:GRG401 3.9 34.8 1.0
O2B A:GRG401 3.9 38.8 1.0
NZ A:LYS239 4.3 43.2 1.0
OD1 A:ASP90 4.3 49.2 1.0
O2A A:GRG401 4.7 28.0 1.0
CZ A:ARG324 4.8 28.7 1.0
C4 A:GRG401 4.8 37.7 1.0
CB A:ASP89 4.9 38.6 1.0
O3B A:GRG401 5.0 31.6 1.0

Reference:

B.Xing, H.Xu, A.Li, T.Lou, M.Xu, K.Wang, Z.Xu, J.S.Dickschat, D.Yang, M.Ma. Crystal Structure Based Mutagenesis of Cattleyene Synthase Leads to the Generation of Rearranged Polycyclic Diterpenes. Angew.Chem.Int.Ed.Engl. V. 61 09785 2022.
ISSN: ESSN 1521-3773
PubMed: 35819825
DOI: 10.1002/ANIE.202209785
Page generated: Thu Oct 3 14:37:23 2024

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