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Magnesium in PDB 8h72: Class I Sesquiterpene Synthase Dbpros (Complex)

Enzymatic activity of Class I Sesquiterpene Synthase Dbpros (Complex)

All present enzymatic activity of Class I Sesquiterpene Synthase Dbpros (Complex):
4.2.3.135;

Protein crystallography data

The structure of Class I Sesquiterpene Synthase Dbpros (Complex), PDB code: 8h72 was solved by T.T.Lou, M.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.56 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.844, 88.421, 201.936, 90, 90, 90
R / Rfree (%) 17.9 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Class I Sesquiterpene Synthase Dbpros (Complex) (pdb code 8h72). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Class I Sesquiterpene Synthase Dbpros (Complex), PDB code: 8h72:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8h72

Go back to Magnesium Binding Sites List in 8h72
Magnesium binding site 1 out of 3 in the Class I Sesquiterpene Synthase Dbpros (Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Class I Sesquiterpene Synthase Dbpros (Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:37.6
occ:1.00
OD1 A:ASP234 2.7 22.8 1.0
OG A:SER237 2.8 25.1 1.0
O A:HOH667 3.0 39.3 1.0
O A:ASN233 3.6 22.3 1.0
CA A:ASP234 3.6 21.5 1.0
CB A:SER237 3.6 29.1 1.0
C A:ASN233 3.6 24.1 1.0
N A:ASP234 3.7 23.1 1.0
CG A:ASP234 3.8 22.3 1.0
O A:HOH506 4.1 31.8 1.0
CB A:ASN233 4.1 21.4 1.0
CB A:ASP234 4.3 22.3 1.0
OE2 A:GLU241 4.3 39.5 1.0
CA A:ASN233 4.5 25.5 1.0
NH2 A:ARG189 4.6 38.5 1.0
C A:ASP234 4.8 24.1 1.0
OD2 A:ASP234 4.8 23.8 1.0
OH A:TYR323 4.9 24.9 1.0
CD A:GLU241 4.9 32.4 1.0
ND2 A:ASN250 4.9 22.6 1.0
CA A:SER237 4.9 28.1 1.0

Magnesium binding site 2 out of 3 in 8h72

Go back to Magnesium Binding Sites List in 8h72
Magnesium binding site 2 out of 3 in the Class I Sesquiterpene Synthase Dbpros (Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Class I Sesquiterpene Synthase Dbpros (Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:51.6
occ:1.00
OD2 A:ASP97 2.7 39.9 1.0
CG A:ASP97 3.7 38.3 1.0
O A:HOH746 3.7 33.8 1.0
C5 A:BTM403 3.7 39.8 1.0
OD1 A:ASP97 3.9 39.6 1.0
C6 A:BTM403 3.9 40.6 1.0
O A:HOH576 4.1 31.0 1.0
O A:HOH625 4.7 34.0 1.0
C7 A:BTM403 4.8 37.7 1.0
N A:BTM403 4.8 40.3 1.0
C4 A:BTM403 4.8 38.6 1.0
C1 A:BTM403 5.0 39.9 1.0

Magnesium binding site 3 out of 3 in 8h72

Go back to Magnesium Binding Sites List in 8h72
Magnesium binding site 3 out of 3 in the Class I Sesquiterpene Synthase Dbpros (Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Class I Sesquiterpene Synthase Dbpros (Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:37.4
occ:1.00
OD1 B:ASP234 2.7 23.8 1.0
OG B:SER237 2.7 26.5 1.0
O B:HOH635 3.0 37.6 1.0
O B:ASN233 3.5 23.8 1.0
CB B:SER237 3.6 24.9 1.0
CA B:ASP234 3.7 23.9 1.0
C B:ASN233 3.7 24.0 1.0
N B:ASP234 3.7 21.9 1.0
CG B:ASP234 3.8 24.8 1.0
O B:HOH543 3.9 30.3 1.0
O B:HOH655 4.1 35.2 1.0
OE2 B:GLU241 4.2 30.0 1.0
CB B:ASN233 4.3 24.9 1.0
NH2 B:ARG189 4.3 30.7 1.0
CB B:ASP234 4.3 24.9 1.0
ND2 B:ASN250 4.6 20.4 1.0
CA B:ASN233 4.6 24.4 1.0
OE1 B:GLU241 4.7 27.2 1.0
CD B:GLU241 4.7 28.6 1.0
OD2 B:ASP234 4.8 27.0 1.0
C B:ASP234 4.8 23.6 1.0
CA B:SER237 4.9 28.3 1.0

Reference:

T.Lou, A.Li, H.Xu, J.Pan, B.Xing, R.Wu, J.S.Dickschat, D.Yang, M.Ma. Structural Insights Into Three Sesquiterpene Synthases For the Biosynthesis of Tricyclic Sesquiterpenes and Chemical Space Expansion By Structure-Based Mutagenesis. J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
PubMed: 37018048
DOI: 10.1021/JACS.3C00278
Page generated: Fri Oct 4 04:26:02 2024

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