Magnesium in PDB 8yl9: Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic

Enzymatic activity of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic

All present enzymatic activity of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic:
2.5.1.29; 2.5.1.81;

Protein crystallography data

The structure of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic, PDB code: 8yl9 was solved by M.Xu, M.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.32 / 2.75
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 146.99, 146.99, 146.99, 90, 90, 90
R / Rfree (%) 18.7 / 26.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic (pdb code 8yl9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic, PDB code: 8yl9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 8yl9

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Magnesium binding site 1 out of 9 in the Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:18.6
occ:1.00
 O31 A:PPV404 2.1 12.0 1.0
OD2 A:ASP105 2.3 18.1 1.0
O22 A:PPV404 2.4 18.0 1.0
OD2 A:ASP109 2.6 20.6 1.0
OD1 A:ASP109 3.1 23.6 1.0
CG A:ASP109 3.2 27.5 1.0
CG A:ASP105 3.3 18.6 1.0
NZ A:LYS244 3.3 20.1 1.0
P1 A:PPV404 3.4 18.8 1.0
P2 A:PPV404 3.5 21.1 1.0
OD1 A:ASP105 3.6 23.4 1.0
O A:HOH537 3.6 21.1 1.0
O12 A:PPV404 3.8 21.1 1.0
OPP A:PPV404 3.8 17.7 1.0
NH2 A:ARG334 3.9 17.7 1.0
O11 A:PPV404 3.9 19.4 1.0
OE2 A:GLU245 4.0 20.0 1.0
MG A:MG402 4.2 18.1 1.0
OD1 A:ASP106 4.3 18.3 1.0
H3 A:BTM405 4.3 43.6 1.0
CE A:LYS244 4.5 15.3 1.0
O21 A:PPV404 4.6 14.9 1.0
H4A A:BTM405 4.6 41.1 1.0
CB A:ASP105 4.7 14.4 1.0
CB A:ASP109 4.7 21.6 1.0
O A:ASP105 4.7 16.4 1.0
MG A:MG403 4.7 19.6 1.0
O32 A:PPV404 4.8 23.0 1.0
CG A:GLU245 4.8 15.4 1.0
CD A:GLU245 4.8 15.4 1.0
C A:ASP105 4.9 20.6 1.0
CZ A:ARG334 5.0 14.0 1.0

Magnesium binding site 2 out of 9 in 8yl9

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Magnesium binding site 2 out of 9 in the Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:18.1
occ:1.00
 O22 A:PPV404 2.3 18.0 1.0
OD1 A:ASP105 2.3 23.4 1.0
OD2 A:ASP109 2.5 20.6 1.0
H5A A:BTM405 2.9 50.3 1.0
O32 A:PPV404 3.0 23.0 1.0
P2 A:PPV404 3.1 21.1 1.0
CG A:ASP105 3.5 18.6 1.0
CG A:ASP109 3.6 27.5 1.0
H5 A:BTM405 3.6 50.3 1.0
C5 A:BTM405 3.7 43.0 1.0
H4A A:BTM405 3.8 41.1 1.0
O12 A:PPV404 3.9 21.1 1.0
CB A:ASP109 3.9 21.6 1.0
OE1 A:GLU196 4.0 38.5 1.0
OD2 A:ASP105 4.0 18.1 1.0
OE2 A:GLU196 4.2 29.3 1.0
MG A:MG401 4.2 18.6 1.0
C4 A:BTM405 4.3 35.4 1.0
CD A:GLU196 4.5 30.4 1.0
H4 A:BTM405 4.5 41.1 1.0
OPP A:PPV404 4.5 17.7 1.0
NH1 A:ARG193 4.5 12.5 1.0
H5B A:BTM405 4.6 50.3 1.0
CB A:ASP105 4.6 14.4 1.0
OD1 A:ASP109 4.7 23.6 1.0
O A:GLU196 4.8 26.5 1.0

Magnesium binding site 3 out of 9 in 8yl9

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Magnesium binding site 3 out of 9 in the Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:19.6
occ:1.00
 O12 A:PPV404 2.0 21.1 1.0
OD1 A:ASN237 2.2 15.6 1.0
OE2 A:GLU245 2.2 20.0 1.0
O11 A:PPV404 2.4 19.4 1.0
OG A:SER241 2.5 14.3 1.0
OPP A:PPV404 3.0 17.7 1.0
P2 A:PPV404 3.1 21.1 1.0
CG A:ASN237 3.2 14.8 1.0
CD A:GLU245 3.3 15.4 1.0
P1 A:PPV404 3.3 18.8 1.0
NH2 A:ARG193 3.4 14.8 1.0
CB A:SER241 3.4 15.3 1.0
ND2 A:ASN237 3.5 16.9 1.0
OE1 A:GLU245 3.7 13.4 1.0
O32 A:PPV404 4.0 23.0 1.0
O22 A:PPV404 4.1 18.0 1.0
O31 A:PPV404 4.2 12.0 1.0
O A:ASN237 4.3 17.2 1.0
CZ A:ARG193 4.4 14.8 1.0
OD1 A:ASP238 4.5 16.9 1.0
O21 A:PPV404 4.5 14.9 1.0
C A:ASN237 4.5 12.8 1.0
CG A:GLU245 4.5 15.4 1.0
CB A:ASN237 4.5 11.7 1.0
N A:ASP238 4.7 13.6 1.0
MG A:MG401 4.7 18.6 1.0
CA A:ASP238 4.8 13.3 1.0
CA A:SER241 4.8 16.2 1.0

Magnesium binding site 4 out of 9 in 8yl9

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Magnesium binding site 4 out of 9 in the Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:16.4
occ:1.00
 OE2 B:GLU245 2.1 17.5 1.0
OG B:SER241 2.2 13.0 1.0
OD1 B:ASN237 2.2 11.5 1.0
O32 B:PPV404 2.3 15.2 1.0
O11 B:PPV404 2.4 11.1 1.0
CD B:GLU245 2.9 15.2 1.0
OE1 B:GLU245 3.1 13.0 1.0
NH2 B:ARG193 3.2 12.7 1.0
CG B:ASN237 3.4 10.0 1.0
CB B:SER241 3.4 17.3 1.0
P2 B:PPV404 3.8 16.5 1.0
O B:ASN237 3.8 11.4 1.0
P1 B:PPV404 3.9 17.0 1.0
OD1 B:ASP238 3.9 11.5 1.0
C B:ASN237 4.1 10.9 1.0
ND2 B:ASN237 4.1 12.2 1.0
CA B:ASP238 4.2 10.6 1.0
N B:ASP238 4.3 8.9 1.0
OPP B:PPV404 4.3 17.1 1.0
CG B:GLU245 4.3 18.0 1.0
CZ B:ARG193 4.3 11.9 1.0
O12 B:PPV404 4.3 13.2 1.0
ND2 B:ASN260 4.4 18.5 1.0
CB B:ASN237 4.5 7.8 1.0
O B:GLN259 4.5 17.0 1.0
O31 B:PPV404 4.6 19.4 1.0
O B:SER241 4.6 16.2 1.0
CA B:SER241 4.6 15.6 1.0
C B:SER241 4.7 16.4 1.0
O22 B:PPV404 4.8 9.8 1.0
CG B:ASP238 4.9 11.9 1.0
O21 B:PPV404 4.9 18.0 1.0
CA B:ASN237 4.9 10.6 1.0
NH1 B:ARG193 4.9 7.7 1.0
MG B:MG402 5.0 13.5 1.0

Magnesium binding site 5 out of 9 in 8yl9

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Magnesium binding site 5 out of 9 in the Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:13.5
occ:1.00
 OD2 B:ASP105 2.1 20.0 1.0
O31 B:PPV404 2.4 19.4 1.0
OD2 B:ASP109 2.5 12.0 1.0
O22 B:PPV404 2.6 9.8 1.0
OPP B:PPV404 3.2 17.1 1.0
P2 B:PPV404 3.2 16.5 1.0
CG B:ASP105 3.3 17.3 1.0
P1 B:PPV404 3.3 17.0 1.0
O32 B:PPV404 3.4 15.2 1.0
CG B:ASP109 3.5 10.9 1.0
NZ B:LYS244 3.5 16.4 1.0
OD1 B:ASP109 3.8 16.1 1.0
OD1 B:ASP105 3.8 16.0 1.0
MG B:MG403 3.9 12.8 1.0
O11 B:PPV404 3.9 11.1 1.0
OE2 B:GLU245 3.9 17.5 1.0
NH2 B:ARG334 4.1 16.8 1.0
CE B:LYS244 4.3 14.3 1.0
O B:HOH530 4.4 13.2 1.0
CB B:ASP105 4.5 12.8 1.0
O21 B:PPV404 4.6 18.0 1.0
CD B:GLU245 4.7 15.2 1.0
CG B:GLU245 4.7 18.0 1.0
O12 B:PPV404 4.7 13.2 1.0
OD1 B:ASP106 4.8 18.4 1.0
CB B:ASP109 4.8 13.8 1.0
H3A B:BTM405 4.9 24.7 1.0
MG B:MG401 5.0 16.4 1.0

Magnesium binding site 6 out of 9 in 8yl9

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Magnesium binding site 6 out of 9 in the Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:12.8
occ:1.00
 OD1 B:ASP105 2.0 16.0 1.0
O B:HOH530 2.0 13.2 1.0
O22 B:PPV404 2.1 9.8 1.0
O B:HOH514 2.2 15.4 1.0
OD2 B:ASP109 2.4 12.0 1.0
O B:HOH549 2.6 17.2 1.0
CG B:ASP105 2.9 17.3 1.0
CB B:ASP109 3.2 13.8 1.0
CG B:ASP109 3.2 10.9 1.0
OD2 B:ASP105 3.3 20.0 1.0
P2 B:PPV404 3.5 16.5 1.0
MG B:MG402 3.9 13.5 1.0
O B:HOH513 3.9 15.2 1.0
O12 B:PPV404 4.1 13.2 1.0
OE2 B:GLU196 4.2 22.1 1.0
CB B:ASP105 4.3 12.8 1.0
O32 B:PPV404 4.4 15.2 1.0
OD1 B:ASP109 4.4 16.1 1.0
OPP B:PPV404 4.5 17.1 1.0
H5A B:BTM405 4.6 26.3 1.0
O B:HOH558 4.7 14.7 1.0
H3A B:BTM405 4.7 24.7 1.0
CD B:GLU196 4.7 17.7 1.0
H5 B:BTM405 4.7 26.3 1.0
CA B:ASP109 4.7 11.2 1.0
H5B B:BTM405 4.8 26.3 1.0
CA B:ASP105 4.8 10.4 1.0
O B:GLU196 4.8 11.7 1.0
O B:ASP105 4.9 13.4 1.0
OE1 B:GLU196 5.0 11.9 1.0
C5 B:BTM405 5.0 22.2 1.0

Magnesium binding site 7 out of 9 in 8yl9

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Magnesium binding site 7 out of 9 in the Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg401

b:22.6
occ:1.00
 O I:HOH507 2.1 17.2 1.0
O22 I:PPV404 2.5 22.7 1.0
OD2 I:ASP109 2.5 23.7 1.0
OD1 I:ASP105 2.7 28.4 1.0
CB I:ASP109 3.3 26.7 1.0
CG I:ASP109 3.3 28.0 1.0
MG I:MG402 3.4 30.0 1.0
P2 I:PPV404 3.5 25.0 1.0
CG I:ASP105 3.6 27.0 1.0
OE2 I:GLU196 3.7 34.1 1.0
OD2 I:ASP105 3.8 29.4 1.0
O32 I:PPV404 3.8 20.0 1.0
O12 I:PPV404 4.0 24.5 1.0
OE1 I:GLU196 4.1 29.3 1.0
CD I:GLU196 4.1 30.6 1.0
OD1 I:ASP109 4.5 28.8 1.0
NH1 I:ARG193 4.5 19.4 1.0
O I:HOH503 4.6 17.5 1.0
O21 I:PPV404 4.7 29.4 1.0
CA I:ASP109 4.8 20.2 1.0
H7A I:BTM405 4.9 37.3 1.0
OPP I:PPV404 5.0 23.3 1.0

Magnesium binding site 8 out of 9 in 8yl9

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Magnesium binding site 8 out of 9 in the Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg402

b:30.0
occ:1.00
 OD2 I:ASP109 1.9 23.7 1.0
O21 I:PPV404 2.1 29.4 1.0
OD2 I:ASP105 2.3 29.4 1.0
O22 I:PPV404 2.4 22.7 1.0
CG I:ASP109 2.9 28.0 1.0
OD1 I:ASP109 3.3 28.8 1.0
CG I:ASP105 3.4 27.0 1.0
MG I:MG401 3.4 22.6 1.0
P1 I:PPV404 3.5 27.7 1.0
P2 I:PPV404 3.6 25.0 1.0
OD1 I:ASP105 3.7 28.4 1.0
NZ I:LYS244 3.8 22.2 1.0
O12 I:PPV404 3.9 24.5 1.0
OPP I:PPV404 4.1 23.3 1.0
OE2 I:GLU245 4.1 29.6 1.0
O11 I:PPV404 4.1 26.8 1.0
CB I:ASP109 4.3 26.7 1.0
H7A I:BTM405 4.5 37.3 1.0
O31 I:PPV404 4.5 23.4 1.0
O I:HOH507 4.6 17.2 1.0
OD1 I:ASP106 4.7 21.1 1.0
CB I:ASP105 4.7 16.2 1.0
NH2 I:ARG334 4.7 20.2 1.0
CE I:LYS244 4.8 30.3 1.0
CD I:GLU245 4.8 29.3 1.0
CG I:GLU245 4.8 30.7 1.0
O I:ASP105 4.8 21.9 1.0
O32 I:PPV404 4.8 20.0 1.0

Magnesium binding site 9 out of 9 in 8yl9

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Magnesium binding site 9 out of 9 in the Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg403

b:29.4
occ:1.00
 OE2 I:GLU245 2.0 29.6 1.0
OD1 I:ASN237 2.1 22.9 1.0
OG I:SER241 2.1 27.5 1.0
O12 I:PPV404 2.3 24.5 1.0
O11 I:PPV404 2.4 26.8 1.0
CD I:GLU245 2.9 29.3 1.0
CB I:SER241 3.1 29.0 1.0
CG I:ASN237 3.2 23.7 1.0
OE1 I:GLU245 3.2 26.6 1.0
NH2 I:ARG193 3.3 26.4 1.0
OPP I:PPV404 3.4 23.3 1.0
P1 I:PPV404 3.4 27.7 1.0
P2 I:PPV404 3.5 25.0 1.0
ND2 I:ASN237 3.7 23.5 1.0
O I:ASN237 3.8 26.8 1.0
O21 I:PPV404 4.1 29.4 1.0
OD1 I:ASP238 4.1 32.3 1.0
C I:ASN237 4.2 27.6 1.0
CG I:GLU245 4.3 30.7 1.0
CA I:SER241 4.4 31.4 1.0
O22 I:PPV404 4.4 22.7 1.0
CB I:ASN237 4.4 21.8 1.0
CZ I:ARG193 4.4 25.1 1.0
O32 I:PPV404 4.5 20.0 1.0
O I:SER241 4.5 32.1 1.0
N I:ASP238 4.5 29.7 1.0
CA I:ASP238 4.5 25.1 1.0
ND2 I:ASN260 4.6 29.0 1.0
C I:SER241 4.6 29.3 1.0
O31 I:PPV404 4.7 23.4 1.0
O I:GLN259 4.8 31.1 1.0
CA I:ASN237 5.0 23.5 1.0
N I:SER241 5.0 28.2 1.0
NH1 I:ARG193 5.0 19.4 1.0

Reference:

M.Ma, M.Xu, H.Xu, Z.Lei, B.Xing, J.S.Dickschat, D.Yang. Structural Insights Into the Terpene Cyclization Domains of Two Fungal Sesterterpene Synthases and Enzymatic Engineering For Sesterterpene Diversification. Angew.Chem.Int.Ed.Engl. 05140 2024.
ISSN: ESSN 1521-3773
PubMed: 38584136
DOI: 10.1002/ANIE.202405140
Page generated: Sat Oct 5 08:37:40 2024

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