Magnesium in PDB 8yla: 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; 4.2.3.176;

Protein crystallography data

The structure of Crystal Structures of Terpene Synthases Complexed with A Substrate Mimic, PDB code: 8yla 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) 28.65 / 1.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.308, 83.623, 80.055, 90, 122.8, 90
R / Rfree (%) 17.5 / 19.1

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 8yla

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Magnesium binding site 1 out of 6 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:7.7
occ:1.00
 OD2 A:ASP95 2.1 8.9 1.0
O31 A:PPV404 2.1 8.3 1.0
O A:HOH655 2.1 8.1 1.0
O A:HOH561 2.1 9.3 1.0
O A:HOH536 2.1 8.6 1.0
OE2 A:GLU99 2.3 10.6 1.0
CG A:ASP95 3.1 9.2 1.0
CD A:GLU99 3.2 11.2 1.0
MG A:MG402 3.2 8.4 1.0
P1 A:PPV404 3.3 8.0 1.0
OD1 A:ASP95 3.5 9.4 1.0
O A:HOH549 3.6 8.8 1.0
O11 A:PPV404 3.6 8.8 1.0
CG A:GLU99 3.7 11.2 1.0
OD2 A:ASP190 3.9 8.9 1.0
OD1 A:ASP190 4.1 9.5 1.0
O21 A:PPV404 4.1 8.0 1.0
O A:HOH539 4.2 8.8 1.0
OE1 A:GLU99 4.2 12.5 1.0
O A:HOH693 4.2 8.7 1.0
CG A:ASP190 4.4 8.6 1.0
CB A:ASP95 4.4 8.9 1.0
O A:HOH619 4.4 12.9 1.0
OPP A:PPV404 4.5 7.7 1.0
O A:ASP190 4.6 9.1 1.0
NH1 A:ARG187 4.7 8.9 1.0
O A:HOH636 4.8 9.5 1.0
O22 A:PPV404 4.8 8.9 1.0
O A:ASP95 4.9 9.2 1.0

Magnesium binding site 2 out of 6 in 8yla

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Magnesium binding site 2 out of 6 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:8.4
occ:1.00
 OE2 A:GLU99 1.9 10.6 1.0
O22 A:PPV404 2.0 8.9 1.0
O A:HOH539 2.1 8.8 1.0
O A:HOH636 2.1 9.5 1.0
O A:HOH549 2.1 8.8 1.0
O31 A:PPV404 2.1 8.3 1.0
CD A:GLU99 3.0 11.2 1.0
P1 A:PPV404 3.2 8.0 1.0
MG A:MG401 3.2 7.7 1.0
P2 A:PPV404 3.2 8.1 1.0
OPP A:PPV404 3.4 7.7 1.0
OE1 A:GLU99 3.5 12.5 1.0
NH2 A:ARG324 3.5 20.0 1.0
OD2 A:ASP95 3.6 8.9 1.0
O21 A:PPV404 3.8 8.0 1.0
OD1 A:ASP96 3.9 11.9 1.0
NH1 A:ARG238 4.0 10.8 1.0
O32 A:PPV404 4.1 8.1 1.0
CG A:GLU99 4.2 11.2 1.0
OE2 A:GLU239 4.2 8.7 1.0
O A:HOH536 4.3 8.6 1.0
O12 A:PPV404 4.4 8.3 1.0
O A:HOH774 4.4 12.8 1.0
O11 A:PPV404 4.5 8.8 1.0
O A:HOH693 4.7 8.7 1.0
CZ A:ARG324 4.7 14.8 1.0
MG A:MG403 4.8 8.1 1.0
CG A:ASP95 4.8 9.2 1.0
O A:HOH561 4.8 9.3 1.0
CZ A:ARG238 5.0 9.9 1.0

Magnesium binding site 3 out of 6 in 8yla

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Magnesium binding site 3 out of 6 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:8.1
occ:1.00
 OE2 A:GLU239 2.0 8.7 1.0
O21 A:PPV404 2.0 8.0 1.0
O32 A:PPV404 2.0 8.1 1.0
O A:HOH589 2.1 8.3 1.0
OD1 A:ASN231 2.1 8.2 1.0
OG A:SER235 2.2 8.8 1.0
CD A:GLU239 3.1 8.7 1.0
CG A:ASN231 3.1 8.2 1.0
CB A:SER235 3.1 9.3 1.0
P2 A:PPV404 3.2 8.1 1.0
P1 A:PPV404 3.3 8.0 1.0
OPP A:PPV404 3.4 7.7 1.0
OE1 A:GLU239 3.5 9.5 1.0
ND2 A:ASN231 3.5 11.0 1.0
O A:HOH693 3.8 8.7 1.0
NH2 A:ARG187 3.8 8.7 1.0
O22 A:PPV404 3.9 8.9 1.0
O A:HOH539 4.0 8.8 1.0
O A:ASN231 4.1 8.5 1.0
O31 A:PPV404 4.2 8.3 1.0
O11 A:PPV404 4.3 8.8 1.0
CG A:GLU239 4.3 9.8 1.0
C A:ASN231 4.4 8.2 1.0
O12 A:PPV404 4.4 8.3 1.0
OD1 A:ASP232 4.5 8.0 1.0
CB A:ASN231 4.5 9.8 1.0
CA A:SER235 4.5 9.3 1.0
NH2 A:ARG238 4.6 10.3 1.0
CA A:ASP232 4.7 8.9 1.0
N A:ASP232 4.7 8.3 1.0
CZ A:ARG187 4.7 8.2 1.0
MG A:MG402 4.8 8.4 1.0
ND2 A:ASN252 4.9 8.3 1.0
C A:SER235 5.0 9.0 1.0

Magnesium binding site 4 out of 6 in 8yla

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Magnesium binding site 4 out of 6 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:8.6
occ:1.00
 O B:HOH551 2.1 9.3 1.0
O B:HOH621 2.1 8.5 1.0
O11 B:PPV404 2.1 8.7 1.0
OD2 B:ASP95 2.1 9.7 1.0
O B:HOH546 2.1 8.5 1.0
OE2 B:GLU99 2.2 10.7 1.0
CD B:GLU99 3.1 10.8 1.0
CG B:ASP95 3.1 9.3 1.0
MG B:MG402 3.2 8.6 1.0
P1 B:PPV404 3.3 8.1 1.0
OD1 B:ASP95 3.5 9.6 1.0
O B:HOH555 3.5 9.3 1.0
O31 B:PPV404 3.6 8.3 1.0
CG B:GLU99 3.7 11.2 1.0
OD2 B:ASP190 3.9 9.7 1.0
OE1 B:GLU99 4.0 10.5 1.0
OD1 B:ASP190 4.1 10.1 1.0
O21 B:PPV404 4.2 8.1 1.0
O B:HOH627 4.2 8.7 1.0
O B:HOH565 4.2 8.2 1.0
O B:HOH636 4.3 10.3 1.0
CG B:ASP190 4.4 9.8 1.0
CB B:ASP95 4.5 10.0 1.0
OPP B:PPV404 4.5 8.5 1.0
O B:HOH654 4.5 9.8 1.0
O B:ASP190 4.6 10.0 1.0
NH1 B:ARG187 4.6 8.9 1.0
O B:HOH651 4.8 9.3 1.0
O22 B:PPV404 4.8 8.4 1.0
C5 B:BTM405 4.9 21.5 1.0
O B:ASP95 5.0 10.3 1.0
C3 B:BTM405 5.0 22.4 1.0

Magnesium binding site 5 out of 6 in 8yla

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Magnesium binding site 5 out of 6 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:8.6
occ:1.00
 OE2 B:GLU99 2.0 10.7 1.0
O B:HOH565 2.0 8.2 1.0
O22 B:PPV404 2.1 8.4 1.0
O B:HOH555 2.1 9.3 1.0
O B:HOH651 2.1 9.3 1.0
O11 B:PPV404 2.1 8.7 1.0
CD B:GLU99 3.0 10.8 1.0
MG B:MG401 3.2 8.6 1.0
P1 B:PPV404 3.2 8.1 1.0
P2 B:PPV404 3.3 8.2 1.0
OPP B:PPV404 3.5 8.5 1.0
OE1 B:GLU99 3.5 10.5 1.0
OD2 B:ASP95 3.7 9.7 1.0
O21 B:PPV404 3.8 8.1 1.0
NH2 B:ARG324 3.9 11.5 1.0
OD1 B:ASP96 3.9 14.0 1.0
NH1 B:ARG238 3.9 9.4 1.0
O32 B:PPV404 4.2 8.2 1.0
OE2 B:GLU239 4.2 8.2 1.0
CG B:GLU99 4.2 11.2 1.0
O B:HOH546 4.2 8.5 1.0
O B:HOH742 4.3 11.1 1.0
O12 B:PPV404 4.4 9.8 1.0
O31 B:PPV404 4.5 8.3 1.0
O B:HOH627 4.5 8.7 1.0
O B:HOH551 4.7 9.3 1.0
MG B:MG403 4.8 8.2 1.0
CG B:ASP95 4.8 9.3 1.0
C3 B:BTM405 4.9 22.4 1.0
CZ B:ARG238 5.0 8.8 1.0
O B:HOH621 5.0 8.5 1.0

Magnesium binding site 6 out of 6 in 8yla

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Magnesium binding site 6 out of 6 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:8.2
occ:1.00
 OE2 B:GLU239 2.0 8.2 1.0
O32 B:PPV404 2.0 8.2 1.0
O21 B:PPV404 2.0 8.1 1.0
O B:HOH585 2.1 8.5 1.0
OD1 B:ASN231 2.2 7.6 1.0
OG B:SER235 2.2 8.1 1.0
CD B:GLU239 3.0 8.2 1.0
CG B:ASN231 3.1 8.3 1.0
CB B:SER235 3.2 7.9 1.0
P2 B:PPV404 3.2 8.2 1.0
P1 B:PPV404 3.3 8.1 1.0
OPP B:PPV404 3.4 8.5 1.0
OE1 B:GLU239 3.4 8.6 1.0
ND2 B:ASN231 3.5 9.4 1.0
O B:HOH627 3.7 8.7 1.0
NH2 B:ARG187 3.8 8.3 1.0
O22 B:PPV404 3.8 8.4 1.0
O B:HOH565 4.0 8.2 1.0
O B:ASN231 4.1 7.7 1.0
O11 B:PPV404 4.2 8.7 1.0
CG B:GLU239 4.3 8.1 1.0
O31 B:PPV404 4.3 8.3 1.0
C B:ASN231 4.4 7.7 1.0
O12 B:PPV404 4.4 9.8 1.0
OD1 B:ASP232 4.5 8.7 1.0
CB B:ASN231 4.5 9.0 1.0
CA B:SER235 4.6 8.6 1.0
NH2 B:ARG238 4.7 10.9 1.0
CA B:ASP232 4.7 7.7 1.0
N B:ASP232 4.7 8.0 1.0
CZ B:ARG187 4.8 8.9 1.0
MG B:MG402 4.8 8.6 1.0
ND2 B:ASN252 4.9 8.3 1.0
NH1 B:ARG238 4.9 9.4 1.0
C B:SER235 4.9 7.9 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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