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Magnesium in PDB 7ofl: Crystal Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate

Protein crystallography data

The structure of Crystal Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate, PDB code: 7ofl was solved by N.Dimos, B.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.31 / 1.83
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.455, 76.622, 135.108, 90, 90, 90
R / Rfree (%) 18.3 / 23.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate (pdb code 7ofl). 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 Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate, PDB code: 7ofl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7ofl

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Magnesium binding site 1 out of 6 in the Crystal Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate


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 the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:21.1
occ:1.00
 O11 A:AHD401 2.0 18.3 1.0
O A:HOH610 2.1 22.0 1.0
OD2 A:ASP98 2.1 17.5 1.0
O A:HOH556 2.1 15.5 1.0
O15 A:AHD401 2.2 17.4 1.0
O A:HOH618 2.4 18.2 1.0
CG A:ASP98 3.0 18.1 1.0
P9 A:AHD401 3.3 21.3 1.0
P14 A:AHD401 3.3 19.9 1.0
MG A:MG404 3.3 17.6 1.0
OD1 A:ASP98 3.3 19.1 1.0
C8 A:AHD401 3.6 25.5 1.0
C7 A:AHD401 3.7 22.6 1.0
NZ A:LYS241 3.8 19.4 1.0
O16 A:AHD401 3.9 21.5 1.0
NH2 A:ARG322 3.9 19.2 1.0
O10 A:AHD401 4.0 17.4 1.0
O A:HOH524 4.2 20.2 1.0
OE2 A:GLU242 4.2 22.2 1.0
OD2 A:ASP102 4.2 23.0 1.0
O A:HOH578 4.3 27.7 1.0
OD1 A:ASP102 4.4 18.7 1.0
O12 A:AHD401 4.4 19.5 1.0
CB A:ASP98 4.4 21.3 1.0
O A:HOH718 4.5 18.3 1.0
OD1 A:ASP99 4.5 20.4 1.0
O17 A:AHD401 4.6 19.7 1.0
MG A:MG403 4.7 19.1 1.0
CG A:ASP102 4.7 20.1 1.0
O A:HOH533 4.8 17.9 1.0
O A:HOH632 4.8 16.3 1.0
CE A:LYS241 4.9 21.2 1.0
C2 A:AHD401 4.9 33.5 1.0
O A:HOH522 5.0 21.3 1.0
O A:HOH623 5.0 18.4 1.0

Magnesium binding site 2 out of 6 in 7ofl

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate


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 the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:19.1
occ:1.00
 O10 A:AHD401 1.9 17.4 1.0
O16 A:AHD401 2.0 21.5 1.0
O A:HOH583 2.0 20.8 1.0
OE2 A:GLU242 2.1 22.2 1.0
OD1 A:ASN234 2.1 20.4 1.0
OG A:SER238 2.2 19.4 1.0
CD A:GLU242 3.1 22.1 1.0
CB A:SER238 3.1 15.3 1.0
CG A:ASN234 3.1 21.4 1.0
P9 A:AHD401 3.2 21.3 1.0
P14 A:AHD401 3.3 19.9 1.0
ND2 A:ASN234 3.5 19.7 1.0
OE1 A:GLU242 3.5 17.8 1.0
C8 A:AHD401 3.7 25.5 1.0
NH2 A:ARG188 3.7 14.6 1.0
O11 A:AHD401 3.9 18.3 1.0
O A:HOH632 3.9 16.3 1.0
O13 A:AHD401 3.9 29.6 1.0
O A:HOH556 3.9 15.5 1.0
O A:ASN234 4.1 19.4 1.0
O15 A:AHD401 4.2 17.4 1.0
CG A:GLU242 4.3 19.2 1.0
O17 A:AHD401 4.3 19.7 1.0
O12 A:AHD401 4.4 19.5 1.0
OD1 A:ASP235 4.5 21.1 1.0
C A:ASN234 4.5 20.3 1.0
CB A:ASN234 4.5 17.9 1.0
CA A:SER238 4.5 19.7 1.0
MG A:MG402 4.7 21.1 1.0
CZ A:ARG188 4.8 15.9 1.0
N A:ASP235 4.9 21.2 1.0
CA A:ASP235 4.9 22.4 1.0
C A:SER238 4.9 22.6 1.0
O A:SER238 4.9 21.8 1.0

Magnesium binding site 3 out of 6 in 7ofl

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate


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 the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:17.6
occ:1.00
 OD1 A:ASP98 2.0 19.1 1.0
O A:HOH718 2.0 18.3 1.0
O15 A:AHD401 2.1 17.4 1.0
O A:HOH623 2.1 18.4 1.0
O A:HOH533 2.2 17.9 1.0
O A:HOH618 2.2 18.2 1.0
CG A:ASP98 3.0 18.1 1.0
P14 A:AHD401 3.3 19.9 1.0
MG A:MG402 3.3 21.1 1.0
OD2 A:ASP98 3.4 17.5 1.0
O17 A:AHD401 3.5 19.7 1.0
O A:HOH524 4.0 20.2 1.0
O A:HOH552 4.0 22.3 1.0
OE1 A:GLN169 4.0 22.1 1.0
O A:HOH632 4.1 16.3 1.0
O16 A:AHD401 4.2 21.5 1.0
CB A:ASP98 4.3 21.3 1.0
C7 A:AHD401 4.5 22.6 1.0
NE2 A:GLN169 4.5 20.1 1.0
OD1 A:ASP102 4.5 18.7 1.0
O A:HOH556 4.6 15.5 1.0
O A:THR191 4.6 18.9 1.0
C8 A:AHD401 4.6 25.5 1.0
NH1 A:ARG188 4.7 18.2 1.0
CD A:GLN169 4.7 25.4 1.0
O A:HOH610 4.8 22.0 1.0
C2 A:AHD401 4.8 33.5 1.0
O11 A:AHD401 4.9 18.3 1.0

Magnesium binding site 4 out of 6 in 7ofl

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate


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 the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:23.5
occ:1.00
 O B:HOH530 2.0 20.4 1.0
OD2 B:ASP98 2.0 21.9 1.0
O12 B:AHD401 2.1 23.4 1.0
O16 B:AHD401 2.1 22.4 1.0
O B:HOH549 2.1 25.0 1.0
O B:HOH526 2.2 24.1 1.0
CG B:ASP98 2.9 22.3 1.0
OD1 B:ASP98 3.2 21.7 1.0
MG B:MG403 3.2 23.9 1.0
P14 B:AHD401 3.2 26.0 1.0
P9 B:AHD401 3.3 25.1 1.0
C8 B:AHD401 3.7 26.1 1.0
C7 B:AHD401 3.8 25.9 1.0
NZ B:LYS241 3.8 27.3 1.0
O17 B:AHD401 3.8 21.6 1.0
O10 B:AHD401 4.0 25.2 1.0
NH2 B:ARG322 4.0 21.6 1.0
O B:HOH592 4.1 23.5 1.0
OD2 B:ASP102 4.1 28.7 1.0
OE2 B:GLU242 4.2 23.1 1.0
O B:HOH673 4.3 25.5 1.0
CB B:ASP98 4.3 22.5 1.0
OD1 B:ASP102 4.4 23.0 1.0
O B:HOH615 4.4 28.1 1.0
O15 B:AHD401 4.4 22.0 1.0
O11 B:AHD401 4.4 25.6 1.0
OD1 B:ASP99 4.6 24.7 1.0
CG B:ASP102 4.7 26.3 1.0
O B:HOH527 4.7 23.6 1.0
MG B:MG404 4.7 23.1 1.0
O B:HOH611 4.8 21.2 1.0
CE B:LYS241 4.9 25.4 1.0
O B:HOH619 4.9 20.6 1.0

Magnesium binding site 5 out of 6 in 7ofl

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Magnesium binding site 5 out of 6 in the Crystal Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:23.9
occ:1.00
 OD1 B:ASP98 1.9 21.7 1.0
O B:HOH673 2.0 25.5 1.0
O B:HOH527 2.1 23.6 1.0
O B:HOH619 2.1 20.6 1.0
O16 B:AHD401 2.1 22.4 1.0
O B:HOH549 2.2 25.0 1.0
CG B:ASP98 3.0 22.3 1.0
MG B:MG402 3.2 23.5 1.0
P14 B:AHD401 3.4 26.0 1.0
OD2 B:ASP98 3.4 21.9 1.0
O15 B:AHD401 3.4 22.0 1.0
O B:HOH592 3.9 23.5 1.0
O B:HOH555 4.0 26.0 1.0
OE1 B:GLN169 4.1 21.9 1.0
O17 B:AHD401 4.2 21.6 1.0
O B:HOH611 4.2 21.2 1.0
CB B:ASP98 4.3 22.5 1.0
O B:HOH530 4.4 20.4 1.0
OD1 B:ASP102 4.5 23.0 1.0
O B:THR191 4.6 19.9 1.0
C7 B:AHD401 4.6 25.9 1.0
C8 B:AHD401 4.7 26.1 1.0
NE2 B:GLN169 4.7 21.7 1.0
NH1 B:ARG188 4.8 20.2 1.0
CD B:GLN169 4.8 24.4 1.0
O B:HOH526 4.8 24.1 1.0
O12 B:AHD401 4.8 23.4 1.0
CA B:ASP98 4.9 19.7 1.0
C2 B:AHD401 5.0 32.4 1.0

Magnesium binding site 6 out of 6 in 7ofl

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Magnesium binding site 6 out of 6 in the Crystal Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Sesquiterpene Synthase COPU9 From Coniophora Puteana in Complex with Alendronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:23.1
occ:1.00
 O10 B:AHD401 2.0 25.2 1.0
O17 B:AHD401 2.0 21.6 1.0
O B:HOH533 2.0 21.6 1.0
OE2 B:GLU242 2.1 23.1 1.0
OD1 B:ASN234 2.2 25.4 1.0
OG B:SER238 2.3 21.5 1.0
CD B:GLU242 3.1 25.8 1.0
P14 B:AHD401 3.2 26.0 1.0
CB B:SER238 3.2 23.6 1.0
CG B:ASN234 3.2 24.0 1.0
P9 B:AHD401 3.2 25.1 1.0
OE1 B:GLU242 3.4 24.6 1.0
NH2 B:ARG188 3.7 26.8 1.0
ND2 B:ASN234 3.7 20.2 1.0
C8 B:AHD401 3.8 26.1 1.0
O B:HOH611 3.8 21.2 1.0
O B:HOH530 3.9 20.4 1.0
O12 B:AHD401 3.9 23.4 1.0
O13 B:AHD401 3.9 30.9 1.0
O16 B:AHD401 4.1 22.4 1.0
O B:ASN234 4.1 27.5 1.0
O15 B:AHD401 4.3 22.0 1.0
OD1 B:ASP235 4.4 22.3 1.0
CG B:GLU242 4.4 22.0 1.0
O11 B:AHD401 4.5 25.6 1.0
C B:ASN234 4.5 24.0 1.0
CB B:ASN234 4.6 24.6 1.0
CA B:SER238 4.6 27.4 1.0
CZ B:ARG188 4.7 24.4 1.0
MG B:MG402 4.7 23.5 1.0
N B:ASP235 4.8 23.2 1.0
CA B:ASP235 4.9 26.0 1.0
C B:SER238 5.0 26.2 1.0
O B:SER238 5.0 26.8 1.0

Reference:

M.Ringel, N.Dimos, S.Himpich, M.Haack, C.Huber, W.Eisenreich, G.Schenk, B.Loll, T.Bruck. Biotechnological Potential and Initial Characterization of Two Novel Sesquiterpene Synthases From Basidiomycota Coniophora Puteana For Heterologous Production of Delta-Cadinol. Microb Cell Fact V. 21 64 2022.
ISSN: ESSN 1475-2859
PubMed: 35440053
DOI: 10.1186/S12934-022-01791-8
Page generated: Thu Apr 6 18:09:50 2023

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