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Magnesium in PDB 5dz2: Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid

Enzymatic activity of Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid

All present enzymatic activity of Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid:
4.1.99.16; 4.2.3.22; 4.2.3.75;

Protein crystallography data

The structure of Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid, PDB code: 5dz2 was solved by G.G.Harris, P.M.Lombardi, T.A.Pemberton, T.Matsui, T.M.Weiss, K.E.Cole, M.Koksal, F.V.Murphy, L.S.Vedula, W.K.W.Chou, D.E.Cane, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.17 / 2.11
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.213, 67.213, 345.388, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid (pdb code 5dz2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid, PDB code: 5dz2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5dz2

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Magnesium binding site 1 out of 6 in the Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:37.0
occ:1.00
 O A:HOH515 2.0 37.9 1.0
O A:HOH529 2.1 35.2 1.0
O A:HOH543 2.1 37.5 1.0
OD1 A:ASP86 2.1 36.0 1.0
O9 A:212404 2.2 33.9 1.0
O A:HOH522 2.2 33.8 1.0
MG A:MG403 3.0 40.6 1.0
CG A:ASP86 3.1 36.9 1.0
OD2 A:ASP86 3.3 35.4 1.0
P8 A:212404 3.4 38.5 1.0
O12 A:212404 3.6 34.4 1.0
O A:HOH501 3.6 42.5 1.0
OE1 A:GLU165 3.9 48.4 1.0
OE2 A:GLU165 4.1 51.6 1.0
O A:HOH528 4.1 36.8 1.0
NZ A:LYS94 4.1 44.6 1.0
O10 A:212404 4.3 36.8 1.0
CD A:GLU165 4.4 51.4 1.0
O A:HOH519 4.5 36.2 1.0
CB A:ASP86 4.5 38.5 1.0
O A:HOH541 4.5 40.1 1.0
C19 A:212404 4.6 37.9 1.0
C16 A:212404 4.7 34.7 1.0
C7 A:212404 4.7 38.3 1.0
OE1 A:GLU243 4.7 51.9 1.0
O A:HOH553 4.8 42.2 1.0
O3 A:212404 4.9 35.2 1.0

Magnesium binding site 2 out of 6 in 5dz2

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Magnesium binding site 2 out of 6 in the Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:37.5
occ:1.00
 O10 A:212404 1.9 36.8 1.0
OD1 A:ASN229 2.0 37.3 1.0
O2 A:212404 2.1 40.8 1.0
O A:HOH508 2.1 34.7 1.0
OE2 A:GLU237 2.2 40.9 1.0
OG A:SER233 2.5 31.8 1.0
CG A:ASN229 3.1 35.8 1.0
P1 A:212404 3.2 40.4 1.0
P8 A:212404 3.2 38.5 1.0
CD A:GLU237 3.2 45.6 1.0
ND2 A:ASN229 3.5 33.5 1.0
C7 A:212404 3.5 38.3 1.0
CB A:SER233 3.5 33.8 1.0
OE1 A:GLU237 3.6 42.3 1.0
O14 A:212404 3.6 32.9 1.0
O A:HOH528 3.7 36.8 1.0
O3 A:212404 3.9 35.2 1.0
O A:HOH534 4.0 49.1 1.0
O9 A:212404 4.1 33.9 1.0
O12 A:212404 4.2 34.4 1.0
O A:ASN229 4.2 32.2 1.0
O A:HOH519 4.3 36.2 1.0
O5 A:212404 4.4 36.0 1.0
CB A:ASN229 4.4 40.2 1.0
OD1 A:ASP230 4.4 38.0 1.0
C A:ASN229 4.5 36.5 1.0
CG A:GLU237 4.5 41.0 1.0
MG A:MG403 4.7 40.6 1.0
N A:ASP230 4.9 30.6 1.0
CA A:SER233 4.9 35.2 1.0
C16 A:212404 5.0 34.7 1.0
CA A:ASP230 5.0 33.8 1.0

Magnesium binding site 3 out of 6 in 5dz2

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Magnesium binding site 3 out of 6 in the Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:40.6
occ:1.00
 O9 A:212404 1.9 33.9 1.0
O3 A:212404 2.1 35.2 1.0
O A:HOH543 2.1 37.5 1.0
OD2 A:ASP86 2.2 35.4 1.0
O A:HOH519 2.2 36.2 1.0
O A:HOH553 2.3 42.2 1.0
MG A:MG401 3.0 37.0 1.0
CG A:ASP86 3.1 36.9 1.0
P8 A:212404 3.1 38.5 1.0
P1 A:212404 3.3 40.4 1.0
OD1 A:ASP86 3.4 36.0 1.0
C7 A:212404 3.5 38.3 1.0
C16 A:212404 3.6 34.7 1.0
O10 A:212404 3.7 36.8 1.0
O2 A:212404 4.1 40.8 1.0
O A:HOH522 4.1 33.8 1.0
NH2 A:ARG325 4.1 30.9 1.0
NH1 A:ARG236 4.2 33.7 1.0
O A:HOH541 4.2 40.1 1.0
OE2 A:GLU237 4.3 40.9 1.0
O12 A:212404 4.3 34.4 1.0
OE2 A:GLU241 4.4 42.0 1.0
O5 A:212404 4.4 36.0 1.0
O A:HOH529 4.5 35.2 1.0
CB A:ASP86 4.5 38.5 1.0
O A:HOH528 4.5 36.8 1.0
C19 A:212404 4.5 37.9 1.0
OE1 A:GLU241 4.7 46.6 1.0
MG A:MG402 4.7 37.5 1.0
O A:HOH515 4.8 37.9 1.0
O14 A:212404 4.9 32.9 1.0
OD1 A:ASP87 4.9 40.6 1.0
CD A:GLU241 5.0 45.6 1.0

Magnesium binding site 4 out of 6 in 5dz2

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Magnesium binding site 4 out of 6 in the Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:40.6
occ:1.00
 O B:HOH517 2.0 40.7 1.0
O10 B:212404 2.0 35.8 1.0
OD1 B:ASP86 2.0 36.8 1.0
O B:HOH533 2.1 35.1 1.0
O B:HOH513 2.1 40.7 1.0
O B:HOH541 2.2 38.7 1.0
MG B:MG403 2.9 35.5 1.0
CG B:ASP86 2.9 40.2 1.0
OD2 B:ASP86 3.1 35.4 1.0
P8 B:212404 3.2 35.8 1.0
O12 B:212404 3.4 36.9 1.0
O B:HOH522 3.8 46.2 1.0
O B:HOH536 4.1 37.2 1.0
O B:HOH521 4.1 36.2 1.0
O9 B:212404 4.2 36.7 1.0
OE2 B:GLU165 4.2 52.4 1.0
OE1 B:GLU165 4.3 52.1 1.0
CB B:ASP86 4.3 33.9 1.0
C16 B:212404 4.4 35.8 1.0
O B:HOH510 4.4 46.4 1.0
C19 B:212404 4.4 33.4 1.0
C7 B:212404 4.5 37.1 1.0
NZ B:LYS94 4.6 46.0 1.0
O B:HOH518 4.6 33.5 1.0
O3 B:212404 4.7 34.5 1.0
CD B:GLU165 4.7 50.7 1.0
OE1 B:GLU161 4.9 57.5 1.0

Magnesium binding site 5 out of 6 in 5dz2

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Magnesium binding site 5 out of 6 in the Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:36.3
occ:1.00
 OE2 B:GLU237 2.0 38.0 1.0
O9 B:212404 2.0 36.7 1.0
O5 B:212404 2.1 35.6 1.0
OD1 B:ASN229 2.2 32.0 1.0
O B:HOH502 2.2 29.3 1.0
OG B:SER233 2.3 36.3 1.0
CD B:GLU237 3.0 41.0 1.0
CG B:ASN229 3.2 39.2 1.0
CB B:SER233 3.2 34.2 1.0
P1 B:212404 3.3 36.1 1.0
P8 B:212404 3.3 35.8 1.0
OE1 B:GLU237 3.4 40.0 1.0
ND2 B:ASN229 3.6 33.3 1.0
O B:HOH536 3.7 37.2 1.0
C7 B:212404 3.7 37.1 1.0
O3 B:212404 3.9 34.5 1.0
O14 B:212404 3.9 30.5 1.0
O B:HOH521 4.1 36.2 1.0
O10 B:212404 4.2 35.8 1.0
O B:ASN229 4.2 31.8 1.0
NH2 B:ARG184 4.3 50.8 1.0
CG B:GLU237 4.3 43.8 1.0
O12 B:212404 4.4 36.9 1.0
OD1 B:ASP230 4.4 35.6 1.0
O2 B:212404 4.5 37.9 1.0
CB B:ASN229 4.5 33.0 1.0
C B:ASN229 4.5 33.4 1.0
CA B:SER233 4.6 31.1 1.0
MG B:MG403 4.7 35.5 1.0
N B:ASP230 4.9 30.2 1.0
NH2 B:ARG236 4.9 40.2 1.0
CA B:ASP230 5.0 32.6 1.0
O B:SER233 5.0 33.0 1.0
C B:SER233 5.0 34.6 1.0

Magnesium binding site 6 out of 6 in 5dz2

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Magnesium binding site 6 out of 6 in the Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Geosmin Synthase From Streptomyces Coelicolor N-Terminal Domain Complexed with Three MG2+ Ions and Alendronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:35.5
occ:1.00
 O10 B:212404 2.0 35.8 1.0
OD2 B:ASP86 2.1 35.4 1.0
O3 B:212404 2.1 34.5 1.0
O B:HOH521 2.1 36.2 1.0
O B:HOH533 2.2 35.1 1.0
O B:HOH518 2.2 33.5 1.0
MG B:MG401 2.9 40.6 1.0
CG B:ASP86 3.1 40.2 1.0
P8 B:212404 3.1 35.8 1.0
P1 B:212404 3.3 36.1 1.0
OD1 B:ASP86 3.4 36.8 1.0
C7 B:212404 3.5 37.1 1.0
C16 B:212404 3.6 35.8 1.0
O9 B:212404 3.7 36.7 1.0
O B:HOH541 4.0 38.7 1.0
O5 B:212404 4.0 35.6 1.0
NH1 B:ARG236 4.1 33.5 1.0
O B:HOH510 4.1 46.4 1.0
NH2 B:ARG325 4.2 36.2 1.0
OE1 B:GLU241 4.3 40.3 1.0
OE2 B:GLU237 4.3 38.0 1.0
OE2 B:GLU241 4.4 35.9 1.0
O12 B:212404 4.4 36.9 1.0
O2 B:212404 4.4 37.9 1.0
CB B:ASP86 4.4 33.9 1.0
O B:HOH517 4.5 40.7 1.0
O B:HOH536 4.5 37.2 1.0
C19 B:212404 4.7 33.4 1.0
O B:HOH513 4.7 40.7 1.0
MG B:MG402 4.7 36.3 1.0
CD B:GLU241 4.8 42.3 1.0
O14 B:212404 4.9 30.5 1.0
OD1 B:ASP87 4.9 36.5 1.0

Reference:

G.G.Harris, P.M.Lombardi, T.A.Pemberton, T.Matsui, T.M.Weiss, K.E.Cole, M.Koksal, F.V.Murphy, L.S.Vedula, W.K.Chou, D.E.Cane, D.W.Christianson. Structural Studies of Geosmin Synthase, A Bifunctional Sesquiterpene Synthase with Alpha Alpha Domain Architecture That Catalyzes A Unique Cyclization-Fragmentation Reaction Sequence. Biochemistry V. 54 7142 2015.
ISSN: ISSN 0006-2960
PubMed: 26598179
DOI: 10.1021/ACS.BIOCHEM.5B01143
Page generated: Sun Sep 29 03:27:07 2024

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