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Magnesium in PDB 6oh6: Crystal Structure of (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi

Enzymatic activity of Crystal Structure of (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi

All present enzymatic activity of Crystal Structure of (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi:
4.2.3.193;

Protein crystallography data

The structure of Crystal Structure of (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi, PDB code: 6oh6 was solved by S.Centeno-Leija, H.Serrano-Posada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.35 / 2.07
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.050, 107.050, 88.821, 90.00, 90.00, 120.00
R / Rfree (%) 23.3 / 25.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi (pdb code 6oh6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi, PDB code: 6oh6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6oh6

Go back to Magnesium Binding Sites List in 6oh6
Magnesium binding site 1 out of 3 in the Crystal Structure of (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi


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 (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:54.2
occ:0.55
 OE1 A:GLU238 2.0 72.4 1.0
O21 A:PPV401 2.0 51.6 0.6
OD1 A:ASN230 2.1 61.4 1.0
OG A:SER234 2.1 52.2 1.0
O22 A:PPV401 2.1 53.8 0.6
CB A:SER234 2.7 45.9 1.0
CD A:GLU238 3.3 75.5 1.0
CG A:ASN230 3.3 61.2 1.0
O A:ASN230 3.3 38.2 1.0
P2 A:PPV401 3.4 59.1 0.6
P1 A:PPV401 3.4 59.2 0.6
OPP A:PPV401 3.6 54.9 0.6
OE2 A:GLU238 3.8 56.6 1.0
O A:HOH561 3.8 56.0 1.0
C A:ASN230 3.8 42.8 1.0
NH2 A:ARG184 3.8 36.3 1.0
O32 A:PPV401 4.0 56.5 0.6
CA A:SER234 4.1 48.1 1.0
NH2 A:ARG237 4.2 59.5 0.4
CB A:ASN230 4.2 40.1 1.0
O31 A:PPV401 4.3 53.3 0.6
ND2 A:ASN230 4.3 63.0 1.0
O A:HOH537 4.3 64.5 1.0
N A:ASP231 4.3 34.5 1.0
O11 A:PPV401 4.4 52.8 0.6
CA A:ASP231 4.5 33.2 1.0
O12 A:PPV401 4.5 57.1 0.6
CG A:GLU238 4.5 62.6 1.0
OD1 A:ASP231 4.6 37.1 1.0
CA A:ASN230 4.6 38.0 1.0
N A:SER234 4.7 43.1 1.0
CE1 A:TYR317 4.8 63.1 1.0
C A:SER234 4.9 50.1 1.0
MG A:MG403 5.0 56.6 0.6

Magnesium binding site 2 out of 3 in 6oh6

Go back to Magnesium Binding Sites List in 6oh6
Magnesium binding site 2 out of 3 in the Crystal Structure of (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi


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 (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:56.6
occ:0.55
 O A:HOH537 1.9 64.5 1.0
OE1 A:GLU95 2.0 68.5 1.0
O32 A:PPV401 2.0 56.5 0.6
O11 A:PPV401 2.0 52.8 0.6
O A:HOH540 2.1 60.2 1.0
P1 A:PPV401 3.1 59.2 0.6
CD A:GLU95 3.2 75.8 1.0
P2 A:PPV401 3.2 59.1 0.6
OPP A:PPV401 3.2 54.9 0.6
O21 A:PPV401 3.6 51.6 0.6
MG A:MG404 3.7 61.1 0.6
OD2 A:ASP90 3.7 52.9 1.0
O A:HOH569 3.8 59.4 1.0
OE2 A:GLU95 3.8 76.1 1.0
OD1 A:ASP91 3.9 53.7 1.0
NH2 A:ARG316 3.9 62.7 1.0
O22 A:PPV401 4.0 53.8 0.6
NH2 A:ARG237 4.2 59.5 0.4
NH1 A:ARG237 4.3 62.2 0.4
O12 A:PPV401 4.3 57.1 0.6
CG A:GLU95 4.4 71.8 1.0
O31 A:PPV401 4.4 53.3 0.6
O A:HOH561 4.5 56.0 1.0
NH2 A:ARG237 4.6 59.9 0.6
O A:HOH532 4.6 65.0 1.0
CG A:ASP90 4.7 43.1 1.0
OE1 A:GLU238 4.7 72.4 1.0
CZ A:ARG237 4.7 64.0 0.4
O A:HOH526 4.8 54.0 1.0
O A:HOH517 4.8 50.0 1.0
CG A:ASP91 5.0 60.8 1.0
MG A:MG402 5.0 54.2 0.6

Magnesium binding site 3 out of 3 in 6oh6

Go back to Magnesium Binding Sites List in 6oh6
Magnesium binding site 3 out of 3 in the Crystal Structure of (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi


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 (E)-Biformene Synthase Lrdc From Streptomyces Sp. Strain K155 in Complex with Mg and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:61.1
occ:0.55
 O A:HOH526 1.9 54.0 1.0
OD2 A:ASP90 2.0 52.9 1.0
OE2 A:GLU95 2.1 76.1 1.0
O A:HOH517 2.1 50.0 1.0
O11 A:PPV401 2.3 52.8 0.6
O A:HOH501 2.4 55.0 1.0
CD A:GLU95 2.9 75.8 1.0
OE1 A:GLU95 3.0 68.5 1.0
CG A:ASP90 3.1 43.1 1.0
P1 A:PPV401 3.3 59.2 0.6
O31 A:PPV401 3.4 53.3 0.6
OD1 A:ASP90 3.4 49.6 1.0
MG A:MG403 3.7 56.6 0.6
O A:HOH561 3.7 56.0 1.0
OE1 A:GLU165 3.9 53.1 1.0
OE2 A:GLU165 4.0 68.2 1.0
O21 A:PPV401 4.1 51.6 0.6
O A:HOH569 4.2 59.4 1.0
CG A:GLU95 4.3 71.8 1.0
O A:THR187 4.4 39.1 1.0
CD A:GLU165 4.4 50.5 1.0
CB A:ASP90 4.5 48.4 1.0
O A:HOH537 4.5 64.5 1.0
OPP A:PPV401 4.5 54.9 0.6
NH1 A:ARG184 4.6 37.4 1.0
CD2 A:LEU162 4.7 31.3 1.0
CB A:GLU95 4.7 65.5 1.0
CB A:THR187 4.9 38.8 1.0

Reference:

S.Centeno-Leija, S.Tapia-Cabrera, S.Guzman-Trampe, B.Esquivel, N.Esturau-Escofet, V.H.Tierrafria, R.Rodriguez-Sanoja, A.Zarate-Romero, V.Stojanoff, E.Rudino-Pinera, S.Sanchez, H.Serrano-Posada. The Structure of (E)-Biformene Synthase Provides Insights Into the Biosynthesis of Bacterial Bicyclic Labdane-Related Diterpenoids. J.Struct.Biol. V. 207 29 2019.
ISSN: ESSN 1095-8657
PubMed: 30981884
DOI: 10.1016/J.JSB.2019.04.010
Page generated: Tue Oct 1 13:23:15 2024

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