Magnesium in PDB 8a74: PCIDS1_F315A in Complex with MG2+ and Gpp

Enzymatic activity of PCIDS1_F315A in Complex with MG2+ and Gpp

All present enzymatic activity of PCIDS1_F315A in Complex with MG2+ and Gpp:
2.5.1.1;

Protein crystallography data

The structure of PCIDS1_F315A in Complex with MG2+ and Gpp, PDB code: 8a74 was solved by F.Ecker, W.Boland, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.21, 78.25, 89.26, 90, 101.84, 90
R / Rfree (%) 20 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PCIDS1_F315A in Complex with MG2+ and Gpp (pdb code 8a74). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the PCIDS1_F315A in Complex with MG2+ and Gpp, PDB code: 8a74:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8a74

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Magnesium binding site 1 out of 8 in the PCIDS1_F315A in Complex with MG2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PCIDS1_F315A in Complex with MG2+ and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:33.8
occ:1.00
 O A:HOH672 1.9 32.6 1.0
O A:HOH669 2.0 28.8 1.0
OD2 A:ASP319 2.0 34.2 1.0
O A:HOH609 2.1 27.4 1.0
O A:HOH655 2.1 33.5 1.0
O A:HOH651 2.1 45.1 1.0
CG A:ASP319 3.2 32.3 1.0
OD1 A:ASP319 3.7 33.7 1.0
O A:HOH656 3.9 42.1 1.0
OD1 A:ASP337 4.0 33.4 1.0
OD1 A:ASP323 4.1 35.4 1.0
NE2 A:GLN316 4.1 29.1 1.0
OD2 A:ASP337 4.2 34.5 1.0
O A:HOH606 4.2 39.5 1.0
O A:HOH666 4.2 33.3 1.0
O A:ASP319 4.3 29.9 1.0
OD1 A:ASP320 4.4 27.3 1.0
CB A:ASP319 4.4 30.9 1.0
NZ A:LYS342 4.5 39.5 1.0
CG A:ASP337 4.6 34.0 1.0
C A:ASP319 4.6 28.6 1.0
O3B A:GPP505 4.8 40.3 1.0
CG A:ASP323 4.8 33.6 1.0
N A:ASP320 4.9 27.8 1.0
CB A:ASP323 4.9 32.8 1.0

Magnesium binding site 2 out of 8 in 8a74

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Magnesium binding site 2 out of 8 in the PCIDS1_F315A in Complex with MG2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PCIDS1_F315A in Complex with MG2+ and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:35.3
occ:1.00
 OD1 A:ASP183 2.0 37.2 1.0
O A:HOH632 2.1 36.3 1.0
O A:HOH648 2.1 33.2 1.0
OD1 A:ASP179 2.1 35.3 1.0
O1B A:GPP505 2.1 41.1 1.0
O1A A:GPP505 2.2 37.9 1.0
CG A:ASP179 3.1 34.2 1.0
CG A:ASP183 3.1 37.7 1.0
MG A:MG503 3.3 31.0 1.0
PB A:GPP505 3.4 39.9 1.0
OD2 A:ASP179 3.4 35.3 1.0
PA A:GPP505 3.4 38.0 1.0
O3A A:GPP505 3.6 38.9 1.0
CB A:ASP183 3.7 38.1 1.0
NH2 A:ARG188 3.9 36.6 1.0
O A:HOH639 3.9 51.1 1.0
O3B A:GPP505 4.0 40.3 1.0
O A:ASP179 4.1 36.0 1.0
O A:HOH680 4.2 38.7 1.0
OD2 A:ASP183 4.2 39.6 1.0
C1 A:GPP505 4.3 35.9 1.0
OG A:SER185 4.3 40.4 1.0
O1 A:GPP505 4.3 37.6 1.0
CB A:ASP179 4.4 32.0 1.0
C A:ASP179 4.5 34.0 1.0
O2B A:GPP505 4.6 38.2 1.0
O2A A:GPP505 4.6 38.5 1.0
OD1 A:ASP180 4.6 37.8 1.0
CE A:LYS342 4.8 39.1 1.0
O A:HOH602 4.8 35.5 1.0
O A:HOH653 4.9 37.1 1.0
O A:HOH630 4.9 35.4 1.0
NZ A:LYS342 4.9 39.5 1.0
N A:ASP180 5.0 33.2 1.0

Magnesium binding site 3 out of 8 in 8a74

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Magnesium binding site 3 out of 8 in the PCIDS1_F315A in Complex with MG2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PCIDS1_F315A in Complex with MG2+ and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:31.0
occ:1.00
 O A:HOH653 2.0 37.1 1.0
O A:HOH680 2.1 38.7 1.0
O A:HOH630 2.1 35.4 1.0
OD2 A:ASP179 2.2 35.3 1.0
O1A A:GPP505 2.3 37.9 1.0
OD1 A:ASP183 2.3 37.2 1.0
CG A:ASP183 3.0 37.7 1.0
OD2 A:ASP183 3.0 39.6 1.0
CG A:ASP179 3.1 34.2 1.0
MG A:MG502 3.3 35.3 1.0
PA A:GPP505 3.4 38.0 1.0
OD1 A:ASP179 3.4 35.3 1.0
O2A A:GPP505 3.9 38.5 1.0
O1 A:GPP505 4.0 37.6 1.0
NE2 A:GLN247 4.1 33.5 1.0
OE1 A:GLN247 4.1 34.4 1.0
O A:HOH674 4.2 45.5 1.0
OD2 A:ASP250 4.2 34.8 1.0
O A:HOH648 4.3 33.2 1.0
CD A:GLN247 4.5 32.8 1.0
CB A:ASP183 4.5 38.1 1.0
C1 A:GPP505 4.5 35.9 1.0
CB A:ASP179 4.5 32.0 1.0
O A:ASP179 4.5 36.0 1.0
C2 A:GPP505 4.6 36.6 1.0
O3A A:GPP505 4.8 38.9 1.0
O1B A:GPP505 4.8 41.1 1.0
O A:HOH632 4.9 36.3 1.0
CA A:ASP179 5.0 33.4 1.0

Magnesium binding site 4 out of 8 in 8a74

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Magnesium binding site 4 out of 8 in the PCIDS1_F315A in Complex with MG2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PCIDS1_F315A in Complex with MG2+ and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:39.1
occ:1.00
 O A:HOH700 1.9 36.2 1.0
O A:HOH662 2.0 40.4 1.0
O A:HOH666 2.2 33.3 1.0
O3B A:GPP505 2.2 40.3 1.0
O A:HOH689 2.2 39.3 1.0
O A:HOH639 2.3 51.1 1.0
PB A:GPP505 3.5 39.9 1.0
NZ A:LYS342 3.7 39.5 1.0
O A:HOH603 3.8 38.0 1.0
O1B A:GPP505 3.9 41.1 1.0
O A:HOH602 4.1 35.5 1.0
O A:HOH672 4.2 32.6 1.0
O A:HOH648 4.2 33.2 1.0
O2B A:GPP505 4.2 38.2 1.0
OE2 A:GLU340 4.2 48.0 1.0
O A:HOH606 4.3 39.5 1.0
OG1 A:THR336 4.5 41.0 1.0
OE1 A:GLU340 4.6 52.2 1.0
O3A A:GPP505 4.7 38.9 1.0
CE A:LYS342 4.8 39.1 1.0
CD A:GLU340 4.8 46.5 1.0

Magnesium binding site 5 out of 8 in 8a74

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Magnesium binding site 5 out of 8 in the PCIDS1_F315A in Complex with MG2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of PCIDS1_F315A in Complex with MG2+ and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:29.8
occ:1.00
 OD2 B:ASP319 1.9 31.4 1.0
O B:HOH665 2.0 31.6 1.0
O B:HOH613 2.0 27.3 1.0
O B:HOH630 2.1 32.4 1.0
O B:HOH627 2.1 33.0 1.0
O B:HOH652 2.1 35.6 1.0
CG B:ASP319 3.0 31.2 1.0
OD1 B:ASP319 3.6 34.4 1.0
O B:HOH635 3.8 42.8 1.0
OD1 B:ASP323 4.0 34.7 1.0
OD1 B:ASP337 4.1 28.4 1.0
NE2 B:GLN316 4.2 25.6 1.0
CB B:ASP319 4.3 29.9 1.0
OD2 B:ASP337 4.3 28.8 1.0
O B:ASP319 4.3 27.4 1.0
OD1 B:ASP320 4.4 27.6 1.0
C B:ASP319 4.5 28.6 1.0
O B:HOH643 4.5 45.9 1.0
CG B:ASP337 4.6 30.1 1.0
NZ B:LYS342 4.6 38.8 1.0
CG B:ASP323 4.7 31.4 1.0
CB B:ASP323 4.8 30.3 1.0
N B:ASP320 4.8 27.7 1.0
CA B:ASP319 4.9 29.2 1.0
O3B B:GPP505 5.0 38.8 0.7

Magnesium binding site 6 out of 8 in 8a74

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Magnesium binding site 6 out of 8 in the PCIDS1_F315A in Complex with MG2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of PCIDS1_F315A in Complex with MG2+ and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:46.5
occ:1.00
 O B:HOH669 1.9 49.1 1.0
O B:HOH620 2.0 43.5 1.0
O2B B:GPP505 2.0 39.0 0.7
OD1 B:ASP183 2.2 47.5 1.0
OD1 B:ASP179 2.2 43.0 1.0
O2A B:GPP505 2.4 37.0 0.7
PB B:GPP505 3.2 39.3 0.7
CG B:ASP183 3.3 47.9 1.0
CG B:ASP179 3.3 40.3 1.0
O3A B:GPP505 3.4 39.0 0.7
PA B:GPP505 3.4 38.3 0.7
MG B:MG503 3.6 43.6 1.0
CB B:ASP183 3.6 48.5 1.0
OD2 B:ASP179 3.7 43.7 1.0
O B:HOH679 3.8 40.3 1.0
O3B B:GPP505 3.9 38.8 0.7
NH2 B:ARG188 4.1 43.3 1.0
OG B:SER185 4.2 49.1 1.0
O1 B:GPP505 4.3 39.7 0.7
O B:ASP179 4.3 43.8 1.0
C1 B:GPP505 4.3 38.6 0.7
OD2 B:ASP183 4.4 49.5 1.0
O B:HOH688 4.4 50.0 1.0
O1B B:GPP505 4.4 39.8 0.7
CE B:LYS342 4.5 38.4 1.0
CB B:ASP179 4.6 39.4 1.0
OD1 B:ASP180 4.6 44.9 1.0
NZ B:LYS342 4.6 38.8 1.0
O1A B:GPP505 4.7 36.2 0.7
MG B:MG504 4.7 49.1 1.0
C B:ASP179 4.7 39.2 1.0
OE1 B:GLU340 4.9 46.5 1.0

Magnesium binding site 7 out of 8 in 8a74

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Magnesium binding site 7 out of 8 in the PCIDS1_F315A in Complex with MG2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of PCIDS1_F315A in Complex with MG2+ and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:43.6
occ:1.00
 O B:HOH629 2.0 47.4 1.0
O2A B:GPP505 2.2 37.0 0.7
O B:HOH688 2.3 50.0 1.0
O B:HOH647 2.3 42.6 1.0
OD2 B:ASP179 2.3 43.7 1.0
OD1 B:ASP183 2.5 47.5 1.0
CG B:ASP179 3.3 40.3 1.0
CG B:ASP183 3.3 47.9 1.0
PA B:GPP505 3.3 38.3 0.7
OD2 B:ASP183 3.4 49.5 1.0
OD1 B:ASP179 3.6 43.0 1.0
MG B:MG502 3.6 46.5 1.0
O1A B:GPP505 3.7 36.2 0.7
NE2 B:GLN247 3.9 38.3 1.0
C1 B:GPP505 3.9 38.6 0.7
OD2 B:ASP250 3.9 32.9 1.0
OE1 B:GLN247 4.0 34.6 1.0
O1 B:GPP505 4.1 39.7 0.7
CD B:GLN247 4.3 33.6 1.0
O B:HOH669 4.6 49.1 1.0
O3A B:GPP505 4.6 39.0 0.7
CB B:ASP179 4.7 39.4 1.0
CB B:ASP183 4.7 48.5 1.0
NZ B:LYS276 4.7 36.9 1.0
C2 B:GPP505 4.8 38.0 0.7
O2B B:GPP505 4.9 39.0 0.7
O B:ASP179 4.9 43.8 1.0

Magnesium binding site 8 out of 8 in 8a74

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Magnesium binding site 8 out of 8 in the PCIDS1_F315A in Complex with MG2+ and Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of PCIDS1_F315A in Complex with MG2+ and Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:49.1
occ:1.00
 O3B B:GPP505 1.9 38.8 0.7
O B:HOH702 2.0 52.2 1.0
O B:HOH679 2.1 40.3 1.0
O B:HOH675 2.2 39.3 1.0
O B:HOH635 2.4 42.8 1.0
PB B:GPP505 3.2 39.3 0.7
O2B B:GPP505 3.6 39.0 0.7
O B:HOH616 3.7 47.7 1.0
O B:HOH669 3.8 49.1 1.0
NZ B:LYS342 3.9 38.8 1.0
O B:HOH643 3.9 45.9 1.0
O B:HOH637 4.0 34.4 1.0
O1B B:GPP505 4.0 39.8 0.7
O B:HOH665 4.2 31.6 1.0
O3A B:GPP505 4.4 39.0 0.7
OE1 B:GLU340 4.4 46.5 1.0
MG B:MG502 4.7 46.5 1.0
OE2 B:GLU340 4.7 45.7 1.0
CE B:LYS342 4.8 38.4 1.0
O B:HOH620 5.0 43.5 1.0
OG1 B:THR336 5.0 38.4 1.0

Reference:

F.Ecker, W.Boland, M.Groll. Metal-Dependent Enzyme Symmetry Guides the Biosynthetic Flux of Terpene Precursors To Be Published 2023.
DOI: 10.1038/S41557-023-01235-9
Page generated: Thu Oct 3 17:56:32 2024

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