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Magnesium in PDB 8a6v: PCIDS1 in Complex with MG2+ and Ipp

Enzymatic activity of PCIDS1 in Complex with MG2+ and Ipp

All present enzymatic activity of PCIDS1 in Complex with MG2+ and Ipp:
2.5.1.1;

Protein crystallography data

The structure of PCIDS1 in Complex with MG2+ and Ipp, PDB code: 8a6v 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 (°) 57.4, 72.4, 84.9, 90, 101.53, 90
R / Rfree (%) 16.4 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PCIDS1 in Complex with MG2+ and Ipp (pdb code 8a6v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the PCIDS1 in Complex with MG2+ and Ipp, PDB code: 8a6v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8a6v

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Magnesium binding site 1 out of 7 in the PCIDS1 in Complex with MG2+ and Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PCIDS1 in Complex with MG2+ and Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:32.6
occ:1.00
 O A:HOH612 2.0 27.8 1.0
O1B A:IPE505 2.0 29.2 1.0
O A:HOH644 2.1 33.3 1.0
OD2 A:ASP319 2.1 26.8 1.0
O A:HOH608 2.2 29.3 1.0
O1A A:IPE505 2.3 39.4 1.0
CG A:ASP319 3.2 26.8 1.0
PB A:IPE505 3.3 28.6 1.0
PA A:IPE505 3.4 39.4 1.0
O3A A:IPE505 3.5 31.8 1.0
OD1 A:ASP319 3.6 24.4 1.0
OD1 A:ASP323 3.8 36.6 1.0
O A:HOH666 4.0 35.5 1.0
O3B A:IPE505 4.1 27.0 1.0
NE2 A:GLN316 4.2 25.6 1.0
O A:ASP319 4.2 27.3 1.0
OD2 A:ASP337 4.3 31.0 1.0
O2A A:IPE505 4.3 33.2 1.0
NZ A:LYS333 4.3 30.9 1.0
O A:HOH659 4.4 27.8 1.0
OD1 A:ASP337 4.4 31.9 1.0
CB A:ASP319 4.4 27.9 1.0
O2B A:IPE505 4.4 28.9 1.0
C A:ASP319 4.5 28.1 1.0
OD1 A:ASP320 4.5 28.8 1.0
O1 A:IPE505 4.6 40.1 1.0
CG A:ASP323 4.6 33.1 1.0
CB A:ASP323 4.7 31.3 1.0
CG A:ASP337 4.7 31.1 1.0
CE A:LYS333 4.8 32.1 1.0
C5 A:IPE504 4.8 29.4 1.0
N A:ASP320 4.9 27.3 1.0
MG A:MG502 5.0 25.3 1.0

Magnesium binding site 2 out of 7 in 8a6v

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Magnesium binding site 2 out of 7 in the PCIDS1 in Complex with MG2+ and Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PCIDS1 in Complex with MG2+ and Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:25.3
occ:1.00
 O A:HOH659 1.9 27.8 1.0
O3B A:IPE505 2.0 27.0 1.0
OD2 A:ASP179 2.0 26.8 1.0
O A:HOH610 2.1 26.0 1.0
OD2 A:ASP183 2.2 25.3 1.0
O2A A:IPE505 2.4 33.2 1.0
CG A:ASP179 3.1 26.7 1.0
PB A:IPE505 3.3 28.6 1.0
CG A:ASP183 3.3 26.1 1.0
MG A:MG503 3.3 27.6 1.0
O3A A:IPE505 3.4 31.8 1.0
PA A:IPE505 3.4 39.4 1.0
OD1 A:ASP179 3.5 26.9 1.0
CB A:ASP183 3.6 27.1 1.0
O A:HOH642 3.8 31.2 1.0
O1B A:IPE505 4.1 29.2 1.0
O A:HOH612 4.2 27.8 1.0
NH2 A:ARG188 4.2 27.9 1.0
O A:HOH660 4.3 35.4 1.0
O1A A:IPE505 4.3 39.4 1.0
CB A:ASP179 4.4 25.7 1.0
O A:HOH649 4.4 33.1 1.0
OD1 A:ASP183 4.4 25.4 1.0
O2B A:IPE505 4.4 28.9 1.0
O A:ASP179 4.4 26.6 1.0
OG A:SER185 4.4 32.7 1.0
OD1 A:ASP180 4.5 27.4 1.0
O1 A:IPE505 4.6 40.1 1.0
C A:ASP179 4.7 26.3 1.0
C1 A:IPE505 4.8 45.1 1.0
O A:HOH609 4.9 30.2 1.0
O A:HOH616 4.9 25.8 1.0
MG A:MG501 5.0 32.6 1.0

Magnesium binding site 3 out of 7 in 8a6v

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Magnesium binding site 3 out of 7 in the PCIDS1 in Complex with MG2+ and Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PCIDS1 in Complex with MG2+ and Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:27.6
occ:1.00
 O A:HOH609 1.9 30.2 1.0
OD1 A:ASP179 2.0 26.9 1.0
O2A A:IPE505 2.1 33.2 1.0
O A:HOH616 2.1 25.8 1.0
O A:HOH660 2.1 35.4 1.0
OD2 A:ASP183 2.3 25.3 1.0
CG A:ASP179 3.0 26.7 1.0
CG A:ASP183 3.2 26.1 1.0
OD2 A:ASP179 3.3 26.8 1.0
MG A:MG502 3.3 25.3 1.0
OD1 A:ASP183 3.4 25.4 1.0
PA A:IPE505 3.4 39.4 1.0
O1 A:IPE505 3.7 40.1 1.0
C1 A:IPE505 3.9 45.1 1.0
NE2 A:GLN247 3.9 36.4 1.0
OE1 A:GLN247 4.0 35.9 1.0
OD2 A:ASP250 4.1 38.9 1.0
O A:HOH659 4.2 27.8 1.0
CD A:GLN247 4.3 34.4 1.0
O1A A:IPE505 4.3 39.4 1.0
CB A:ASP179 4.4 25.7 1.0
O A:HOH622 4.4 41.5 1.0
O A:HOH666 4.4 35.5 1.0
O3A A:IPE505 4.4 31.8 1.0
NZ A:LYS342 4.5 40.6 1.0
CB A:ASP183 4.6 27.1 1.0
CG A:ASP250 4.6 34.6 1.0
CE A:LYS342 4.7 38.3 1.0
OD1 A:ASP250 4.7 38.5 1.0
NZ A:LYS276 4.8 40.8 1.0
O A:ASP179 4.8 26.6 1.0
O3B A:IPE505 4.8 27.0 1.0
C2 A:IPE505 4.9 46.6 1.0
CA A:ASP179 5.0 25.6 1.0
O A:HOH649 5.0 33.1 1.0
O A:HOH610 5.0 26.0 1.0

Magnesium binding site 4 out of 7 in 8a6v

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Magnesium binding site 4 out of 7 in the PCIDS1 in Complex with MG2+ and Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PCIDS1 in Complex with MG2+ and Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:32.6
occ:1.00
 O B:HOH653 2.0 32.9 1.0
O B:HOH608 2.0 26.0 1.0
OD2 B:ASP319 2.1 32.5 1.0
O B:HOH648 2.1 33.1 1.0
O B:HOH660 2.1 33.8 1.0
O B:HOH639 2.2 35.5 1.0
CG B:ASP319 3.2 32.1 1.0
OD1 B:ASP319 3.7 34.6 1.0
OD1 B:ASP323 4.0 36.8 1.0
O B:HOH663 4.0 35.6 1.0
O B:HOH654 4.0 39.6 1.0
OD2 B:ASP337 4.0 31.9 1.0
OD1 B:ASP337 4.2 33.1 1.0
NE2 B:GLN316 4.3 28.8 1.0
O B:ASP319 4.3 29.6 1.0
CB B:ASP319 4.4 30.1 1.0
OD1 B:ASP320 4.4 27.0 1.0
O B:HOH638 4.5 36.3 1.0
C B:ASP319 4.5 28.9 1.0
CG B:ASP337 4.5 31.8 1.0
NZ B:LYS342 4.6 45.7 1.0
CG B:ASP323 4.7 34.6 1.0
O3B B:IPE505 4.8 35.9 1.0
CB B:ASP323 4.8 33.2 1.0
N B:ASP320 4.8 27.2 1.0
O B:HOH633 4.9 43.7 1.0

Magnesium binding site 5 out of 7 in 8a6v

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Magnesium binding site 5 out of 7 in the PCIDS1 in Complex with MG2+ and Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of PCIDS1 in Complex with MG2+ and Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:53.3
occ:1.00
 O3B B:IPE505 2.0 35.9 1.0
O B:HOH673 2.1 37.8 1.0
O B:HOH679 2.1 41.0 1.0
O B:HOH632 2.2 36.7 1.0
O B:HOH628 2.3 38.2 1.0
O B:HOH663 2.4 35.6 1.0
PB B:IPE505 3.2 35.6 1.0
O2B B:IPE505 3.6 33.0 1.0
O B:HOH616 3.8 37.7 1.0
O B:HOH638 3.8 36.3 1.0
O B:HOH653 4.0 32.9 1.0
O B:HOH650 4.0 30.9 1.0
O1B B:IPE505 4.0 36.0 1.0
O B:HOH629 4.0 33.3 1.0
OE1 B:GLU340 4.2 42.6 1.0
NZ B:LYS342 4.3 45.7 1.0
OE2 B:GLU340 4.4 42.4 1.0
O3A B:IPE505 4.4 35.0 1.0
OG1 B:THR336 4.4 40.9 1.0
O B:HOH675 4.5 36.5 1.0
CD B:GLU340 4.7 40.3 1.0
MG B:MG503 4.9 36.0 1.0
CE B:LYS342 5.0 43.1 1.0

Magnesium binding site 6 out of 7 in 8a6v

Go back to Magnesium Binding Sites List in 8a6v
Magnesium binding site 6 out of 7 in the PCIDS1 in Complex with MG2+ and Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of PCIDS1 in Complex with MG2+ and Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:36.0
occ:1.00
 O B:HOH650 2.0 30.9 1.0
O2B B:IPE505 2.0 33.0 1.0
OD2 B:ASP179 2.0 32.1 1.0
O B:HOH610 2.2 32.7 1.0
OD2 B:ASP183 2.2 32.2 1.0
O1A B:IPE505 2.3 31.7 1.0
CG B:ASP179 3.1 30.2 1.0
PB B:IPE505 3.2 35.6 1.0
CG B:ASP183 3.3 32.3 1.0
MG B:MG504 3.3 30.3 1.0
PA B:IPE505 3.4 34.7 1.0
O3A B:IPE505 3.4 35.0 1.0
OD1 B:ASP179 3.5 30.8 1.0
CB B:ASP183 3.7 32.8 1.0
NH2 B:ARG188 3.8 34.6 1.0
O B:HOH632 3.9 36.7 1.0
O3B B:IPE505 4.0 35.9 1.0
O1 B:IPE505 4.0 37.5 1.0
O B:HOH652 4.2 33.6 1.0
OG B:SER185 4.3 34.4 1.0
O B:ASP179 4.3 27.9 1.0
CB B:ASP179 4.4 29.2 1.0
O1B B:IPE505 4.4 36.0 1.0
OD1 B:ASP183 4.4 33.7 1.0
OD1 B:ASP180 4.5 31.8 1.0
CE B:LYS342 4.5 43.1 1.0
C B:ASP179 4.5 28.8 1.0
O2A B:IPE505 4.7 35.3 1.0
O B:HOH629 4.8 33.3 1.0
C1 B:IPE505 4.8 39.4 1.0
MG B:MG502 4.9 53.3 1.0
O B:HOH612 5.0 31.3 1.0
N B:ASP180 5.0 29.4 1.0
O B:HOH626 5.0 29.8 1.0

Magnesium binding site 7 out of 7 in 8a6v

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Magnesium binding site 7 out of 7 in the PCIDS1 in Complex with MG2+ and Ipp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of PCIDS1 in Complex with MG2+ and Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:30.3
occ:1.00
 O B:HOH612 2.0 31.3 1.0
O1A B:IPE505 2.0 31.7 1.0
O B:HOH652 2.1 33.6 1.0
OD1 B:ASP179 2.1 30.8 1.0
O B:HOH626 2.1 29.8 1.0
OD2 B:ASP183 2.3 32.2 1.0
CG B:ASP179 3.0 30.2 1.0
CG B:ASP183 3.1 32.3 1.0
PA B:IPE505 3.2 34.7 1.0
OD2 B:ASP179 3.3 32.1 1.0
OD1 B:ASP183 3.3 33.7 1.0
MG B:MG503 3.3 36.0 1.0
O B:HOH602 3.8 45.0 1.0
O2A B:IPE505 3.8 35.3 1.0
C1 B:IPE505 3.9 39.4 1.0
OD2 B:ASP250 4.0 37.0 1.0
O1 B:IPE505 4.0 37.5 1.0
NE2 B:GLN247 4.0 33.0 1.0
OE1 B:GLN247 4.1 32.4 1.0
O B:HOH657 4.2 37.5 1.0
O B:HOH650 4.3 30.9 1.0
CB B:ASP179 4.4 29.2 1.0
CD B:GLN247 4.5 30.6 1.0
O3A B:IPE505 4.5 35.0 1.0
CB B:ASP183 4.5 32.8 1.0
O B:ASP179 4.7 27.9 1.0
O2B B:IPE505 4.7 33.0 1.0
NZ B:LYS276 4.9 34.4 1.0
CA B:ASP179 4.9 29.2 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 17:20:28 2024

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