Atomistry » Magnesium » PDB 8a63-8ac1 » 8a7k
Atomistry »
  Magnesium »
    PDB 8a63-8ac1 »
      8a7k »

Magnesium in PDB 8a7k: PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol

Enzymatic activity of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol

All present enzymatic activity of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol:
2.5.1.1;

Protein crystallography data

The structure of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol, PDB code: 8a7k 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 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.08, 70.48, 94.9, 90, 91.29, 90
R / Rfree (%) 14.2 / 16.8

Other elements in 8a7k:

The structure of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol (pdb code 8a7k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol, PDB code: 8a7k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8a7k

Go back to Magnesium Binding Sites List in 8a7k
Magnesium binding site 1 out of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol


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+/MN2+, Ipp, and Zol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:17.2
occ:0.50
MN A:MN501 0.1 13.6 0.5
O11 A:ZOL510 1.9 12.4 1.0
O A:HOH656 2.0 11.4 1.0
O A:HOH734 2.1 11.6 1.0
OD2 A:ASP179 2.1 11.0 1.0
OD2 A:ASP183 2.2 11.4 1.0
O16 A:ZOL510 2.3 11.9 1.0
CG A:ASP179 3.2 11.8 1.0
P9 A:ZOL510 3.2 11.4 1.0
P14 A:ZOL510 3.4 11.6 1.0
CG A:ASP183 3.4 12.3 1.0
MN A:MN502 3.5 13.3 0.5
MG A:MG505 3.6 17.4 0.5
OD1 A:ASP179 3.6 11.5 1.0
O A:HOH716 3.6 13.8 1.0
C8 A:ZOL510 3.7 11.0 1.0
CB A:ASP183 3.8 12.0 1.0
O10 A:ZOL510 3.9 11.2 1.0
C7 A:ZOL510 4.0 11.5 1.0
O15 A:ZOL510 4.0 11.5 1.0
NH2 A:ARG188 4.0 13.2 1.0
O A:HOH636 4.2 13.2 1.0
O12 A:ZOL510 4.3 11.6 1.0
OD1 A:ASP180 4.4 13.3 1.0
OG A:SER185 4.4 13.8 1.0
O A:ASP179 4.4 11.8 1.0
CB A:ASP179 4.5 11.2 1.0
O A:HOH664 4.5 15.8 1.0
O A:HOH687 4.5 12.2 1.0
OD1 A:ASP183 4.5 12.3 1.0
O A:HOH674 4.6 13.7 1.0
C A:ASP179 4.7 10.7 1.0
O17 A:ZOL510 4.7 11.9 1.0
MG A:MG506 4.8 17.2 0.5
MN A:MN503 4.8 14.0 0.5
O A:HOH625 5.0 12.5 1.0

Magnesium binding site 2 out of 6 in 8a7k

Go back to Magnesium Binding Sites List in 8a7k
Magnesium binding site 2 out of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol


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+/MN2+, Ipp, and Zol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:17.4
occ:0.50
MN A:MN502 0.1 13.3 0.5
O A:HOH625 1.8 12.5 1.0
O A:HOH653 2.1 11.9 1.0
O A:HOH687 2.1 12.2 1.0
OD1 A:ASP179 2.1 11.5 1.0
O16 A:ZOL510 2.2 11.9 1.0
OD2 A:ASP183 2.3 11.4 1.0
CG A:ASP183 3.1 12.3 1.0
OD1 A:ASP183 3.2 12.3 1.0
CG A:ASP179 3.2 11.8 1.0
OD2 A:ASP179 3.4 11.0 1.0
MN A:MN501 3.4 13.6 0.5
P14 A:ZOL510 3.5 11.6 1.0
MG A:MG504 3.6 17.2 0.5
O17 A:ZOL510 3.6 11.9 1.0
OD1 A:ASP250 3.8 14.0 1.0
NE2 A:GLN247 3.9 15.8 1.0
O A:HOH640 4.1 13.8 1.0
OE1 A:GLN247 4.2 14.6 1.0
NZ A:LYS342 4.3 16.0 1.0
CD A:GLN247 4.3 15.2 1.0
O A:HOH734 4.4 11.6 1.0
O A:HOH676 4.4 13.8 1.0
CB A:ASP179 4.4 11.2 1.0
CB A:ASP183 4.5 12.0 1.0
C19 A:ZOL510 4.5 12.3 1.0
CG A:ASP250 4.5 13.0 1.0
O15 A:ZOL510 4.6 11.5 1.0
C7 A:ZOL510 4.7 11.5 1.0
O A:ASP179 4.7 11.8 1.0
C8 A:ZOL510 4.8 11.0 1.0
OD2 A:ASP250 4.8 14.9 1.0
N15 A:ZOL510 4.8 11.6 1.0
CA A:ASP179 4.9 11.3 1.0
O A:HOH674 4.9 13.7 1.0
O11 A:ZOL510 5.0 12.4 1.0

Magnesium binding site 3 out of 6 in 8a7k

Go back to Magnesium Binding Sites List in 8a7k
Magnesium binding site 3 out of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol


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+/MN2+, Ipp, and Zol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:17.2
occ:0.50
MN A:MN503 0.0 14.0 0.5
O10 A:ZOL510 2.0 11.2 1.0
O15 A:ZOL510 2.0 11.5 1.0
O A:HOH755 2.1 12.6 1.0
O A:HOH648 2.1 12.1 1.0
OD2 A:ASP319 2.1 12.4 1.0
O A:HOH636 2.2 13.2 1.0
CG A:ASP319 3.2 11.9 1.0
P9 A:ZOL510 3.3 11.4 1.0
P14 A:ZOL510 3.4 11.6 1.0
O13 A:ZOL510 3.5 12.2 1.0
C8 A:ZOL510 3.5 11.0 1.0
OD1 A:ASP319 3.6 13.1 1.0
O A:HOH774 4.0 15.8 1.0
O11 A:ZOL510 4.0 12.4 1.0
O A:HOH676 4.1 13.8 1.0
O A:ASP319 4.1 11.9 1.0
OD2 A:ASP337 4.2 13.6 1.0
O A:HOH734 4.2 11.6 1.0
NE2 A:GLN316 4.3 13.2 1.0
OD1 A:ASP323 4.3 17.1 1.0
O16 A:ZOL510 4.4 11.9 1.0
NZ A:LYS333 4.4 12.1 1.0
CB A:ASP319 4.4 11.9 1.0
O12 A:ZOL510 4.4 11.6 1.0
OD1 A:ASP337 4.4 12.6 1.0
OD1 A:ASP320 4.5 12.9 1.0
O17 A:ZOL510 4.5 11.9 1.0
C A:ASP319 4.5 10.5 1.0
CB A:ASP323 4.6 12.8 1.0
CG A:ASP337 4.7 12.7 1.0
O A:HOH716 4.8 13.8 1.0
CE A:LYS333 4.8 14.6 1.0
MG A:MG504 4.8 17.2 0.5
MN A:MN501 4.8 13.6 0.5
CG A:ASP323 4.9 14.1 1.0
N A:ASP320 4.9 11.2 1.0

Magnesium binding site 4 out of 6 in 8a7k

Go back to Magnesium Binding Sites List in 8a7k
Magnesium binding site 4 out of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol


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+/MN2+, Ipp, and Zol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:16.2
occ:0.50
MN B:MN501 0.1 13.8 0.5
O B:HOH625 1.9 13.5 1.0
O B:HOH647 2.0 12.3 1.0
OD1 B:ASP179 2.1 10.9 1.0
O B:HOH752 2.1 12.5 1.0
O15 B:ZOL509 2.2 10.8 1.0
OD2 B:ASP183 2.2 11.1 1.0
CG B:ASP183 3.1 12.4 1.0
CG B:ASP179 3.1 10.6 1.0
OD1 B:ASP183 3.2 12.6 1.0
MN B:MN503 3.4 13.3 0.5
OD2 B:ASP179 3.4 10.3 1.0
P14 B:ZOL509 3.4 11.8 1.0
MG B:MG505 3.5 15.7 0.5
O16 B:ZOL509 3.5 12.6 1.0
NE2 B:GLN247 3.9 12.1 0.5
OD1 B:ASP250 3.9 14.9 1.0
OE1 B:GLN247 4.1 12.4 0.5
NE2 B:GLN247 4.2 14.1 0.5
O B:HOH628 4.2 15.3 1.0
OE1 B:GLN247 4.3 11.5 0.5
NZ B:LYS342 4.3 17.3 1.0
CD B:GLN247 4.3 10.9 0.5
O B:HOH739 4.3 11.7 1.0
O B:HOH683 4.4 13.7 1.0
C19 B:ZOL509 4.4 13.5 1.0
CB B:ASP179 4.4 10.6 1.0
CB B:ASP183 4.5 11.5 1.0
CG B:ASP250 4.5 13.2 1.0
O17 B:ZOL509 4.5 11.8 1.0
CD B:GLN247 4.7 11.4 0.5
O B:ASP179 4.7 11.6 1.0
C7 B:ZOL509 4.7 11.0 1.0
C8 B:ZOL509 4.7 10.7 1.0
OD2 B:ASP250 4.7 15.5 1.0
N15 B:ZOL509 4.8 11.9 1.0
O12 B:ZOL509 4.9 10.2 1.0
CA B:ASP179 4.9 11.3 1.0
O B:HOH667 5.0 11.1 1.0

Magnesium binding site 5 out of 6 in 8a7k

Go back to Magnesium Binding Sites List in 8a7k
Magnesium binding site 5 out of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol


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+/MN2+, Ipp, and Zol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:15.7
occ:0.50
MN B:MN503 0.1 13.3 0.5
O12 B:ZOL509 1.9 10.2 1.0
O B:HOH667 2.0 11.1 1.0
O B:HOH739 2.1 11.7 1.0
OD2 B:ASP179 2.1 10.3 1.0
OD2 B:ASP183 2.2 11.1 1.0
O15 B:ZOL509 2.2 10.8 1.0
CG B:ASP179 3.2 10.6 1.0
P9 B:ZOL509 3.2 11.5 1.0
MN B:MN501 3.4 13.8 0.5
CG B:ASP183 3.4 12.4 1.0
P14 B:ZOL509 3.4 11.8 1.0
MG B:MG504 3.5 16.2 0.5
OD1 B:ASP179 3.5 10.9 1.0
C8 B:ZOL509 3.7 10.7 1.0
O B:HOH743 3.7 14.1 1.0
CB B:ASP183 3.8 11.5 1.0
O11 B:ZOL509 4.0 12.3 1.0
O17 B:ZOL509 4.0 11.8 1.0
C7 B:ZOL509 4.0 11.0 1.0
NH2 B:ARG188 4.1 13.2 1.0
O B:HOH621 4.3 13.4 1.0
O10 B:ZOL509 4.3 11.4 1.0
O B:ASP179 4.4 11.6 1.0
OD1 B:ASP180 4.4 12.8 1.0
OG B:SER185 4.4 13.2 1.0
O B:HOH752 4.4 12.5 1.0
CB B:ASP179 4.5 10.6 1.0
OD1 B:ASP183 4.5 12.6 1.0
O B:HOH677 4.6 14.9 1.0
O B:HOH689 4.6 14.7 1.0
O16 B:ZOL509 4.7 12.6 1.0
C B:ASP179 4.7 10.5 1.0
MN B:MN502 4.8 15.0 0.5
MG B:MG506 4.8 16.1 0.5
O B:HOH625 5.0 13.5 1.0
O B:HOH647 5.0 12.3 1.0

Magnesium binding site 6 out of 6 in 8a7k

Go back to Magnesium Binding Sites List in 8a7k
Magnesium binding site 6 out of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol


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+/MN2+, Ipp, and Zol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:16.1
occ:0.50
MN B:MN502 0.0 15.0 0.5
O11 B:ZOL509 2.0 12.3 1.0
O17 B:ZOL509 2.1 11.8 1.0
O B:HOH757 2.1 14.3 1.0
O B:HOH639 2.1 12.9 1.0
OD2 B:ASP319 2.1 12.2 1.0
O B:HOH621 2.1 13.4 1.0
CG B:ASP319 3.1 12.8 1.0
P9 B:ZOL509 3.3 11.5 1.0
P14 B:ZOL509 3.4 11.8 1.0
OD1 B:ASP319 3.5 13.7 1.0
O13 B:ZOL509 3.6 12.3 1.0
C8 B:ZOL509 3.6 10.7 1.0
O12 B:ZOL509 4.0 10.2 1.0
O B:HOH683 4.0 13.7 1.0
O B:HOH760 4.1 17.5 1.0
OD1 B:ASP323 4.2 19.2 1.0
O B:ASP319 4.2 12.4 1.0
O B:HOH739 4.2 11.7 1.0
OD2 B:ASP337 4.2 12.9 1.0
NE2 B:GLN316 4.3 12.5 1.0
O15 B:ZOL509 4.3 10.8 1.0
OD1 B:ASP337 4.4 13.8 1.0
CB B:ASP319 4.4 12.5 1.0
OD1 B:ASP320 4.4 13.6 1.0
O10 B:ZOL509 4.4 11.4 1.0
O16 B:ZOL509 4.5 12.6 1.0
C B:ASP319 4.5 11.4 1.0
NZ B:LYS333 4.5 12.4 1.0
CB B:ASP323 4.6 12.6 1.0
CG B:ASP337 4.7 12.5 1.0
O B:HOH743 4.8 14.1 1.0
CG B:ASP323 4.8 16.1 1.0
MG B:MG505 4.8 15.7 0.5
CE B:LYS333 4.8 13.5 1.0
MN B:MN503 4.9 13.3 0.5
N B:ASP320 4.9 12.0 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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy