Atomistry » Manganese » PDB 7z03-8awv » 8a7k
Atomistry »
  Manganese »
    PDB 7z03-8awv »
      8a7k »

Manganese 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:

Magnesium (Mg) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 6 binding sites of Manganese where determined in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol, PDB code: 8a7k:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 8a7k

Go back to Manganese Binding Sites List in 8a7k
Manganese 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 Manganese with other atoms in the Mn 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:Mn501

b:13.6
occ:0.50
 MG A:MG504 0.1 17.2 0.5
O11 A:ZOL510 2.0 12.4 1.0
O A:HOH734 2.1 11.6 1.0
OD2 A:ASP179 2.1 11.0 1.0
O A:HOH656 2.1 11.4 1.0
OD2 A:ASP183 2.1 11.4 1.0
O16 A:ZOL510 2.2 11.9 1.0
CG A:ASP179 3.1 11.8 1.0
P9 A:ZOL510 3.2 11.4 1.0
MN A:MN502 3.3 13.3 0.5
CG A:ASP183 3.3 12.3 1.0
P14 A:ZOL510 3.4 11.6 1.0
MG A:MG505 3.4 17.4 0.5
OD1 A:ASP179 3.5 11.5 1.0
C8 A:ZOL510 3.7 11.0 1.0
O A:HOH716 3.7 13.8 1.0
CB A:ASP183 3.8 12.0 1.0
O10 A:ZOL510 4.0 11.2 1.0
O15 A:ZOL510 4.0 11.5 1.0
C7 A:ZOL510 4.0 11.5 1.0
NH2 A:ARG188 4.1 13.2 1.0
O A:HOH636 4.2 13.2 1.0
O12 A:ZOL510 4.4 11.6 1.0
O A:ASP179 4.4 11.8 1.0
O A:HOH687 4.4 12.2 1.0
OD1 A:ASP183 4.4 12.3 1.0
CB A:ASP179 4.4 11.2 1.0
OG A:SER185 4.5 13.8 1.0
OD1 A:ASP180 4.5 13.3 1.0
O A:HOH674 4.5 13.7 1.0
O A:HOH664 4.6 15.8 1.0
O17 A:ZOL510 4.6 11.9 1.0
C A:ASP179 4.6 10.7 1.0
MG A:MG506 4.8 17.2 0.5
O A:HOH625 4.8 12.5 1.0
MN A:MN503 4.9 14.0 0.5
O A:HOH653 4.9 11.9 1.0

Manganese binding site 2 out of 6 in 8a7k

Go back to Manganese Binding Sites List in 8a7k
Manganese 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 Manganese with other atoms in the Mn 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:Mn502

b:13.3
occ:0.50
 MG A:MG505 0.1 17.4 0.5
O A:HOH625 1.9 12.5 1.0
O A:HOH653 2.1 11.9 1.0
O16 A:ZOL510 2.1 11.9 1.0
O A:HOH687 2.1 12.2 1.0
OD1 A:ASP179 2.1 11.5 1.0
OD2 A:ASP183 2.2 11.4 1.0
CG A:ASP183 3.1 12.3 1.0
CG A:ASP179 3.2 11.8 1.0
OD1 A:ASP183 3.2 12.3 1.0
MN A:MN501 3.3 13.6 0.5
OD2 A:ASP179 3.4 11.0 1.0
P14 A:ZOL510 3.4 11.6 1.0
MG A:MG504 3.5 17.2 0.5
O17 A:ZOL510 3.5 11.9 1.0
OD1 A:ASP250 3.9 14.0 1.0
NE2 A:GLN247 3.9 15.8 1.0
OE1 A:GLN247 4.2 14.6 1.0
O A:HOH640 4.3 13.8 1.0
NZ A:LYS342 4.3 16.0 1.0
O A:HOH734 4.3 11.6 1.0
O A:HOH676 4.3 13.8 1.0
CD A:GLN247 4.4 15.2 1.0
C19 A:ZOL510 4.4 12.3 1.0
CB A:ASP179 4.5 11.2 1.0
CB A:ASP183 4.5 12.0 1.0
O15 A:ZOL510 4.5 11.5 1.0
CG A:ASP250 4.5 13.0 1.0
C7 A:ZOL510 4.6 11.5 1.0
C8 A:ZOL510 4.6 11.0 1.0
O A:ASP179 4.7 11.8 1.0
N15 A:ZOL510 4.7 11.6 1.0
OD2 A:ASP250 4.8 14.9 1.0
O11 A:ZOL510 4.9 12.4 1.0
O A:HOH674 4.9 13.7 1.0
CA A:ASP179 4.9 11.3 1.0
O A:HOH656 5.0 11.4 1.0

Manganese binding site 3 out of 6 in 8a7k

Go back to Manganese Binding Sites List in 8a7k
Manganese 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 Manganese with other atoms in the Mn 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:Mn503

b:14.0
occ:0.50
 MG A:MG506 0.0 17.2 0.5
O15 A:ZOL510 2.0 11.5 1.0
O10 A:ZOL510 2.1 11.2 1.0
O A:HOH648 2.1 12.1 1.0
O A:HOH755 2.1 12.6 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
NE2 A:GLN316 4.2 13.2 1.0
O A:HOH734 4.2 11.6 1.0
OD1 A:ASP323 4.3 17.1 1.0
O16 A:ZOL510 4.4 11.9 1.0
CB A:ASP319 4.4 11.9 1.0
OD1 A:ASP337 4.4 12.6 1.0
NZ A:LYS333 4.4 12.1 1.0
O12 A:ZOL510 4.4 11.6 1.0
OD1 A:ASP320 4.4 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 4.9 13.6 0.5
CG A:ASP323 4.9 14.1 1.0
N A:ASP320 4.9 11.2 1.0

Manganese binding site 4 out of 6 in 8a7k

Go back to Manganese Binding Sites List in 8a7k
Manganese 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 Manganese with other atoms in the Mn 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:Mn501

b:13.8
occ:0.50
 MG B:MG504 0.1 16.2 0.5
O B:HOH625 2.0 13.5 1.0
O B:HOH647 2.1 12.3 1.0
O15 B:ZOL509 2.1 10.8 1.0
O B:HOH752 2.1 12.5 1.0
OD1 B:ASP179 2.1 10.9 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 3.3 13.3 0.5
P14 B:ZOL509 3.4 11.8 1.0
OD2 B:ASP179 3.4 10.3 1.0
MG B:MG505 3.4 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 4.0 14.9 1.0
OE1 B:GLN247 4.2 12.4 0.5
NE2 B:GLN247 4.2 14.1 0.5
O B:HOH739 4.3 11.7 1.0
O B:HOH628 4.3 15.3 1.0
O B:HOH683 4.3 13.7 1.0
NZ B:LYS342 4.3 17.3 1.0
OE1 B:GLN247 4.3 11.5 0.5
C19 B:ZOL509 4.4 13.5 1.0
CD B:GLN247 4.4 10.9 0.5
O17 B:ZOL509 4.4 11.8 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
C8 B:ZOL509 4.6 10.7 1.0
C7 B:ZOL509 4.6 11.0 1.0
O B:ASP179 4.7 11.6 1.0
N15 B:ZOL509 4.7 11.9 1.0
CD B:GLN247 4.7 11.4 0.5
OD2 B:ASP250 4.7 15.5 1.0
O12 B:ZOL509 4.8 10.2 1.0
CA B:ASP179 4.9 11.3 1.0
O B:HOH667 4.9 11.1 1.0

Manganese binding site 5 out of 6 in 8a7k

Go back to Manganese Binding Sites List in 8a7k
Manganese 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 Manganese with other atoms in the Mn 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:Mn502

b:15.0
occ:0.50
 MG B:MG506 0.0 16.1 0.5
O11 B:ZOL509 2.0 12.3 1.0
O17 B:ZOL509 2.0 11.8 1.0
O B:HOH639 2.1 12.9 1.0
OD2 B:ASP319 2.1 12.2 1.0
O B:HOH757 2.1 14.3 1.0
O B:HOH621 2.2 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
O13 B:ZOL509 3.5 12.3 1.0
C8 B:ZOL509 3.6 10.7 1.0
OD1 B:ASP319 3.6 13.7 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
O B:HOH739 4.2 11.7 1.0
O B:ASP319 4.2 12.4 1.0
OD1 B:ASP323 4.2 19.2 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 4.9 13.5 1.0
MN B:MN503 4.9 13.3 0.5
N B:ASP320 4.9 12.0 1.0

Manganese binding site 6 out of 6 in 8a7k

Go back to Manganese Binding Sites List in 8a7k
Manganese 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 Manganese with other atoms in the Mn 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:Mn503

b:13.3
occ:0.50
 MG B:MG505 0.1 15.7 0.5
O12 B:ZOL509 2.0 10.2 1.0
O B:HOH667 2.1 11.1 1.0
OD2 B:ASP179 2.1 10.3 1.0
O B:HOH739 2.1 11.7 1.0
OD2 B:ASP183 2.1 11.1 1.0
O15 B:ZOL509 2.2 10.8 1.0
CG B:ASP179 3.1 10.6 1.0
P9 B:ZOL509 3.3 11.5 1.0
MN B:MN501 3.3 13.8 0.5
CG B:ASP183 3.3 12.4 1.0
MG B:MG504 3.4 16.2 0.5
P14 B:ZOL509 3.4 11.8 1.0
OD1 B:ASP179 3.5 10.9 1.0
C8 B:ZOL509 3.7 10.7 1.0
CB B:ASP183 3.7 11.5 1.0
O B:HOH743 3.8 14.1 1.0
O17 B:ZOL509 4.0 11.8 1.0
C7 B:ZOL509 4.0 11.0 1.0
O11 B:ZOL509 4.0 12.3 1.0
NH2 B:ARG188 4.1 13.2 1.0
O B:ASP179 4.3 11.6 1.0
O B:HOH621 4.3 13.4 1.0
O B:HOH752 4.4 12.5 1.0
O10 B:ZOL509 4.4 11.4 1.0
OD1 B:ASP183 4.4 12.6 1.0
CB B:ASP179 4.4 10.6 1.0
OG B:SER185 4.4 13.2 1.0
OD1 B:ASP180 4.4 12.8 1.0
O B:HOH677 4.6 14.9 1.0
C B:ASP179 4.6 10.5 1.0
O16 B:ZOL509 4.6 12.6 1.0
O B:HOH689 4.7 14.7 1.0
O B:HOH625 4.9 13.5 1.0
MN B:MN502 4.9 15.0 0.5
MG B:MG506 4.9 16.1 0.5
O B:HOH647 4.9 12.3 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: Sun Oct 6 11:17:59 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy