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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

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