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Magnesium in PDB 8a7b: PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp

Enzymatic activity of PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp

All present enzymatic activity of PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp:
2.5.1.1;

Protein crystallography data

The structure of PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp, PDB code: 8a7b 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 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.31, 77.97, 88.71, 90, 101.26, 90
R / Rfree (%) 15.6 / 17.5

Other elements in 8a7b:

The structure of PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp also contains other interesting chemical elements:

Bromine (Br) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp (pdb code 8a7b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp, PDB code: 8a7b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8a7b

Go back to Magnesium Binding Sites List in 8a7b
Magnesium binding site 1 out of 5 in the PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:22.5
occ:1.00
 O A:HOH620 2.0 22.3 1.0
OD1 A:ASP179 2.1 20.8 1.0
O2A A:L7X508 2.1 22.2 1.0
O A:HOH629 2.1 22.6 1.0
O A:HOH711 2.1 23.4 1.0
OD2 A:ASP183 2.2 21.4 1.0
CG A:ASP183 3.0 23.2 1.0
CG A:ASP179 3.0 21.1 1.0
MG A:MG504 3.2 23.3 1.0
OD1 A:ASP183 3.2 23.3 1.0
OD2 A:ASP179 3.3 22.2 1.0
PA A:L7X508 3.3 23.5 1.0
O1A A:L7X508 3.8 25.1 1.0
O1 A:L7X508 3.9 23.1 1.0
NE2 A:GLN247 4.0 22.5 1.0
OE1 A:GLN247 4.1 22.2 1.0
O A:HOH612 4.2 30.5 1.0
OD2 A:ASP250 4.2 29.4 1.0
O A:HOH717 4.2 29.3 1.0
O A:HOH705 4.3 24.9 1.0
C2 A:L7X508 4.3 26.5 1.0
C1 A:L7X508 4.3 24.5 1.0
CB A:ASP179 4.4 19.9 1.0
CD A:GLN247 4.4 21.6 1.0
CB A:ASP183 4.4 23.4 1.0
O A:HOH732 4.6 39.3 1.0
O A:ASP179 4.7 21.1 1.0
O3A A:L7X508 4.7 23.5 1.0
O3B A:L7X508 4.7 22.6 1.0
O A:HOH631 4.9 22.4 1.0
CA A:ASP179 5.0 20.1 1.0

Magnesium binding site 2 out of 5 in 8a7b

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Magnesium binding site 2 out of 5 in the PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:25.4
occ:1.00
 O A:HOH651 2.1 24.9 1.0
O A:HOH695 2.1 24.1 1.0
O A:HOH706 2.1 24.7 1.0
OD1 A:ASN319 2.1 25.2 1.0
O A:HOH605 2.1 23.8 1.0
O A:HOH615 2.1 27.6 1.0
CG A:ASN319 3.1 24.4 1.0
ND2 A:ASN319 3.6 26.5 1.0
O A:HOH616 4.0 28.2 1.0
OD1 A:ASP323 4.1 25.5 1.0
OD2 A:ASP337 4.1 25.7 1.0
O A:HOH668 4.2 24.4 1.0
OD1 A:ASP337 4.2 25.8 1.0
O A:HOH603 4.2 28.5 1.0
NE2 A:GLN316 4.3 25.7 1.0
O A:ASN319 4.3 23.9 1.0
O A:HOH618 4.4 32.6 1.0
CB A:ASN319 4.5 23.2 1.0
NZ A:LYS342 4.5 28.1 1.0
OD1 A:ASP320 4.5 23.4 1.0
C A:ASN319 4.5 23.3 1.0
CG A:ASP337 4.6 26.2 1.0
O A:HOH647 4.6 28.7 1.0
CG A:ASP323 4.7 24.9 1.0
CB A:ASP323 4.9 24.4 1.0
N A:ASP320 4.9 23.4 1.0

Magnesium binding site 3 out of 5 in 8a7b

Go back to Magnesium Binding Sites List in 8a7b
Magnesium binding site 3 out of 5 in the PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:25.9
occ:1.00
 O2B A:L7X508 1.9 24.2 1.0
O A:HOH668 2.0 24.4 1.0
O A:HOH621 2.0 27.4 1.0
O A:HOH723 2.1 29.8 1.0
O A:HOH702 2.1 26.6 1.0
O A:HOH692 2.2 29.9 1.0
PB A:L7X508 3.4 23.3 1.0
NZ A:LYS342 3.8 28.1 1.0
O A:HOH624 3.9 27.3 1.0
O3B A:L7X508 3.9 22.6 1.0
O A:HOH651 3.9 24.9 1.0
O A:HOH603 3.9 28.5 1.0
O1B A:L7X508 4.0 23.9 1.0
O A:HOH678 4.1 25.9 1.0
O A:HOH705 4.2 24.9 1.0
OE1 A:GLU340 4.3 37.3 1.0
OE2 A:GLU340 4.3 33.2 1.0
C A:CO3507 4.3 43.6 1.0
O A:HOH648 4.3 49.5 1.0
O3 A:CO3507 4.4 43.8 1.0
O3A A:L7X508 4.5 23.5 1.0
O1 A:CO3507 4.5 42.0 1.0
O2 A:CO3507 4.5 49.0 1.0
OG1 A:THR336 4.6 31.9 1.0
CD A:GLU340 4.7 32.0 1.0
CE A:LYS342 4.8 28.7 1.0

Magnesium binding site 4 out of 5 in 8a7b

Go back to Magnesium Binding Sites List in 8a7b
Magnesium binding site 4 out of 5 in the PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:23.3
occ:1.00
 OD2 A:ASP179 2.0 22.2 1.0
O3B A:L7X508 2.1 22.6 1.0
O A:HOH631 2.1 22.4 1.0
OD2 A:ASP183 2.1 21.4 1.0
O2A A:L7X508 2.1 22.2 1.0
O A:HOH705 2.1 24.9 1.0
CG A:ASP179 3.0 21.1 1.0
MG A:MG501 3.2 22.5 1.0
CG A:ASP183 3.2 23.2 1.0
PB A:L7X508 3.2 23.3 1.0
OD1 A:ASP179 3.3 20.8 1.0
PA A:L7X508 3.4 23.5 1.0
O3A A:L7X508 3.6 23.5 1.0
CB A:ASP183 3.6 23.4 1.0
NH2 A:ARG188 3.9 24.5 1.0
O2B A:L7X508 4.0 24.2 1.0
O A:HOH692 4.1 29.9 1.0
C1 A:L7X508 4.1 24.5 1.0
O A:ASP179 4.2 21.1 1.0
O A:HOH732 4.2 39.3 1.0
O1 A:L7X508 4.2 23.1 1.0
O A:HOH711 4.2 23.4 1.0
OD1 A:ASP183 4.3 23.3 1.0
CB A:ASP179 4.3 19.9 1.0
OG A:SER185 4.4 27.3 1.0
OD1 A:ASP180 4.4 22.8 1.0
C A:ASP179 4.5 20.6 1.0
O1A A:L7X508 4.5 25.1 1.0
O1B A:L7X508 4.6 23.9 1.0
O A:HOH620 4.8 22.3 1.0
O A:HOH629 4.9 22.6 1.0
O A:HOH678 4.9 25.9 1.0
C2 A:L7X508 4.9 26.5 1.0
CE A:LYS342 4.9 28.7 1.0
N A:ASP180 5.0 20.9 1.0
CA A:ASP179 5.0 20.1 1.0

Magnesium binding site 5 out of 5 in 8a7b

Go back to Magnesium Binding Sites List in 8a7b
Magnesium binding site 5 out of 5 in the PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of PCIDS1_D319N in Complex with MG2+ and 3-Br-Gpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:26.3
occ:1.00
 OD1 B:ASN319 2.0 24.9 1.0
O B:HOH646 2.0 29.5 1.0
O B:HOH685 2.1 30.0 1.0
O B:HOH605 2.1 23.1 1.0
O B:HOH680 2.1 30.0 1.0
O B:HOH714 2.1 33.1 1.0
CG B:ASN319 3.1 24.3 1.0
ND2 B:ASN319 3.6 27.4 1.0
OD1 B:ASP323 4.0 27.3 1.0
OD2 B:ASP337 4.2 24.3 1.0
NE2 B:GLN316 4.2 24.1 1.0
O B:ASN319 4.3 21.7 1.0
OD1 B:ASP337 4.3 25.9 1.0
O B:HOH653 4.4 33.7 1.0
CB B:ASN319 4.4 22.7 1.0
OD1 B:ASP320 4.4 21.8 1.0
C B:ASN319 4.5 21.5 1.0
CG B:ASP323 4.7 25.6 1.0
CG B:ASP337 4.7 24.1 1.0
CB B:ASP323 4.7 23.9 1.0
N B:ASP320 4.9 20.7 1.0
O B:HOH655 4.9 48.8 1.0
CA B:ASN319 5.0 22.0 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

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