Magnesium in PDB 8pb3: Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form

The structure of Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form, PDB code: 8pb3 was solved by S.Werten, J.Hudspeth, B.Rupp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.69 / 1.18
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.04, 48.853, 115.452, 90, 131.4, 90
R / Rfree (%)	18.3 / 19.6

The structure of Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form (pdb code 8pb3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form, PDB code: 8pb3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:32.7 occ:1.00 OD1 A:ASN272 1.9 23.1 1.0 O A:HOH574 2.1 31.0 1.0 O A:HOH839 2.1 33.6 1.0 O A:HOH730 2.3 26.1 1.0 O A:HOH640 2.3 26.4 1.0 O A:HOH736 2.3 24.3 1.0 CG A:ASN272 3.0 20.1 1.0 H A:GLU273 3.5 24.3 1.0 HD22 A:ASN272 3.5 31.5 1.0 HA A:ASN272 3.6 23.4 1.0 O A:HOH608 3.7 23.9 1.0 ND2 A:ASN272 3.7 26.2 1.0 O A:GLU273 4.0 24.9 1.0 O A:HOH571 4.0 25.4 1.0 O A:HOH698 4.1 27.0 1.0 CB A:ASN272 4.2 19.4 1.0 N A:GLU273 4.2 20.3 1.0 CA A:ASN272 4.3 19.4 1.0 HD1 A:TRP81 4.4 20.5 1.0 HD21 A:ASN272 4.6 31.5 1.0 CD1 A:TRP81 4.6 17.1 1.0 HB2 A:ASN272 4.6 23.3 1.0 O A:HOH779 4.6 37.1 1.0 O A:GLU296 4.8 25.1 1.0 CL A:CL403 4.8 30.7 1.0 C A:ASN272 4.8 19.4 1.0 HE1 A:TRP81 4.8 21.3 1.0 NE1 A:TRP81 4.9 17.8 1.0 C A:GLU273 4.9 25.0 1.0 HB3 A:ASN272 4.9 23.3 1.0 HA A:LEU297 4.9 25.3 1.0

Magnesium binding site 2 out of 4 in the Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:43.8 occ:1.00 O A:HOH615 2.1 30.6 1.0 O A:GLY58 2.1 21.7 1.0 O A:HOH784 2.1 32.9 1.0 C A:GLY58 3.2 20.4 1.0 HA A:LEU59 3.6 19.5 1.0 HA3 A:GLY58 3.9 25.0 1.0 CA A:GLY58 4.1 20.8 1.0 O A:HOH735 4.2 30.9 1.0 N A:LEU59 4.2 16.5 1.0 HD23 A:LEU59 4.2 22.0 1.0 HA2 A:GLY58 4.2 25.0 1.0 O A:HOH676 4.3 25.7 1.0 OD1 A:ASN147 4.3 17.2 1.0 CA A:LEU59 4.4 16.3 1.0 O A:HOH712 4.4 29.8 1.0 O A:HOH863 4.5 39.2 1.0 H A:THR60 4.6 19.1 1.0 HG23 A:THR60 4.7 22.8 1.0 HA A:ASN147 5.0 17.7 1.0 H A:LEU59 5.0 19.8 1.0

Magnesium binding site 3 out of 4 in the Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:39.9 occ:1.00 O A:HOH849 2.1 39.6 1.0 O A:HOH684 2.3 32.5 1.0 O A:HOH515 3.9 30.5 1.0 HA A:GLU263 4.1 24.3 1.0 HG2 A:GLU265 4.2 32.9 1.0 O A:LYS262 4.3 21.3 1.0 HG3 A:GLU265 4.8 32.9 1.0 O A:GLU263 4.8 23.6 1.0 CG A:GLU265 4.9 27.4 1.0 CA A:GLU263 4.9 20.2 1.0

Magnesium binding site 4 out of 4 in the Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Psim in Complex with Sah and Norbaeocystin, Monoclinic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:24.1 occ:1.00 O B:HOH503 2.0 18.6 1.0 O B:HOH749 2.0 27.9 1.0 O B:HOH542 2.1 24.7 1.0 OE1 B:GLN229 2.1 23.6 1.0 O B:HOH700 2.1 24.8 1.0 OE2 A:GLU170 3.0 28.6 1.0 HE22 B:GLN229 3.1 23.0 1.0 CD B:GLN229 3.1 19.7 1.0 O B:HOH784 3.1 29.8 1.0 NE2 B:GLN229 3.4 19.2 1.0 O B:HOH733 3.5 32.9 1.0 HD11 B:ILE164 3.9 17.7 1.0 CD A:GLU170 4.0 31.9 1.0 O B:HOH770 4.1 26.4 1.0 O B:ILE160 4.1 16.7 0.6 O B:HOH728 4.2 27.1 1.0 O B:ILE160 4.2 15.6 0.4 O B:HOH585 4.2 19.3 1.0 HA B:ASP161 4.2 19.0 1.0 HE21 B:GLN229 4.3 23.0 1.0 HG13 B:ILE164 4.4 19.3 1.0 O B:GLY162 4.4 15.4 1.0 O B:HOH525 4.4 22.9 1.0 CG B:GLN229 4.5 16.4 1.0 O B:HOH608 4.5 30.0 1.0 HB2 B:GLN229 4.5 21.1 1.0 OE1 A:GLU170 4.6 23.1 1.0 HG2 A:GLU170 4.6 37.5 1.0 CD1 B:ILE164 4.8 14.8 1.0 HG3 B:GLN229 4.8 19.6 1.0 CB B:GLN229 4.9 17.5 1.0 HB3 B:GLN229 4.9 21.1 1.0 CG A:GLU170 4.9 31.2 1.0 HG13 A:VAL166 5.0 20.3 1.0

J.Hudspeth, K.Rogge, S.Dorner, M.Mull, D.Hoffmeister, B.Rupp, S.Werten. Methyl Transfer in Psilocybin Biosynthesis Nat Commun V. 15 2709 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-46997-Z