Magnesium in PDB 8ye0: Crystal Structure of Kgpf Prenyltransferase

The structure of Crystal Structure of Kgpf Prenyltransferase, PDB code: 8ye0 was solved by K.Hamada, S.Inoue, Y.Goto, H.Suga, K.Ogata, T.Sengoku, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.64 / 1.94
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.681, 69.344, 86.426, 109.12, 93.1, 104.89
R / Rfree (%)	19.1 / 23.9

The binding sites of Magnesium atom in the Crystal Structure of Kgpf Prenyltransferase (pdb code 8ye0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Kgpf Prenyltransferase, PDB code: 8ye0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Kgpf Prenyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Kgpf Prenyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:18.8 occ:1.00 O4 A:PIS301 2.0 20.4 1.0 O A:HOH473 2.0 22.7 1.0 OE1 A:GLU182 2.1 22.2 1.0 O5 A:PIS301 2.1 18.9 1.0 O A:HOH419 2.2 22.8 1.0 O A:HOH410 2.3 19.9 1.0 CD A:GLU182 3.0 21.0 1.0 P1 A:PIS301 3.3 21.2 1.0 P2 A:PIS301 3.3 23.4 1.0 OE2 A:GLU182 3.4 22.7 1.0 O1 A:PIS301 3.4 26.6 1.0 OH A:TYR184 3.6 22.6 1.0 O A:HOH498 4.0 22.6 1.0 O A:HOH489 4.0 20.7 1.0 O A:HOH431 4.1 20.2 1.0 O6 A:PIS301 4.1 32.0 1.0 O3 A:PIS301 4.1 23.0 1.0 OH A:TYR233 4.1 22.3 1.0 O2 A:PIS301 4.4 21.1 1.0 CG A:GLU182 4.4 17.7 1.0 OD1 A:ASN227 4.4 23.4 1.0 CZ A:TYR184 4.6 23.0 1.0 CB A:GLU182 4.6 15.1 1.0 OD2 A:ASP172 4.7 25.3 1.0 CE2 A:TYR184 4.7 20.4 1.0 S1 A:PIS301 4.7 37.5 1.0 NZ A:LYS133 4.8 31.4 1.0 O A:HOH510 4.8 19.8 1.0 O A:HOH480 4.9 31.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Kgpf Prenyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Kgpf Prenyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:49.1 occ:1.00 O4 B:PIS301 1.9 44.8 1.0 O B:HOH421 2.0 40.8 1.0 OE1 B:GLU182 2.1 48.6 1.0 O2 B:PIS301 2.6 40.0 1.0 CD B:GLU182 3.0 46.9 1.0 P2 B:PIS301 3.2 41.1 1.0 OE2 B:GLU182 3.5 39.3 1.0 O1 B:PIS301 3.6 35.9 1.0 P1 B:PIS301 3.6 33.2 1.0 NZ B:LYS133 3.7 27.5 0.5 OH B:TYR184 3.7 28.4 1.0 O6 B:PIS301 4.0 45.8 1.0 O5 B:PIS301 4.0 36.5 1.0 O B:HOH473 4.2 34.9 1.0 OH B:TYR233 4.3 32.5 1.0 CG B:GLU182 4.3 34.8 1.0 CB B:GLU182 4.4 27.9 1.0 OD1 B:ASN227 4.6 60.5 1.0 OD2 B:ASP172 4.6 46.9 1.0 ND2 B:ASN227 4.7 46.9 1.0 S1 B:PIS301 4.7 56.0 1.0 CZ B:TYR184 4.8 28.9 1.0 O3 B:PIS301 4.9 42.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Kgpf Prenyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Kgpf Prenyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:53.6 occ:1.00 O6 C:PIS301 1.9 33.9 1.0 OE1 C:GLU182 2.1 51.8 1.0 O C:HOH415 2.1 42.3 1.0 O C:HOH403 2.2 44.8 1.0 O5 C:PIS301 2.5 33.3 1.0 CD C:GLU182 3.0 58.3 1.0 P2 C:PIS301 3.2 52.2 1.0 OE2 C:GLU182 3.2 52.6 1.0 O1 C:PIS301 3.4 59.1 1.0 P1 C:PIS301 3.6 47.7 1.0 OH C:TYR184 4.0 51.4 1.0 OD1 C:ASN227 4.1 72.8 1.0 OH C:TYR233 4.2 45.4 1.0 O4 C:PIS301 4.3 49.3 1.0 O2 C:PIS301 4.3 48.0 1.0 S1 C:PIS301 4.3 64.5 1.0 CG C:GLU182 4.4 52.9 1.0 O C:HOH417 4.4 41.0 1.0 NZ C:LYS133 4.4 53.3 1.0 OD2 C:ASP172 4.5 64.7 1.0 ND2 C:ASN227 4.6 66.9 1.0 CB C:GLU182 4.7 56.2 1.0 O3 C:PIS301 4.7 53.7 1.0 CG C:ASN227 4.8 70.0 1.0 CZ C:TYR184 4.9 48.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Kgpf Prenyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Kgpf Prenyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:38.8 occ:1.00 O4 D:PIS301 1.9 32.7 1.0 O D:HOH443 2.0 34.2 1.0 O D:HOH411 2.0 34.0 1.0 O D:HOH430 2.1 39.4 1.0 OE1 D:GLU182 2.2 33.7 1.0 O2 D:PIS301 2.3 31.0 1.0 P2 D:PIS301 3.2 29.4 1.0 CD D:GLU182 3.2 36.0 1.0 O1 D:PIS301 3.3 33.2 1.0 P1 D:PIS301 3.4 30.3 1.0 OE2 D:GLU182 3.6 36.9 1.0 O D:HOH422 3.8 39.8 1.0 OH D:TYR184 3.8 30.9 1.0 O D:HOH454 4.0 35.8 1.0 OH D:TYR233 4.1 36.7 1.0 O D:HOH434 4.1 29.8 1.0 O6 D:PIS301 4.1 34.3 1.0 O5 D:PIS301 4.3 28.7 1.0 OD1 D:ASN227 4.3 43.5 1.0 S1 D:PIS301 4.5 53.2 1.0 O3 D:PIS301 4.5 34.4 1.0 CG D:GLU182 4.6 33.2 1.0 CB D:GLU182 4.7 29.9 1.0 OD2 D:ASP172 4.7 38.3 1.0 CZ D:TYR184 4.8 27.9 1.0 ND2 D:ASN227 4.9 39.3 1.0 CE2 D:TYR184 5.0 30.5 1.0

S.Inoue, D.T.Nguyen, K.Hamada, R.Okuma, C.Okada, M.Okada, I.Abe, T.Sengoku, Y.Goto, H.Suga. De Novo Discovery of Pseudo-Natural Prenylated Macrocyclic Peptide Ligands. Angew.Chem.Int.Ed.Engl. 09973 2024.
ISSN: ESSN 1521-3773
PubMed: 38837490
DOI: 10.1002/ANIE.202409973