Magnesium in PDB 8uyi: Structure of Adp-Bound and Phosphorylated Pediculus Humanus (pH) PINK1 Dimer

The binding sites of Magnesium atom in the Structure of Adp-Bound and Phosphorylated Pediculus Humanus (pH) PINK1 Dimer (pdb code 8uyi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Adp-Bound and Phosphorylated Pediculus Humanus (pH) PINK1 Dimer, PDB code: 8uyi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Adp-Bound and Phosphorylated Pediculus Humanus (pH) PINK1 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Adp-Bound and Phosphorylated Pediculus Humanus (pH) PINK1 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:76.7 occ:1.00 OD1 A:ASP357 2.4 116.3 1.0 O1B A:ADP601 2.4 119.1 1.0 O2P B:SEP202 2.7 123.3 1.0 OD2 A:ASP357 2.7 106.8 1.0 CG A:ASP357 2.9 107.1 1.0 P B:SEP202 3.6 127.1 1.0 O3P B:SEP202 3.7 119.3 1.0 PB A:ADP601 3.9 129.3 1.0 OG B:SEP202 4.0 118.8 1.0 OD2 A:ASP334 4.1 122.1 1.0 CB B:SEP202 4.3 112.6 1.0 MG A:MG603 4.3 104.9 1.0 CB A:ASP357 4.3 102.8 1.0 OE2 A:GLU214 4.4 108.8 1.0 O3A A:ADP601 4.6 122.7 1.0 CA A:GLY359 4.7 75.9 1.0 O3B A:ADP601 4.7 124.5 1.0 N A:GLY359 4.7 81.2 1.0 O2B A:ADP601 4.8 119.7 1.0 O A:ASP357 4.8 109.1 1.0 CG A:ASP334 5.0 121.5 1.0 CA A:ASP357 5.0 102.1 1.0

Magnesium binding site 2 out of 4 in the Structure of Adp-Bound and Phosphorylated Pediculus Humanus (pH) PINK1 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Adp-Bound and Phosphorylated Pediculus Humanus (pH) PINK1 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:104.9 occ:1.00 OD1 A:ASN339 2.1 105.7 1.0 OD2 A:ASP357 2.2 106.8 1.0 O3A A:ADP601 2.9 122.7 1.0 O1A A:ADP601 3.1 117.5 1.0 O2P B:SEP202 3.1 123.3 1.0 CG A:ASN339 3.1 100.8 1.0 CG A:ASP357 3.4 107.1 1.0 ND2 A:ASN339 3.5 105.7 1.0 O1B A:ADP601 3.6 119.1 1.0 PA A:ADP601 3.6 112.0 1.0 PB A:ADP601 3.8 129.3 1.0 CE A:LYS336 4.0 122.7 1.0 CB A:ASP357 4.1 102.8 1.0 O2B A:ADP601 4.2 119.7 1.0 MG A:MG602 4.3 76.7 1.0 OD1 A:ASP357 4.4 116.3 1.0 NZ A:LYS336 4.4 118.0 1.0 CB A:ASN339 4.4 93.7 1.0 P B:SEP202 4.4 127.1 1.0 OD2 A:ASP334 4.5 122.1 1.0 O5' A:ADP601 4.5 117.4 1.0 C5' A:ADP601 4.7 115.7 1.0 O1P B:SEP202 4.7 116.8 1.0 CA A:ASN339 4.8 97.7 1.0 O2A A:ADP601 4.9 110.1 1.0 N A:ASN339 4.9 98.5 1.0 O A:ASP338 4.9 118.5 1.0 CB A:ASP338 5.0 123.3 1.0 C A:ASP338 5.0 115.0 1.0

Magnesium binding site 3 out of 4 in the Structure of Adp-Bound and Phosphorylated Pediculus Humanus (pH) PINK1 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Adp-Bound and Phosphorylated Pediculus Humanus (pH) PINK1 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:90.2 occ:1.00 OD1 B:ASP357 2.1 102.9 1.0 O1B B:ADP601 2.2 109.7 1.0 CG B:ASP357 2.8 94.6 1.0 OD2 B:ASP357 2.8 99.2 1.0 O1P A:SEP202 3.4 129.7 1.0 PB B:ADP601 3.8 112.1 1.0 O3P A:SEP202 4.0 132.6 1.0 P A:SEP202 4.1 140.1 1.0 CB B:ASP357 4.2 80.9 1.0 OG A:SEP202 4.3 133.6 1.0 O3A B:ADP601 4.5 111.5 1.0 OE1 B:GLU214 4.5 104.8 1.0 O3B B:ADP601 4.5 106.0 1.0 O2B B:ADP601 4.6 114.9 1.0 CB A:SEP202 4.7 124.6 1.0 CA B:GLY359 4.7 66.6 1.0 N B:GLY359 4.7 75.5 1.0 O2A B:ADP601 4.7 109.6 1.0 CA B:ASP357 4.8 81.8 1.0 O B:ASP357 4.8 88.0 1.0 NZ B:LYS193 4.8 93.4 1.0 SG B:CYS360 4.8 113.2 1.0 C B:ASP357 5.0 86.0 1.0 MG B:MG603 5.0 85.8 1.0

Magnesium binding site 4 out of 4 in the Structure of Adp-Bound and Phosphorylated Pediculus Humanus (pH) PINK1 Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Adp-Bound and Phosphorylated Pediculus Humanus (pH) PINK1 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:85.8 occ:1.00 O2A B:ADP601 2.1 109.6 1.0 OD1 B:ASN339 2.2 103.2 1.0 OD2 B:ASP357 2.7 99.2 1.0 O3B B:ADP601 3.4 106.0 1.0 CG B:ASN339 3.4 96.7 1.0 O1P A:SEP202 3.5 129.7 1.0 PA B:ADP601 3.5 116.1 1.0 CG B:ASP357 3.6 94.6 1.0 CB B:ASP357 3.9 80.9 1.0 C5' B:ADP601 4.0 112.5 1.0 O5' B:ADP601 4.2 110.5 1.0 ND2 B:ASN339 4.2 102.4 1.0 O1B B:ADP601 4.2 109.7 1.0 PB B:ADP601 4.2 112.1 1.0 O3A B:ADP601 4.3 111.5 1.0 O B:ASP338 4.3 113.4 1.0 CA B:ASN339 4.5 86.8 1.0 CB B:ASN339 4.5 82.0 1.0 OD1 B:ASP357 4.6 102.9 1.0 O1A B:ADP601 4.6 109.0 1.0 N B:ASN339 4.7 98.4 1.0 C B:ASP338 4.7 113.4 1.0 CE B:LYS336 5.0 103.8 1.0 MG B:MG602 5.0 90.2 1.0 P A:SEP202 5.0 140.1 1.0 NZ B:LYS336 5.0 106.7 1.0

Z.Y.Gan, S.Callegari, T.N.Nguyen, N.S.Kirk, A.Leis, M.Lazarou, G.Dewson, D.Komander. Interaction of PINK1 with Nucleotides and Kinetin. Sci Adv V. 10 J7408 2024.
ISSN: ESSN 2375-2548
PubMed: 38241364
DOI: 10.1126/SCIADV.ADJ7408