Magnesium in PDB 8wgy: Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain

The structure of Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain (pdb code 8wgy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain, PDB code: 8wgy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:22.7 occ:1.00 O2G B:ANP801 2.0 32.6 1.0 OG B:SER510 2.0 21.2 1.0 O2B B:ANP801 2.5 26.6 1.0 CB B:SER510 3.3 10.2 1.0 PG B:ANP801 3.4 14.3 1.0 PB B:ANP801 3.7 0.0 1.0 O2A B:ANP801 3.8 28.6 1.0 OE1 B:GLU557 3.9 41.6 1.0 N3B B:ANP801 4.0 29.7 1.0 N B:SER510 4.2 0.0 1.0 O1G B:ANP801 4.2 30.5 1.0 CA B:SER510 4.2 0.0 1.0 OE1 A:GLU579 4.4 36.3 1.0 O3G B:ANP801 4.5 27.0 1.0 O1B B:ANP801 4.5 29.3 1.0 NH2 A:ARG620 4.6 19.6 1.0 OD2 B:ASP603 4.6 15.2 1.0 CD A:GLU579 4.8 36.1 1.0 O3A B:ANP801 4.9 18.1 1.0 OE2 A:GLU579 4.9 32.7 1.0 PA B:ANP801 5.0 4.1 1.0

Magnesium binding site 2 out of 4 in the Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg803 b:36.2 occ:1.00 OG E:SER510 2.0 48.1 1.0 O3G E:ANP801 2.0 59.4 1.0 O2B E:ANP801 2.7 55.2 1.0 CB E:SER510 3.2 43.5 1.0 PG E:ANP801 3.4 70.3 1.0 O2A E:ANP801 3.5 60.0 1.0 N3B E:ANP801 3.7 60.3 1.0 PB E:ANP801 3.8 54.9 1.0 OE2 E:GLU557 4.0 50.5 1.0 OE2 D:GLU579 4.2 39.4 1.0 O2G E:ANP801 4.3 56.4 1.0 CA E:SER510 4.3 39.7 1.0 NH2 D:ARG620 4.3 39.3 1.0 N E:SER510 4.3 43.6 1.0 O1G E:ANP801 4.4 61.6 1.0 OD2 E:ASP603 4.7 51.3 1.0 PA E:ANP801 4.7 60.5 1.0 O1B E:ANP801 4.8 56.4 1.0 O3A E:ANP801 4.8 51.9 1.0 NH1 D:ARG620 4.9 34.1 1.0

Magnesium binding site 3 out of 4 in the Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg802 b:24.2 occ:1.00 OG C:SER510 1.9 23.7 1.0 O3G C:ANP801 2.0 38.5 1.0 O2B C:ANP801 2.3 28.9 1.0 CB C:SER510 3.1 23.8 1.0 PG C:ANP801 3.3 39.5 1.0 PB C:ANP801 3.5 25.2 1.0 O2A C:ANP801 3.6 28.8 1.0 N3B C:ANP801 3.6 33.6 1.0 N C:SER510 3.9 15.0 1.0 CA C:SER510 4.0 17.5 1.0 O2G C:ANP801 4.0 30.3 1.0 O1B C:ANP801 4.4 32.3 1.0 O1G C:ANP801 4.4 34.7 1.0 O3A C:ANP801 4.6 20.4 1.0 NH2 F:ARG620 4.6 34.1 1.0 OE2 C:GLU557 4.7 46.0 1.0 PA C:ANP801 4.8 32.3 1.0 OD2 C:ASP603 4.9 43.0 1.0 CB C:LYS509 4.9 17.7 1.0 C C:LYS509 4.9 15.8 1.0

Magnesium binding site 4 out of 4 in the Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mpox E5 Hexamer Amp-Pnp and Ssdna Bound Form with Clear Primase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:14.9 occ:1.00 O1G A:ANP801 2.1 23.9 1.0 O2B A:ANP801 2.3 3.1 1.0 CB A:SER510 3.0 6.5 1.0 PG A:ANP801 3.5 16.6 1.0 O2A A:ANP801 3.6 10.0 1.0 PB A:ANP801 3.7 0.0 1.0 OG A:SER510 3.8 19.1 1.0 OD2 A:ASP603 3.9 23.4 1.0 OE1 C:GLU579 3.9 33.0 1.0 N A:SER510 4.0 7.4 1.0 CA A:SER510 4.0 0.0 1.0 N3B A:ANP801 4.0 13.0 1.0 OE1 A:GLU557 4.3 39.0 1.0 O1B A:ANP801 4.4 10.4 1.0 O3G A:ANP801 4.4 11.7 1.0 O2G A:ANP801 4.5 21.7 1.0 NH2 C:ARG620 4.5 22.2 1.0 CD C:GLU579 4.6 35.9 1.0 OE2 C:GLU579 4.6 36.2 1.0 O3A A:ANP801 4.7 13.0 1.0 PA A:ANP801 4.8 6.1 1.0 CG A:ASP603 5.0 26.1 1.0

Y.Xu, Y.Wu, Y.Zhang, K.Gao, X.Wu, Y.Yang, D.Li, B.Yang, Z.Zhang, C.Dong. Essential and Multifunctional Mpox Virus E5 Helicase-Primase in Double and Single Hexamer. Sci Adv V. 10 L1150 2024.
ISSN: ESSN 2375-2548
PubMed: 39167653
DOI: 10.1126/SCIADV.ADL1150