Magnesium in PDB 8hwe: Cryo-Em Structure of D5 Atp-Adp Form

The binding sites of Magnesium atom in the Cryo-Em Structure of D5 Atp-Adp Form (pdb code 8hwe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of D5 Atp-Adp Form, PDB code: 8hwe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Cryo-Em Structure of D5 Atp-Adp Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of D5 Atp-Adp Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:12.7 occ:1.00 O2B D:ATP1001 2.0 27.1 1.0 OG D:SER510 2.3 23.2 1.0 PB D:ATP1001 3.2 25.4 1.0 O3B D:ATP1001 3.3 33.1 1.0 O3G D:ATP1001 3.4 36.4 1.0 CB D:SER510 3.5 20.3 1.0 PG D:ATP1001 3.9 40.4 1.0 O1B D:ATP1001 4.1 22.3 1.0 NH2 E:ARG620 4.2 41.9 1.0 O3A D:ATP1001 4.2 25.6 1.0 OD2 D:ASP603 4.3 23.6 1.0 O1G D:ATP1001 4.4 27.9 1.0 N D:SER510 4.4 11.0 1.0 CA D:SER510 4.5 10.5 1.0 NZ E:LYS575 4.5 49.4 1.0 OE2 E:GLU579 4.5 47.6 1.0 O1A D:ATP1001 4.6 27.7 1.0

Magnesium binding site 2 out of 5 in the Cryo-Em Structure of D5 Atp-Adp Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of D5 Atp-Adp Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:22.5 occ:1.00 OG C:SER510 2.0 22.6 1.0 O2G C:ATP1001 2.7 34.0 1.0 O2B C:ATP1001 3.1 23.4 1.0 CB C:SER510 3.3 13.0 1.0 O3B C:ATP1001 3.5 23.2 1.0 O3A C:ATP1001 3.5 22.5 1.0 PB C:ATP1001 3.7 8.6 1.0 PG C:ATP1001 3.8 38.3 1.0 OD1 C:ASP603 4.2 24.0 1.0 NH2 D:ARG620 4.2 27.4 1.0 N C:SER510 4.3 6.8 1.0 CA C:SER510 4.3 7.2 1.0 O3G C:ATP1001 4.4 28.7 1.0 PA C:ATP1001 4.9 34.4 1.0 O2A C:ATP1001 4.9 33.1 1.0 O1G C:ATP1001 5.0 25.8 1.0

Magnesium binding site 3 out of 5 in the Cryo-Em Structure of D5 Atp-Adp Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of D5 Atp-Adp Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:36.2 occ:1.00 O2B A:ATP1001 2.0 51.8 1.0 OG A:SER510 2.5 40.6 1.0 O1G A:ATP1001 3.0 61.4 1.0 PB A:ATP1001 3.4 45.5 1.0 OD2 A:ASP603 3.6 71.1 1.0 CB A:SER510 3.6 40.0 1.0 O3B A:ATP1001 3.7 56.3 1.0 PG A:ATP1001 3.9 61.9 1.0 O1B A:ATP1001 4.3 49.8 1.0 O3A A:ATP1001 4.3 54.2 1.0 N A:SER510 4.4 43.1 1.0 NH2 B:ARG620 4.5 50.0 1.0 CA A:SER510 4.5 41.7 1.0 CG A:ASP603 4.5 69.7 1.0 O2G A:ATP1001 4.7 57.0 1.0 OD1 A:ASP603 4.7 68.1 1.0 OG A:SER556 4.9 75.0 1.0

Magnesium binding site 4 out of 5 in the Cryo-Em Structure of D5 Atp-Adp Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of D5 Atp-Adp Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1002 b:48.4 occ:1.00 OG E:SER510 2.1 54.8 1.0 O1G E:ATP1001 2.4 73.3 1.0 CB E:SER510 3.4 52.8 1.0 O2B E:ATP1001 3.4 75.2 1.0 PG E:ATP1001 3.6 75.4 1.0 O2G E:ATP1001 4.0 73.9 1.0 OD2 E:ASP603 4.0 66.1 1.0 CA E:SER510 4.3 50.1 1.0 O3B E:ATP1001 4.3 72.1 1.0 O1A E:ATP1001 4.4 72.9 1.0 N E:SER510 4.4 45.8 1.0 PB E:ATP1001 4.5 73.2 1.0 OG E:SER556 4.7 75.4 1.0 CG E:ASP603 4.8 66.5 1.0 O3G E:ATP1001 4.9 74.3 1.0 OD1 E:ASP603 4.9 66.6 1.0 NH2 F:ARG620 4.9 85.5 1.0

Magnesium binding site 5 out of 5 in the Cryo-Em Structure of D5 Atp-Adp Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of D5 Atp-Adp Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:30.4 occ:1.00 O2B B:ATP1001 2.0 29.9 1.0 OG B:SER510 2.2 23.5 1.0 O2G B:ATP1001 2.4 37.9 1.0 CB B:SER510 3.3 19.1 1.0 PB B:ATP1001 3.3 15.2 1.0 O3B B:ATP1001 3.5 29.0 1.0 PG B:ATP1001 3.5 47.6 1.0 NH2 C:ARG620 4.2 26.4 1.0 O1A B:ATP1001 4.2 39.0 1.0 O3A B:ATP1001 4.3 27.2 1.0 O1B B:ATP1001 4.3 35.5 1.0 N B:SER510 4.3 19.5 1.0 CA B:SER510 4.3 16.5 1.0 O1G B:ATP1001 4.4 39.0 1.0 OD2 B:ASP603 4.6 33.4 1.0 O3G B:ATP1001 4.6 39.9 1.0 PA B:ATP1001 4.9 33.6 1.0

Y.N.Li, J.Zhu, Y.Y.Guo, R.H.Yan. Structural Insight Into the Assembly and Working Mechanism of Helicase-Primase D5 From Mpox Virus Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-01142-0