Magnesium in PDB 8hwf: Cryo-Em Structure of D5 Adp-Ssdna Form

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

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of D5 Adp-Ssdna 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 Adp-Ssdna Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:82.7 occ:1.00 OG C:SER510 2.1 65.1 1.0 O2B C:ADP1001 2.2 83.0 1.0 CB C:SER510 3.5 58.9 1.0 OE1 D:GLU579 3.5 80.1 1.0 PB C:ADP1001 3.5 77.2 1.0 OD2 C:ASP603 3.7 78.2 1.0 OE2 C:GLU557 3.8 92.6 1.0 O3B C:ADP1001 3.9 68.6 1.0 O3A C:ADP1001 4.3 70.4 1.0 CA C:SER510 4.5 53.3 1.0 N C:SER510 4.5 47.3 1.0 CD D:GLU579 4.5 83.1 1.0 O1B C:ADP1001 4.6 62.2 1.0 CG C:ASP603 4.6 77.2 1.0 OD1 C:ASP603 4.7 75.9 1.0 CD C:GLU557 4.7 92.1 1.0 OE1 C:GLU557 4.8 93.9 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of D5 Adp-Ssdna 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 Adp-Ssdna Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:94.1 occ:1.00 O3B B:ADP1001 2.0 71.0 1.0 OG B:SER510 2.1 57.3 1.0 PB B:ADP1001 3.3 60.4 1.0 CB B:SER510 3.5 48.0 1.0 O2B B:ADP1001 3.7 56.6 1.0 OD2 B:ASP603 4.1 86.9 1.0 N B:SER510 4.1 41.6 1.0 OD1 B:ASP603 4.3 76.1 1.0 CA B:SER510 4.3 45.3 1.0 O3A B:ADP1001 4.3 50.8 1.0 O1B B:ADP1001 4.4 54.3 1.0 OE1 C:GLU579 4.4 76.4 1.0 O2A B:ADP1001 4.5 49.1 1.0 CG B:ASP603 4.6 82.7 1.0 NZ B:LYS509 4.6 47.0 1.0 NH2 C:ARG620 4.6 72.0 1.0 CD C:GLU579 4.8 83.0 1.0 OE2 C:GLU579 4.9 84.5 1.0 CB B:LYS509 5.0 29.6 1.0 PA B:ADP1001 5.0 51.9 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of D5 Adp-Ssdna 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 Adp-Ssdna Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:90.2 occ:1.00 OG A:SER510 2.1 66.1 1.0 O3B A:ADP1001 2.3 85.2 1.0 CB A:SER510 3.2 62.5 1.0 OD2 A:ASP603 3.5 88.9 1.0 OE2 B:GLU579 3.7 79.0 1.0 PB A:ADP1001 3.8 80.2 1.0 CA A:SER510 4.0 62.5 1.0 N A:SER510 4.0 60.7 1.0 O2A A:ADP1001 4.1 83.7 1.0 OE2 A:GLU557 4.3 94.8 1.0 O2B A:ADP1001 4.4 81.4 1.0 CG A:ASP603 4.5 93.4 1.0 O1B A:ADP1001 4.6 80.0 1.0 NH2 B:ARG620 4.6 81.9 1.0 CD B:GLU579 4.6 80.3 1.0 OD1 A:ASP603 4.7 98.8 1.0 O3A A:ADP1001 4.7 80.6 1.0 OE1 B:GLU579 4.7 82.3 1.0 PA A:ADP1001 4.8 79.8 1.0 CD A:GLU557 4.9 91.6 1.0 C A:LYS509 5.0 57.3 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