Magnesium in PDB 8hwa: D5 Atp-Adp-Apo-Ssdna IS1

The binding sites of Magnesium atom in the D5 Atp-Adp-Apo-Ssdna IS1 (pdb code 8hwa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the D5 Atp-Adp-Apo-Ssdna IS1, PDB code: 8hwa:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the D5 Atp-Adp-Apo-Ssdna IS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of D5 Atp-Adp-Apo-Ssdna IS1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:72.2 occ:1.00 O2B A:ATP1001 2.0 78.2 1.0 OG A:SER510 2.0 66.1 1.0 O1G A:ATP1001 2.9 78.2 1.0 PB A:ATP1001 3.2 78.2 1.0 O3B A:ATP1001 3.3 78.2 1.0 CB A:SER510 3.4 66.1 1.0 PG A:ATP1001 3.6 78.2 1.0 O1A A:ATP1001 3.6 78.2 1.0 O3A A:ATP1001 3.9 78.2 1.0 O3G A:ATP1001 4.1 78.2 1.0 NH2 B:ARG620 4.1 75.0 1.0 OE2 A:GLU557 4.2 88.7 1.0 PA A:ATP1001 4.2 78.2 1.0 N A:SER510 4.3 66.1 1.0 CA A:SER510 4.4 66.1 1.0 O1B A:ATP1001 4.4 78.2 1.0 OE1 B:GLU579 4.5 71.9 1.0 O2A A:ATP1001 4.8 78.2 1.0 O2G A:ATP1001 5.0 78.2 1.0

Magnesium binding site 2 out of 4 in the D5 Atp-Adp-Apo-Ssdna IS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of D5 Atp-Adp-Apo-Ssdna IS1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:63.9 occ:1.00 OG B:SER510 2.7 56.6 1.0 O3G B:ATP1001 3.1 63.6 1.0 O2B B:ATP1001 3.3 63.6 1.0 OE2 C:GLU579 3.4 61.9 1.0 OE2 B:GLU557 3.7 73.5 1.0 PG B:ATP1001 4.0 63.6 1.0 CB B:SER510 4.1 56.6 1.0 O1G B:ATP1001 4.1 63.6 1.0 O3B B:ATP1001 4.3 63.6 1.0 PB B:ATP1001 4.4 63.6 1.0 CD B:GLU557 4.6 73.5 1.0 CD C:GLU579 4.7 61.9 1.0 OE1 B:GLU557 4.7 73.5 1.0 CA B:SER510 4.9 56.6 1.0 N B:SER510 4.9 56.6 1.0 NH2 C:ARG620 4.9 61.8 1.0

Magnesium binding site 3 out of 4 in the D5 Atp-Adp-Apo-Ssdna IS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of D5 Atp-Adp-Apo-Ssdna IS1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:61.4 occ:1.00 O2B C:ATP1001 2.0 59.5 1.0 O3G C:ATP1001 2.5 59.5 1.0 OG C:SER510 2.7 52.8 1.0 PB C:ATP1001 3.2 59.5 1.0 O3B C:ATP1001 3.4 59.5 1.0 PG C:ATP1001 3.5 59.5 1.0 OD2 C:ASP603 3.8 59.1 1.0 O1B C:ATP1001 3.9 59.5 1.0 O1G C:ATP1001 4.0 59.5 1.0 CB C:SER510 4.0 52.8 1.0 O3A C:ATP1001 4.4 59.5 1.0 NH2 D:ARG620 4.5 57.4 1.0 O2G C:ATP1001 4.8 59.5 1.0 CG C:ASP603 4.8 59.1 1.0 N C:SER510 4.8 52.8 1.0 OD1 C:ASP603 4.9 59.1 1.0 CA C:SER510 5.0 52.8 1.0

Magnesium binding site 4 out of 4 in the D5 Atp-Adp-Apo-Ssdna IS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of D5 Atp-Adp-Apo-Ssdna IS1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:70.8 occ:1.00 O3A D:ATP1001 2.0 73.3 1.0 O1A D:ATP1001 2.0 73.3 1.0 O2B D:ATP1001 2.2 73.3 1.0 PB D:ATP1001 2.4 73.3 1.0 PA D:ATP1001 2.4 73.3 1.0 CB D:SER510 2.4 63.0 1.0 OG D:SER510 2.5 63.0 1.0 O1B D:ATP1001 3.0 73.3 1.0 O5' D:ATP1001 3.4 73.3 1.0 CA D:SER510 3.5 63.0 1.0 N D:SER510 3.5 63.0 1.0 O2A D:ATP1001 3.6 73.3 1.0 O3B D:ATP1001 3.8 73.3 1.0 N D:THR511 4.1 60.1 1.0 C D:SER510 4.2 63.0 1.0 C5' D:ATP1001 4.7 73.3 1.0 OG1 D:THR511 4.7 60.1 1.0 C D:LYS509 4.8 60.0 1.0 N D:LYS509 4.9 60.0 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