Magnesium in PDB 8hwb: D5 Atp-Adp-Apo-Ssdna IS2

The binding sites of Magnesium atom in the D5 Atp-Adp-Apo-Ssdna IS2 (pdb code 8hwb). 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 IS2, PDB code: 8hwb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the D5 Atp-Adp-Apo-Ssdna IS2


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 IS2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:99.9 occ:1.00 O2B A:ATP1001 2.0 98.3 1.0 OG A:SER510 2.0 96.8 1.0 O1G A:ATP1001 3.0 98.3 1.0 PB A:ATP1001 3.4 98.3 1.0 CB A:SER510 3.4 96.8 1.0 O3B A:ATP1001 3.6 98.3 1.0 OD2 A:ASP603 3.7 110.7 1.0 PG A:ATP1001 3.8 98.3 1.0 O1A A:ATP1001 4.1 98.3 1.0 N A:SER510 4.2 96.8 1.0 O3A A:ATP1001 4.3 98.3 1.0 CA A:SER510 4.3 96.8 1.0 O1B A:ATP1001 4.4 98.3 1.0 O3G A:ATP1001 4.5 98.3 1.0 PA A:ATP1001 4.7 98.3 1.0 CG A:ASP603 4.7 110.7 1.0 NH2 B:ARG620 4.8 78.7 1.0 OD1 A:ASP603 4.9 110.7 1.0

Magnesium binding site 2 out of 4 in the D5 Atp-Adp-Apo-Ssdna IS2


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 IS2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:70.0 occ:1.00 O2B B:ATP1001 2.0 66.2 1.0 O3G B:ATP1001 2.2 66.2 1.0 OG B:SER510 2.2 61.2 1.0 PG B:ATP1001 3.1 66.2 1.0 PB B:ATP1001 3.1 66.2 1.0 O3B B:ATP1001 3.1 66.2 1.0 CB B:SER510 3.6 61.2 1.0 O1G B:ATP1001 3.6 66.2 1.0 O1A B:ATP1001 4.1 66.2 1.0 O3A B:ATP1001 4.1 66.2 1.0 OE2 B:GLU557 4.1 81.5 1.0 O1B B:ATP1001 4.2 66.2 1.0 N B:SER510 4.3 61.2 1.0 NH2 C:ARG620 4.4 63.5 1.0 O2G B:ATP1001 4.4 66.2 1.0 CA B:SER510 4.5 61.2 1.0 PA B:ATP1001 4.7 66.2 1.0

Magnesium binding site 3 out of 4 in the D5 Atp-Adp-Apo-Ssdna IS2


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 IS2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:63.7 occ:1.00 O2B C:ATP1001 1.9 68.6 1.0 O3G C:ATP1001 2.0 68.6 1.0 PB C:ATP1001 2.8 68.6 1.0 O3B C:ATP1001 2.9 68.6 1.0 PG C:ATP1001 2.9 68.6 1.0 OG C:SER510 3.2 57.5 1.0 O1G C:ATP1001 3.5 68.6 1.0 O1B C:ATP1001 3.5 68.6 1.0 NZ D:LYS575 4.0 67.3 1.0 NH2 D:ARG620 4.1 65.7 1.0 O3A C:ATP1001 4.1 68.6 1.0 O2G C:ATP1001 4.2 68.6 1.0 OD2 C:ASP603 4.5 67.9 1.0 CB C:SER510 4.6 57.5 1.0 CE C:LYS509 4.9 57.3 1.0

Magnesium binding site 4 out of 4 in the D5 Atp-Adp-Apo-Ssdna IS2


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 IS2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:86.1 occ:1.00 O3A D:ATP1001 1.9 80.3 1.0 O1A D:ATP1001 2.2 80.3 1.0 PA D:ATP1001 2.3 80.3 1.0 O2B D:ATP1001 2.4 80.3 1.0 PB D:ATP1001 2.6 80.3 1.0 CB D:SER510 2.9 68.5 1.0 O5' D:ATP1001 3.0 80.3 1.0 OG D:SER510 3.1 68.5 1.0 O1B D:ATP1001 3.5 80.3 1.0 O2A D:ATP1001 3.7 80.3 1.0 O3B D:ATP1001 3.8 80.3 1.0 CA D:SER510 4.0 68.5 1.0 N D:SER510 4.0 68.5 1.0 C5' D:ATP1001 4.3 80.3 1.0 N D:THR511 4.4 65.9 1.0 C D:SER510 4.5 68.5 1.0 OG1 D:THR511 4.7 65.9 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