Magnesium in PDB 8hwg: D5 Atprs-Adp-Ssdna Form

The binding sites of Magnesium atom in the D5 Atprs-Adp-Ssdna Form (pdb code 8hwg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the D5 Atprs-Adp-Ssdna Form, PDB code: 8hwg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the D5 Atprs-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 D5 Atprs-Adp-Ssdna Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:47.7 occ:1.00 OG C:SER510 1.8 50.6 1.0 S1G C:AGS1001 2.2 70.0 1.0 O2B C:AGS1001 2.7 53.1 1.0 CB C:SER510 3.2 43.1 1.0 PG C:AGS1001 3.8 59.5 1.0 OE1 D:GLU579 4.0 44.1 1.0 O2A C:AGS1001 4.0 52.0 1.0 OE1 C:GLU557 4.1 55.4 1.0 PB C:AGS1001 4.1 13.3 1.0 OD1 C:ASP603 4.1 43.2 1.0 CA C:SER510 4.2 30.8 1.0 OE2 D:GLU579 4.2 41.4 1.0 N C:SER510 4.3 34.1 1.0 O2G C:AGS1001 4.3 52.1 1.0 O3B C:AGS1001 4.4 54.1 1.0 CD D:GLU579 4.5 43.2 1.0 CD C:GLU557 4.5 59.0 1.0 O1B C:AGS1001 4.8 37.8 1.0 OE2 C:GLU557 4.9 55.5 1.0 OG C:SER556 5.0 47.8 1.0 O3G C:AGS1001 5.0 48.9 1.0

Magnesium binding site 2 out of 6 in the D5 Atprs-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 D5 Atprs-Adp-Ssdna Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:25.9 occ:1.00 O3G B:AGS1001 2.0 51.3 1.0 OG B:SER510 2.1 43.8 1.0 O2B B:AGS1001 2.5 44.9 1.0 PG B:AGS1001 3.4 50.8 1.0 CB B:SER510 3.5 30.8 1.0 OE2 B:GLU557 3.7 58.8 1.0 PB B:AGS1001 3.8 19.4 1.0 O3B B:AGS1001 4.1 40.5 1.0 S1G B:AGS1001 4.2 48.3 1.0 OE2 C:GLU579 4.2 43.9 1.0 O1B B:AGS1001 4.4 26.3 1.0 OE1 C:GLU579 4.4 41.5 1.0 N B:SER510 4.4 21.9 1.0 CA B:SER510 4.5 17.2 1.0 O2G B:AGS1001 4.5 37.6 1.0 O2A B:AGS1001 4.5 45.0 1.0 NH2 C:ARG620 4.6 28.3 1.0 CD B:GLU557 4.6 58.1 1.0 CD C:GLU579 4.6 42.2 1.0 OE1 B:GLU557 4.7 58.3 1.0 O3A B:AGS1001 5.0 39.7 1.0

Magnesium binding site 3 out of 6 in the D5 Atprs-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 D5 Atprs-Adp-Ssdna Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:55.8 occ:1.00 O3G D:AGS1001 2.0 53.1 1.0 O2B D:AGS1001 2.0 53.1 1.0 OG D:SER510 2.1 40.9 1.0 CB D:SER510 3.4 29.7 1.0 PG D:AGS1001 3.4 60.9 1.0 PB D:AGS1001 3.4 46.3 1.0 O3A D:AGS1001 3.9 47.0 1.0 O3B D:AGS1001 4.0 49.4 1.0 OD2 D:ASP603 4.3 54.0 1.0 S1G D:AGS1001 4.3 52.4 1.0 N D:SER510 4.4 25.1 1.0 CA D:SER510 4.4 21.1 1.0 O1B D:AGS1001 4.5 37.0 1.0 O2G D:AGS1001 4.5 46.5 1.0 OE2 E:GLU579 4.7 62.6 1.0 NH2 E:ARG620 4.7 61.8 1.0 OE2 D:GLU557 4.8 69.7 1.0 OE1 E:GLU579 4.8 62.7 1.0 O2A D:AGS1001 4.9 49.2 1.0

Magnesium binding site 4 out of 6 in the D5 Atprs-Adp-Ssdna Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of D5 Atprs-Adp-Ssdna Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:37.7 occ:1.00 OG A:SER510 2.0 42.7 1.0 O3G A:AGS1001 2.0 55.1 1.0 O2B A:AGS1001 2.6 49.4 1.0 CB A:SER510 3.3 37.0 1.0 PG A:AGS1001 3.6 56.5 1.0 PB A:AGS1001 3.8 44.3 1.0 O3A A:AGS1001 4.1 52.9 1.0 O3B A:AGS1001 4.2 53.8 1.0 NH2 B:ARG620 4.2 38.1 1.0 OE2 B:GLU579 4.2 47.0 1.0 O2G A:AGS1001 4.4 46.7 1.0 OE2 A:GLU557 4.4 61.1 1.0 CA A:SER510 4.4 28.3 1.0 N A:SER510 4.5 36.7 1.0 OE1 B:GLU579 4.5 54.8 1.0 O2A A:AGS1001 4.6 50.0 1.0 CD B:GLU579 4.7 52.8 1.0 S1G A:AGS1001 4.7 57.5 1.0

Magnesium binding site 5 out of 6 in the D5 Atprs-Adp-Ssdna Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of D5 Atprs-Adp-Ssdna Form within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1002 b:87.1 occ:1.00 O2B F:ADP1001 2.1 118.7 1.0 O3A F:ADP1001 2.1 118.8 1.0 PB F:ADP1001 2.7 123.1 1.0 PA F:ADP1001 3.6 121.7 1.0 O1B F:ADP1001 3.7 116.2 1.0 CB F:SER510 3.7 106.6 1.0 O3B F:ADP1001 3.7 118.1 1.0 OG F:SER510 3.9 105.9 1.0 O5' F:ADP1001 4.0 117.5 1.0 O2A F:ADP1001 4.1 116.6 1.0 O1A F:ADP1001 4.6 116.7 1.0 NH1 F:ARG514 4.8 104.2 1.0 NH2 A:ARG619 4.9 92.6 1.0

Magnesium binding site 6 out of 6 in the D5 Atprs-Adp-Ssdna Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of D5 Atprs-Adp-Ssdna Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1002 b:76.2 occ:1.00 OG E:SER510 3.0 68.8 1.0 CB E:SER510 4.0 64.8 1.0 O1B E:ADP1001 4.5 84.4 1.0 OG E:SER556 4.6 85.2 1.0 OE1 E:GLU557 4.8 98.7 1.0 O2A E:ADP1001 4.8 79.9 1.0 O3B E:ADP1001 4.9 80.0 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