Magnesium in PDB 8k8u: F8-A22-E4 Complex of Mpxv in Complex with Dna and Dctp

The binding sites of Magnesium atom in the F8-A22-E4 Complex of Mpxv in Complex with Dna and Dctp (pdb code 8k8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the F8-A22-E4 Complex of Mpxv in Complex with Dna and Dctp, PDB code: 8k8u:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the F8-A22-E4 Complex of Mpxv in Complex with Dna and Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of F8-A22-E4 Complex of Mpxv in Complex with Dna and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:25.8 occ:1.00 OD2 A:ASP753 1.9 40.8 1.0 O A:TYR550 2.0 43.0 1.0 OD1 A:ASP549 2.0 53.0 1.0 O1B A:CTP1104 2.3 27.2 1.0 O3G A:CTP1104 2.9 35.7 1.0 CG A:ASP753 2.9 46.0 1.0 CG A:ASP549 3.0 52.3 1.0 C A:TYR550 3.2 29.5 1.0 O1A A:CTP1104 3.2 29.3 1.0 OD2 A:ASP549 3.4 45.0 1.0 OD1 A:ASP753 3.5 50.7 1.0 PB A:CTP1104 3.7 30.8 1.0 N A:TYR550 3.8 29.2 1.0 CA A:TYR550 3.9 21.2 1.0 MG A:MG1102 3.9 54.6 1.0 PG A:CTP1104 4.0 38.4 1.0 CB A:ASP753 4.0 35.6 1.0 O3B A:CTP1104 4.2 28.5 1.0 CB A:TYR550 4.2 29.1 1.0 N A:ASN551 4.3 31.2 1.0 N A:SER552 4.3 40.1 1.0 C A:ASP549 4.3 34.6 1.0 C5' A:CTP1104 4.3 39.0 1.0 CB A:ASP549 4.3 50.5 1.0 PA A:CTP1104 4.3 23.5 1.0 O1G A:CTP1104 4.4 40.8 1.0 O3A A:CTP1104 4.5 41.8 1.0 O A:ASP753 4.5 42.1 1.0 CA A:ASN551 4.5 29.5 1.0 MG A:MG1103 4.7 42.6 1.0 O2B A:CTP1104 4.7 36.5 1.0 O5' A:CTP1104 4.7 39.4 1.0 C A:ASN551 4.8 38.8 1.0 N A:LEU553 4.8 16.8 1.0 CA A:ASP549 4.8 33.9 1.0 O A:ASP549 4.9 43.0 1.0

Magnesium binding site 2 out of 3 in the F8-A22-E4 Complex of Mpxv in Complex with Dna and Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of F8-A22-E4 Complex of Mpxv in Complex with Dna and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:54.6 occ:1.00 OD2 A:ASP549 2.0 45.0 1.0 CG A:ASP549 3.1 52.3 1.0 OD1 A:ASP753 3.1 50.7 1.0 O1A A:CTP1104 3.2 29.3 1.0 OD1 A:ASP549 3.6 53.0 1.0 CG A:ASP753 3.9 46.0 1.0 MG A:MG1101 3.9 25.8 1.0 OD2 A:ASP753 4.0 40.8 1.0 CB A:ASP549 4.3 50.5 1.0 CB A:SER754 4.3 45.9 1.0 OG A:SER754 4.4 53.2 1.0 PA A:CTP1104 4.5 23.5 1.0 C5' E:DC25 4.6 57.2 1.0 C3' E:DC25 4.7 45.6 1.0 O5' A:CTP1104 4.8 39.4 1.0 O2A A:CTP1104 5.0 28.6 1.0

Magnesium binding site 3 out of 3 in the F8-A22-E4 Complex of Mpxv in Complex with Dna and Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of F8-A22-E4 Complex of Mpxv in Complex with Dna and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:42.6 occ:1.00 O1G A:CTP1104 2.8 40.8 1.0 O3G A:CTP1104 3.6 35.7 1.0 PG A:CTP1104 3.8 38.4 1.0 CG A:ASP549 4.0 52.3 1.0 OD2 A:ASP549 4.1 45.0 1.0 CB A:ASP549 4.2 50.5 1.0 OD1 A:ASP549 4.2 53.0 1.0 O2G A:CTP1104 4.5 40.2 1.0 MG A:MG1101 4.7 25.8 1.0 O A:TYR550 4.7 43.0 1.0

Y.Shen, Y.Li, R.Yan. Structural Basis For the Inhibition Mechanism of the Dna Polymerase Holoenzyme From Mpox Virus. Structure 2024.
ISSN: ISSN 0969-2126
PubMed: 38579705
DOI: 10.1016/J.STR.2024.03.004