Magnesium in PDB 9im1: The Cryo-Em Structure of Mpxv E5 in Complex with Ssdna in Intermediate State 1

The binding sites of Magnesium atom in the The Cryo-Em Structure of Mpxv E5 in Complex with Ssdna in Intermediate State 1 (pdb code 9im1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Cryo-Em Structure of Mpxv E5 in Complex with Ssdna in Intermediate State 1, PDB code: 9im1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the The Cryo-Em Structure of Mpxv E5 in Complex with Ssdna in Intermediate State 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Cryo-Em Structure of Mpxv E5 in Complex with Ssdna in Intermediate State 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:125.4 occ:1.00 O3G A:ATP801 2.1 114.3 1.0 OG A:SER510 2.3 91.0 1.0 O2B A:ATP801 2.7 100.2 1.0 PG A:ATP801 3.4 136.1 1.0 CB A:SER510 3.5 84.4 1.0 O3B A:ATP801 3.5 104.3 1.0 PB A:ATP801 3.7 102.1 1.0 O1A A:ATP801 3.9 103.9 1.0 OE2 B:GLU579 4.0 112.7 1.0 O2G A:ATP801 4.1 113.7 1.0 OE2 A:GLU557 4.2 121.8 1.0 N A:SER510 4.3 79.9 1.0 CA A:SER510 4.4 83.1 1.0 OE1 B:GLU579 4.4 113.5 1.0 O1G A:ATP801 4.5 110.9 1.0 O3A A:ATP801 4.6 94.2 1.0 CD B:GLU579 4.7 112.9 1.0 NH2 B:ARG620 4.7 90.6 1.0 PA A:ATP801 4.8 98.2 1.0 O1B A:ATP801 4.8 109.2 1.0 OD1 A:ASP603 5.0 107.4 1.0

Magnesium binding site 2 out of 3 in the The Cryo-Em Structure of Mpxv E5 in Complex with Ssdna in Intermediate State 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Cryo-Em Structure of Mpxv E5 in Complex with Ssdna in Intermediate State 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:126.9 occ:1.00 O2B B:ATP801 2.0 93.3 1.0 O3G B:ATP801 2.1 103.6 1.0 OG B:SER510 2.3 86.4 1.0 PG B:ATP801 2.3 134.6 1.0 O3B B:ATP801 2.3 89.3 1.0 O1G B:ATP801 2.5 103.1 1.0 PB B:ATP801 2.7 82.2 1.0 CB B:SER510 2.9 72.2 1.0 N B:SER510 3.4 68.5 1.0 O3A B:ATP801 3.6 82.3 1.0 CA B:SER510 3.8 67.2 1.0 O1A B:ATP801 3.8 82.3 1.0 O2G B:ATP801 3.8 101.4 1.0 O1B B:ATP801 3.9 89.6 1.0 PA B:ATP801 4.0 79.1 1.0 O2A B:ATP801 4.1 84.8 1.0 C B:LYS509 4.4 69.9 1.0 CB B:LYS509 4.5 66.2 1.0 N B:LYS509 4.7 66.8 1.0 CA B:LYS509 4.8 65.7 1.0 OD2 B:ASP603 5.0 110.8 1.0

Magnesium binding site 3 out of 3 in the The Cryo-Em Structure of Mpxv E5 in Complex with Ssdna in Intermediate State 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Cryo-Em Structure of Mpxv E5 in Complex with Ssdna in Intermediate State 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg802 b:122.5 occ:1.00 O2B C:ATP801 2.0 107.4 1.0 O1G C:ATP801 2.1 121.9 1.0 O3B C:ATP801 2.4 111.8 1.0 PG C:ATP801 2.4 147.3 1.0 OG C:SER510 2.6 86.4 1.0 O3G C:ATP801 2.7 119.0 1.0 PB C:ATP801 2.7 101.2 1.0 CB C:SER510 3.1 80.3 1.0 O1A C:ATP801 3.4 101.7 1.0 N C:SER510 3.5 79.5 1.0 O3A C:ATP801 3.6 98.8 1.0 CA C:SER510 3.9 77.5 1.0 O2G C:ATP801 3.9 112.6 1.0 O1B C:ATP801 3.9 100.0 1.0 PA C:ATP801 4.0 104.1 1.0 OD1 C:ASP603 4.4 114.4 1.0 NZ C:LYS509 4.5 72.8 1.0 CB C:LYS509 4.5 72.3 1.0 C C:LYS509 4.5 78.4 1.0 O2A C:ATP801 4.7 107.9 1.0 N C:LYS509 4.8 73.6 1.0 CA C:LYS509 4.9 71.0 1.0 CE C:LYS509 4.9 75.0 1.0

Y.Cheng, P.Han, Q.Peng, R.Liu, H.Liu, B.Yuan, Y.Zhao, L.Kuai, J.Qi, K.Miao, Y.Shi, G.F.Gao, H.Wang. Assembly and Breakage of Head-to-Head Double Hexamer Reveals Mpox Virus E5-Catalyzed Dna Unwinding Initiation. Nat Commun V. 16 5176 2025.
ISSN: ESSN 2041-1723
PubMed: 40467608
DOI: 10.1038/S41467-025-60539-1