Magnesium in PDB 9im2: The Cryo-Em Structure of Mpxv E5 in Complex with Ssdna in Intermediate State 3

The binding sites of Magnesium atom in the The Cryo-Em Structure of Mpxv E5 in Complex with Ssdna in Intermediate State 3 (pdb code 9im2). 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 3, PDB code: 9im2:
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 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:169.0 occ:1.00 O3B A:ATP801 2.0 155.1 1.0 O2B A:ATP801 2.0 152.8 1.0 O3G A:ATP801 2.2 155.1 1.0 OG A:SER510 2.2 135.7 1.0 PB A:ATP801 2.4 155.8 1.0 PG A:ATP801 2.6 163.2 1.0 O3A A:ATP801 2.9 147.1 1.0 O1A A:ATP801 2.9 148.0 1.0 CB A:SER510 3.1 134.8 1.0 PA A:ATP801 3.2 148.8 1.0 O2G A:ATP801 3.3 152.8 1.0 O2A A:ATP801 3.5 151.4 1.0 N A:SER510 3.6 132.5 1.0 O1B A:ATP801 3.7 154.7 1.0 O1G A:ATP801 3.9 149.2 1.0 CA A:SER510 4.0 133.6 1.0 NH2 B:ARG619 4.5 121.0 1.0 N A:LYS509 4.8 123.5 1.0 C A:LYS509 4.8 123.6 1.0 O5' A:ATP801 4.8 147.4 1.0 CB A:LYS509 4.9 121.4 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 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:114.7 occ:1.00 O3B B:ATP801 1.9 119.6 1.0 PB B:ATP801 2.3 115.8 1.0 O2B B:ATP801 2.3 119.5 1.0 PA B:ATP801 2.3 110.8 1.0 O3A B:ATP801 2.3 114.6 1.0 O1A B:ATP801 2.3 116.8 1.0 O2A B:ATP801 2.4 119.0 1.0 O3G B:ATP801 2.5 127.5 1.0 PG B:ATP801 2.8 146.9 1.0 CB B:SER510 2.9 98.2 1.0 OG B:SER510 3.1 102.3 1.0 N B:SER510 3.6 86.4 1.0 O1B B:ATP801 3.7 123.4 1.0 O2G B:ATP801 3.7 130.0 1.0 CA B:SER510 3.8 89.0 1.0 O5' B:ATP801 3.9 111.0 1.0 O1G B:ATP801 4.0 128.3 1.0 N B:LYS509 4.6 90.9 1.0 NH2 C:ARG619 4.7 112.2 1.0 N B:THR511 4.7 79.7 1.0 C B:LYS509 4.8 87.5 1.0 N B:GLY508 4.8 94.9 1.0 C5' B:ATP801 4.8 112.4 1.0 C B:SER510 4.8 91.5 1.0 C B:GLY508 4.9 105.3 1.0 CA B:GLY508 5.0 100.1 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 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg802 b:135.8 occ:1.00 O2B C:ATP801 1.9 125.1 1.0 O3B C:ATP801 2.0 135.1 1.0 O3G C:ATP801 2.0 133.4 1.0 OG C:SER510 2.3 102.7 1.0 PB C:ATP801 2.3 123.9 1.0 PG C:ATP801 2.5 152.2 1.0 O1A C:ATP801 2.7 127.0 1.0 O3A C:ATP801 2.9 118.6 1.0 CB C:SER510 3.0 92.9 1.0 PA C:ATP801 3.3 124.7 1.0 O2G C:ATP801 3.3 134.5 1.0 O1B C:ATP801 3.7 127.4 1.0 O1G C:ATP801 3.8 132.5 1.0 N C:SER510 4.0 92.0 1.0 O2A C:ATP801 4.1 126.2 1.0 CA C:SER510 4.1 87.5 1.0 O5' C:ATP801 4.6 124.8 1.0 NH1 D:ARG619 4.6 124.8 1.0 CG C:LYS509 4.6 91.7 1.0 NH2 D:ARG620 4.8 122.5 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