Magnesium in PDB 9cdf: Structure of MORC2 Pd Mutant Binding to Amp-Pnp

The structure of Structure of MORC2 Pd Mutant Binding to Amp-Pnp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Structure of MORC2 Pd Mutant Binding to Amp-Pnp (pdb code 9cdf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of MORC2 Pd Mutant Binding to Amp-Pnp, PDB code: 9cdf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of MORC2 Pd Mutant Binding to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of MORC2 Pd Mutant Binding to Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:74.0 occ:1.00 O3G A:ANP1102 1.9 65.2 1.0 HD21 A:ASN39 2.4 64.1 1.0 HD22 A:ASN39 2.6 64.1 1.0 HG22 A:ILE97 2.7 68.1 1.0 HB3 A:ASP38 2.7 65.6 1.0 ND2 A:ASN39 2.8 64.1 1.0 HB2 A:ASP38 2.8 65.6 1.0 HB A:ILE97 3.0 68.1 1.0 CB A:ASP38 3.2 65.6 1.0 HA2 A:GLY98 3.3 68.6 1.0 OD2 A:ASP42 3.4 69.6 1.0 CG2 A:ILE97 3.4 68.1 1.0 PG A:ANP1102 3.5 65.2 1.0 N A:GLY98 3.5 68.6 1.0 HZ2 A:LYS427 3.5 63.2 1.0 H A:GLY98 3.5 68.6 1.0 O1B A:ANP1102 3.6 65.2 1.0 HG21 A:ILE97 3.6 68.1 1.0 CB A:ILE97 3.7 68.1 1.0 HA3 A:GLY98 3.7 68.6 1.0 CA A:GLY98 3.7 68.6 1.0 OE2 A:GLU35 3.7 66.7 1.0 HZ1 A:LYS89 3.7 72.1 1.0 N A:ASN39 3.8 64.1 1.0 HA A:ASN39 3.8 64.1 1.0 C A:ASP38 3.8 65.6 1.0 H A:ASN39 3.9 64.1 1.0 C A:ILE97 3.9 68.1 1.0 CG A:ASN39 3.9 64.1 1.0 O A:GLU35 4.0 66.7 1.0 HZ3 A:LYS89 4.0 72.1 1.0 CA A:ASP38 4.2 65.6 1.0 O A:ASP38 4.2 65.6 1.0 O1G A:ANP1102 4.2 65.2 1.0 NZ A:LYS89 4.2 72.1 1.0 CA A:ASN39 4.2 64.1 1.0 HG23 A:ILE97 4.3 68.1 1.0 O1A A:ANP1102 4.3 65.2 1.0 N3B A:ANP1102 4.3 65.2 1.0 CG A:ASP38 4.3 65.6 1.0 NZ A:LYS427 4.4 63.2 1.0 O A:ILE97 4.4 68.1 1.0 O2G A:ANP1102 4.4 65.2 1.0 OD2 A:ASP38 4.4 65.6 1.0 CG A:ASP42 4.4 69.6 1.0 HZ2 A:LYS89 4.4 72.1 1.0 CA A:ILE97 4.4 68.1 1.0 HZ3 A:LYS427 4.5 63.2 1.0 HA A:GLU35 4.5 66.7 1.0 CD A:GLU35 4.5 66.7 1.0 PB A:ANP1102 4.6 65.2 1.0 HNB1 A:ANP1102 4.6 65.2 1.0 HZ1 A:LYS427 4.7 63.2 1.0 CB A:ASN39 4.7 64.1 1.0 OD1 A:ASN39 4.7 64.1 1.0 HA A:ASP38 4.8 65.6 1.0 HD2 A:LYS427 4.8 63.2 1.0 OE1 A:GLU35 4.9 66.7 1.0 CG1 A:ILE97 4.9 68.1 1.0 OD1 A:ASP42 4.9 69.6 1.0 HG13 A:ILE97 4.9 68.1 1.0 HA3 A:GLY103 5.0 63.7 1.0 C A:GLU35 5.0 66.7 1.0

Magnesium binding site 2 out of 2 in the Structure of MORC2 Pd Mutant Binding to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of MORC2 Pd Mutant Binding to Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1103 b:67.8 occ:1.00 HD22 B:ASN39 1.9 61.4 1.0 O2G B:ANP1102 1.9 61.3 1.0 ND2 B:ASN39 2.2 61.4 1.0 HD21 B:ASN39 2.2 61.4 1.0 PG B:ANP1102 2.8 61.3 1.0 O1B B:ANP1102 2.8 61.3 1.0 O3G B:ANP1102 2.9 61.3 1.0 HB2 B:ASP38 3.2 61.9 1.0 CG B:ASN39 3.3 61.4 1.0 HB3 B:ASP38 3.3 61.9 1.0 HB B:ILE97 3.5 65.7 1.0 N3B B:ANP1102 3.6 61.3 1.0 HG22 B:ILE97 3.7 65.7 1.0 CB B:ASP38 3.7 61.9 1.0 O B:GLU35 3.7 64.1 1.0 O1A B:ANP1102 3.7 61.3 1.0 H B:ASN39 3.7 61.4 1.0 HA B:ASN39 3.8 61.4 1.0 N B:ASN39 3.8 61.4 1.0 PB B:ANP1102 3.8 61.3 1.0 OD1 B:ASN39 3.8 61.4 1.0 OD2 B:ASP42 3.9 65.1 1.0 HA2 B:GLY98 4.0 67.2 1.0 CA B:ASN39 4.1 61.4 1.0 C B:ASP38 4.1 61.9 1.0 HA3 B:GLY103 4.2 62.1 1.0 O1G B:ANP1102 4.2 61.3 1.0 CB B:ASN39 4.3 61.4 1.0 CG2 B:ILE97 4.3 65.7 1.0 CB B:ILE97 4.3 65.7 1.0 HG21 B:ILE97 4.3 65.7 1.0 HA B:GLU35 4.4 64.1 1.0 HNB1 B:ANP1102 4.4 61.3 1.0 HZ2 B:LYS427 4.5 62.0 1.0 O B:ILE97 4.6 65.7 1.0 C B:ILE97 4.6 65.7 1.0 O3A B:ANP1102 4.6 61.3 1.0 CA B:ASP38 4.6 61.9 1.0 HB3 B:ASN39 4.6 61.4 1.0 O B:ASP38 4.6 61.9 1.0 OE2 B:GLU35 4.7 64.1 1.0 C B:GLU35 4.7 64.1 1.0 CA B:GLY98 4.7 67.2 1.0 HB3 B:GLU35 4.7 64.1 1.0 N B:GLY98 4.7 67.2 1.0 PA B:ANP1102 4.7 61.3 1.0 OD2 B:ASP38 4.8 61.9 1.0 HA3 B:GLY98 4.8 67.2 1.0 CG B:ASP38 4.8 61.9 1.0 HD2 B:LYS427 4.8 62.0 1.0 CG B:ASP42 4.9 65.1 1.0 CD B:GLU35 5.0 64.1 1.0 CA B:GLU35 5.0 64.1 1.0

W.Tan, J.Park, H.Venugopal, J.Lou, P.S.Dias, P.L.Baldoni, K.W.Moon, T.A.Dite, C.R.Keenan, A.D.Gurzau, J.Lee, T.M.Johanson, A.Leis, J.Yousef, V.Vaibhav, L.F.Dagley, C.S.Ang, L.D.Corso, C.Davidovich, S.J.Vervoort, G.K.Smyth, M.E.Blewitt, R.S.Allan, E.Hinde, S.D'arcy, J.K.Ryu, S.Shakeel. MORC2 Is A Phosphorylation-Dependent Dna Compaction Machine. Nat Commun V. 16 5606 2025.
ISSN: ESSN 2041-1723
PubMed: 40593625
DOI: 10.1038/S41467-025-60751-Z