Magnesium in PDB 7nyz: Cryo-Em Structure of the Mukbef-Matp-Dna Monomer (Partially Open Conformation)

The binding sites of Magnesium atom in the Cryo-Em Structure of the Mukbef-Matp-Dna Monomer (Partially Open Conformation) (pdb code 7nyz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of the Mukbef-Matp-Dna Monomer (Partially Open Conformation), PDB code: 7nyz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of the Mukbef-Matp-Dna Monomer (Partially Open Conformation)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Mukbef-Matp-Dna Monomer (Partially Open Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1501 b:111.3 occ:1.00 O3B A:ATP1502 1.8 109.9 1.0 O2B A:ATP1502 1.9 109.9 1.0 O2G A:ATP1502 1.9 109.9 1.0 PB A:ATP1502 2.3 109.9 1.0 PG A:ATP1502 2.4 109.9 1.0 HB3 A:SER41 2.4 111.8 1.0 H A:SER41 2.6 111.8 1.0 CB A:SER41 3.1 111.8 1.0 O3G A:ATP1502 3.1 109.9 1.0 HG A:SER41 3.1 111.8 1.0 OG A:SER41 3.2 111.8 1.0 O3A A:ATP1502 3.2 109.9 1.0 N A:SER41 3.4 111.8 1.0 O1A A:ATP1502 3.5 109.9 1.0 O1B A:ATP1502 3.5 109.9 1.0 O1G A:ATP1502 3.6 109.9 1.0 HE2 A:LYS40 3.8 114.3 1.0 PA A:ATP1502 3.8 109.9 1.0 CA A:SER41 3.9 111.8 1.0 HB2 A:SER41 3.9 111.8 1.0 H A:LYS40 3.9 114.3 1.0 HB2 A:LYS40 3.9 114.3 1.0 H B:THR1367 3.9 104.0 1.0 OG B:SER1366 4.0 109.0 1.0 HG B:SER1366 4.1 109.0 1.0 HE22 A:GLN1407 4.1 30.0 1.0 O2A A:ATP1502 4.1 109.9 1.0 HZ3 A:LYS40 4.3 114.3 1.0 HA A:SER41 4.3 111.8 1.0 HB2 B:SER1366 4.4 109.0 1.0 N A:LYS40 4.5 114.3 1.0 HA B:SER1366 4.5 109.0 1.0 HG3 A:LYS40 4.5 114.3 1.0 HZ1 A:LYS40 4.5 114.3 1.0 HE21 A:GLN1407 4.5 30.0 1.0 C A:LYS40 4.5 114.3 1.0 OD1 A:ASP1406 4.5 110.7 1.0 NE2 A:GLN1407 4.6 30.0 1.0 CE A:LYS40 4.6 114.3 1.0 NZ A:LYS40 4.6 114.3 1.0 CB A:LYS40 4.7 114.3 1.0 CB B:SER1366 4.7 109.0 1.0 HG1 B:THR1367 4.7 104.0 1.0 H A:GLY39 4.7 113.0 1.0 OG1 B:THR1367 4.7 104.0 1.0 N B:THR1367 4.8 104.0 1.0 CA A:LYS40 4.8 114.3 1.0 HB B:THR1367 4.8 104.0 1.0 H A:THR42 4.9 114.5 1.0 H A:GLY37 4.9 115.6 1.0 OD2 A:ASP1406 4.9 110.7 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of the Mukbef-Matp-Dna Monomer (Partially Open Conformation)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Mukbef-Matp-Dna Monomer (Partially Open Conformation) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1501 b:99.8 occ:1.00 O2B B:ATP1502 1.8 108.5 1.0 O2G B:ATP1502 1.9 108.5 1.0 HG B:SER41 2.0 106.6 1.0 OG B:SER41 2.1 106.6 1.0 PG B:ATP1502 2.5 108.5 1.0 O3B B:ATP1502 2.6 108.5 1.0 O3G B:ATP1502 2.7 108.5 1.0 PB B:ATP1502 2.8 108.5 1.0 H B:SER41 3.2 106.6 1.0 CB B:SER41 3.4 106.6 1.0 HB2 B:SER41 3.6 106.6 1.0 H A:THR1367 3.6 108.8 1.0 HB2 A:SER1366 3.7 111.0 1.0 HE2 B:LYS40 3.7 112.2 1.0 HE21 B:GLN1407 3.8 30.0 1.0 O1B B:ATP1502 3.8 108.5 1.0 HE22 B:GLN1407 3.8 30.0 1.0 O3A B:ATP1502 3.8 108.5 1.0 N B:SER41 3.9 106.6 1.0 OD2 B:ASP1406 3.9 106.9 1.0 O1G B:ATP1502 4.0 108.5 1.0 HB2 B:LYS40 4.0 112.2 1.0 HB3 B:SER41 4.0 106.6 1.0 O1A B:ATP1502 4.0 108.5 1.0 NE2 B:GLN1407 4.1 30.0 1.0 OD1 B:ASP1406 4.2 106.9 1.0 HB A:THR1367 4.2 108.8 1.0 CA B:SER41 4.2 106.6 1.0 HG1 A:THR1367 4.4 108.8 1.0 OG1 A:THR1367 4.4 108.8 1.0 CG B:ASP1406 4.5 106.9 1.0 N A:THR1367 4.5 108.8 1.0 PA B:ATP1502 4.5 108.5 1.0 CB A:SER1366 4.5 111.0 1.0 HA B:SER41 4.6 106.6 1.0 HA A:SER1366 4.6 111.0 1.0 HB3 A:SER1366 4.7 111.0 1.0 CE B:LYS40 4.7 112.2 1.0 H B:LYS40 4.7 112.2 1.0 CB A:THR1367 4.8 108.8 1.0 CB B:LYS40 4.9 112.2 1.0 H B:GLY37 4.9 112.1 1.0 HZ1 B:LYS40 5.0 112.2 1.0 HG3 B:LYS40 5.0 112.2 1.0

F.Buermann, L.F.H.Funke, J.W.Chin, J.Lowe. Dna Entrapment Revealed By the Structure of Bacterial Condensin Mukbef Biorxiv 2021.
DOI: 10.1101/2021.06.29.450292