Magnesium in PDB 6qem: E. Coli Dnabc Complex Bound to Ssdna

All present enzymatic activity of E. Coli Dnabc Complex Bound to Ssdna:
3.6.4.12;

The structure of E. Coli Dnabc Complex Bound to Ssdna also contains other interesting chemical elements:

Fluorine

(F)

15 atoms

The binding sites of Magnesium atom in the E. Coli Dnabc Complex Bound to Ssdna (pdb code 6qem). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the E. Coli Dnabc Complex Bound to Ssdna, PDB code: 6qem:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the E. Coli Dnabc Complex Bound to Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Dnabc Complex Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:10.6 occ:1.00 OG1 A:THR238 2.0 25.0 1.0 F2 A:08T1001 2.3 37.9 1.0 O2B A:08T1001 2.3 37.9 1.0 OE1 A:GLU262 2.8 22.0 1.0 OD1 A:ASP343 3.3 20.5 1.0 OD2 A:ASP343 3.3 20.5 1.0 CB A:THR238 3.3 25.0 1.0 HE3 A:MET263 3.4 19.6 1.0 HG21 A:THR238 3.5 25.0 1.0 BE A:08T1001 3.5 37.9 1.0 HB A:THR238 3.6 25.0 1.0 PB A:08T1001 3.7 37.9 1.0 CD A:GLU262 3.7 22.0 1.0 CG A:ASP343 3.7 20.5 1.0 O3B A:08T1001 3.9 37.9 1.0 CG2 A:THR238 3.9 25.0 1.0 OE2 A:GLU262 4.0 22.0 1.0 HE2 A:LYS237 4.1 37.9 1.0 H A:THR238 4.1 25.0 1.0 CE A:MET263 4.2 19.6 1.0 HE1 A:MET263 4.2 19.6 1.0 HD3 F:ARG442 4.2 21.7 1.0 F3 A:08T1001 4.3 37.9 1.0 HG23 A:THR238 4.3 25.0 1.0 HG3 A:LYS237 4.3 37.9 1.0 F1 A:08T1001 4.3 37.9 1.0 HE2 A:MET263 4.3 19.6 1.0 HB3 A:GLU262 4.4 22.0 1.0 HD23 A:LEU382 4.4 37.9 1.0 CA A:THR238 4.4 25.0 1.0 HB2 A:TYR344 4.5 20.7 1.0 HZ3 A:LYS237 4.6 37.9 1.0 N A:THR238 4.6 25.0 1.0 HD22 A:LEU382 4.6 37.9 1.0 HA A:THR238 4.6 25.0 1.0 O3A A:08T1001 4.6 37.9 1.0 O1B A:08T1001 4.7 37.9 1.0 HD2 F:ARG442 4.7 21.7 1.0 HG22 A:THR238 4.8 25.0 1.0 CG A:GLU262 4.8 22.0 1.0 HZ1 A:LYS237 4.8 37.9 1.0 CD2 A:LEU382 4.9 37.9 1.0 O1A A:08T1001 4.9 37.9 1.0 CE A:LYS237 4.9 37.9 1.0 HB2 A:GLU262 4.9 22.0 1.0 CD F:ARG442 4.9 21.7 1.0 CB A:GLU262 4.9 22.0 1.0 NZ A:LYS237 5.0 37.9 1.0

Magnesium binding site 2 out of 5 in the E. Coli Dnabc Complex Bound to Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Dnabc Complex Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:5.8 occ:1.00 OG1 B:THR238 2.0 26.8 1.0 F2 B:08T1001 2.2 37.9 1.0 O2B B:08T1001 2.3 37.9 1.0 OE1 B:GLU262 2.5 23.3 1.0 HG21 B:THR238 3.1 26.8 1.0 CB B:THR238 3.2 26.8 1.0 HB B:THR238 3.5 26.8 1.0 BE B:08T1001 3.5 37.9 1.0 CD B:GLU262 3.5 23.3 1.0 PB B:08T1001 3.6 37.9 1.0 OD1 B:ASP343 3.7 26.9 1.0 CG2 B:THR238 3.7 26.8 1.0 OD2 B:ASP343 3.8 26.9 1.0 O3B B:08T1001 3.9 37.9 1.0 HD3 A:ARG442 3.9 37.9 1.0 OE2 B:GLU262 4.0 23.3 1.0 HG23 B:THR238 4.1 26.8 1.0 CG B:ASP343 4.1 26.9 1.0 F1 B:08T1001 4.2 37.9 1.0 HE2 B:LYS237 4.2 37.9 1.0 F3 B:08T1001 4.3 37.9 1.0 HE2 B:MET263 4.3 20.9 1.0 H B:THR238 4.3 26.8 1.0 O3A B:08T1001 4.4 37.9 1.0 HB3 B:GLU262 4.4 23.3 1.0 CA B:THR238 4.4 26.8 1.0 HG22 B:THR238 4.4 26.8 1.0 HH21 A:ARG442 4.5 37.9 1.0 HG3 B:LYS237 4.6 37.9 1.0 HA B:THR238 4.6 26.8 1.0 HB2 B:TYR344 4.7 21.7 1.0 O1A B:08T1001 4.7 37.9 1.0 O1B B:08T1001 4.7 37.9 1.0 N B:THR238 4.7 26.8 1.0 CG B:GLU262 4.7 23.3 1.0 HZ3 B:LYS237 4.8 37.9 1.0 NH2 A:ARG442 4.8 37.9 1.0 HB2 B:GLU262 4.8 23.3 1.0 CD A:ARG442 4.9 37.9 1.0 HZ1 B:LYS237 4.9 37.9 1.0 CB B:GLU262 4.9 23.3 1.0 HG2 B:GLU262 4.9 23.3 1.0 HD22 B:LEU382 5.0 37.9 1.0

Magnesium binding site 3 out of 5 in the E. Coli Dnabc Complex Bound to Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Dnabc Complex Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:37.9 occ:1.00 OG1 C:THR238 2.0 26.2 1.0 O2B C:08T1001 2.0 37.9 1.0 F2 C:08T1001 2.2 37.9 1.0 OE1 C:GLU262 3.1 26.2 1.0 CB C:THR238 3.2 26.2 1.0 PB C:08T1001 3.4 37.9 1.0 HB C:THR238 3.4 26.2 1.0 BE C:08T1001 3.4 37.9 1.0 HE3 C:MET263 3.5 21.9 1.0 HG21 C:THR238 3.5 26.2 1.0 HD3 B:ARG442 3.5 37.9 1.0 O3B C:08T1001 3.7 37.9 1.0 CD C:GLU262 3.8 26.2 1.0 OD2 C:ASP343 3.9 23.4 1.0 H C:THR238 3.9 26.2 1.0 CG2 C:THR238 3.9 26.2 1.0 OD1 C:ASP343 3.9 23.4 1.0 OE2 C:GLU262 4.0 26.2 1.0 HE1 C:MET263 4.1 21.9 1.0 CE C:MET263 4.1 21.9 1.0 O3A C:08T1001 4.1 37.9 1.0 F1 C:08T1001 4.1 37.9 1.0 HH21 B:ARG442 4.2 37.9 1.0 HE2 C:MET263 4.3 21.9 1.0 HG23 C:THR238 4.3 26.2 1.0 CG C:ASP343 4.3 23.4 1.0 O1A C:08T1001 4.3 37.9 1.0 F3 C:08T1001 4.3 37.9 1.0 CA C:THR238 4.3 26.2 1.0 CD B:ARG442 4.4 37.9 1.0 HG3 C:LYS237 4.5 37.9 1.0 HE2 C:LYS237 4.5 37.9 1.0 O1B C:08T1001 4.5 37.9 1.0 N C:THR238 4.5 26.2 1.0 HZ3 C:LYS237 4.5 37.9 1.0 HD2 B:ARG442 4.5 37.9 1.0 HA C:THR238 4.6 26.2 1.0 HB3 C:GLU262 4.6 26.2 1.0 HG22 C:THR238 4.7 26.2 1.0 PA C:08T1001 4.7 37.9 1.0 HD23 C:LEU382 4.7 28.6 1.0 NH2 B:ARG442 4.8 37.9 1.0 HG2 B:ARG442 4.9 37.9 1.0 CG C:GLU262 4.9 26.2 1.0 HZ1 C:LYS237 4.9 37.9 1.0 HG2 C:GLU262 5.0 26.2 1.0

Magnesium binding site 4 out of 5 in the E. Coli Dnabc Complex Bound to Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Coli Dnabc Complex Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:9.0 occ:1.00 O2B D:08T1001 1.9 37.9 1.0 OG1 D:THR238 2.0 24.2 1.0 F2 D:08T1001 2.3 37.9 1.0 OE1 D:GLU262 3.1 21.3 1.0 PB D:08T1001 3.2 37.9 1.0 CB D:THR238 3.2 24.2 1.0 OD1 D:ASP343 3.3 24.2 1.0 HB D:THR238 3.3 24.2 1.0 H D:THR238 3.4 24.2 1.0 BE D:08T1001 3.5 37.9 1.0 OD2 D:ASP343 3.6 24.2 1.0 O3B D:08T1001 3.6 37.9 1.0 HE2 D:LYS237 3.8 37.9 1.0 HB2 D:LYS237 3.8 37.9 1.0 CG D:ASP343 3.8 24.2 1.0 HG21 D:THR238 3.9 24.2 1.0 N D:THR238 4.0 24.2 1.0 O1B D:08T1001 4.1 37.9 1.0 HD23 D:LEU382 4.2 37.9 1.0 CA D:THR238 4.2 24.2 1.0 CG2 D:THR238 4.2 24.2 1.0 CD D:GLU262 4.2 21.3 1.0 O3A D:08T1001 4.2 37.9 1.0 F3 D:08T1001 4.3 37.9 1.0 F1 D:08T1001 4.4 37.9 1.0 HA D:THR238 4.4 24.2 1.0 HD3 C:ARG442 4.5 37.9 1.0 HD22 D:LEU382 4.5 37.9 1.0 O1A D:08T1001 4.5 37.9 1.0 HE2 D:MET263 4.5 24.3 1.0 HD21 D:LEU382 4.6 37.9 1.0 OE2 D:GLU262 4.6 21.3 1.0 CD2 D:LEU382 4.6 37.9 1.0 HG23 D:THR238 4.6 24.2 1.0 CB D:LYS237 4.7 37.9 1.0 HB2 D:TYR344 4.7 20.9 1.0 CE D:LYS237 4.8 37.9 1.0 PA D:08T1001 4.8 37.9 1.0 HG22 D:THR238 4.9 24.2 1.0 HB3 D:LYS237 4.9 37.9 1.0 O2A D:08T1001 5.0 37.9 1.0

Magnesium binding site 5 out of 5 in the E. Coli Dnabc Complex Bound to Ssdna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of E. Coli Dnabc Complex Bound to Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1002 b:21.6 occ:1.00 HG1 E:THR238 1.7 28.9 1.0 O2B E:08T1001 2.0 26.6 1.0 F2 E:08T1001 2.0 26.6 1.0 OE1 E:GLU262 2.3 42.1 1.0 OG1 E:THR238 2.4 28.9 1.0 CD E:GLU262 3.2 42.1 1.0 BE E:08T1001 3.2 26.6 1.0 PB E:08T1001 3.3 26.6 1.0 OE2 E:GLU262 3.5 42.1 1.0 HG21 E:THR238 3.5 28.9 1.0 CB E:THR238 3.6 28.9 1.0 O3B E:08T1001 3.6 26.6 1.0 HB E:THR238 3.7 28.9 1.0 OD1 E:ASP343 3.8 46.8 1.0 HD3 D:ARG442 3.9 22.2 1.0 F1 E:08T1001 3.9 26.6 1.0 HD2 D:ARG442 4.0 22.2 1.0 CG2 E:THR238 4.0 28.9 1.0 O3A E:08T1001 4.1 26.6 1.0 F3 E:08T1001 4.1 26.6 1.0 O1B E:08T1001 4.4 26.6 1.0 CD D:ARG442 4.4 22.2 1.0 HG23 E:THR238 4.4 28.9 1.0 OD2 E:ASP343 4.5 46.8 1.0 O1A E:08T1001 4.5 26.6 1.0 H E:THR238 4.5 28.9 1.0 HE2 E:LYS237 4.5 31.3 1.0 HZ3 E:LYS237 4.5 31.3 1.0 CG E:ASP343 4.6 46.8 1.0 HB3 E:GLU262 4.6 42.1 1.0 CG E:GLU262 4.6 42.1 1.0 HB2 E:TYR344 4.6 43.7 1.0 HE2 E:MET263 4.7 39.5 1.0 HZ1 E:LYS237 4.7 31.3 1.0 HB2 E:GLU262 4.8 42.1 1.0 HG22 E:THR238 4.8 28.9 1.0 PA E:08T1001 4.8 26.6 1.0 CA E:THR238 4.8 28.9 1.0 HH21 D:ARG442 4.8 22.2 1.0 HD22 E:LEU382 4.8 35.7 1.0 HG3 E:LYS237 4.9 31.3 1.0 CB E:GLU262 4.9 42.1 1.0 HG2 E:GLU262 5.0 42.1 1.0 NZ E:LYS237 5.0 31.3 1.0

E.Arias-Palomo, N.Puri, V.L.O'shea Murray, Q.Yan, J.M.Berger. Physical Basis For the Loading of A Bacterial Replicative Helicase Onto Dna. Mol.Cell V. 74 173 2019.
ISSN: ISSN 1097-2765
PubMed: 30797687
DOI: 10.1016/J.MOLCEL.2019.01.023