Magnesium in PDB 7tib: Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Open Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) and Primer-Template Dna

The binding sites of Magnesium atom in the Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Open Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) and Primer-Template Dna (pdb code 7tib). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Open Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) and Primer-Template Dna, PDB code: 7tib:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Open Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) and Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Open Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) and Primer-Template Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:37.4 occ:1.00 O1B A:AGS901 2.3 47.2 1.0 O3G A:AGS901 2.3 47.2 1.0 OG1 A:THR360 2.3 45.0 1.0 S1G A:AGS901 2.8 47.2 1.0 PG A:AGS901 3.0 47.2 1.0 OD2 A:ASP424 3.2 48.6 1.0 CB A:THR360 3.4 45.0 1.0 PB A:AGS901 3.4 47.2 1.0 OD1 A:ASP424 3.6 48.6 1.0 O3B A:AGS901 3.7 47.2 1.0 O1A A:AGS901 3.8 47.2 1.0 CG A:ASP424 3.8 48.6 1.0 O3A A:AGS901 4.1 47.2 1.0 CG2 A:THR360 4.2 45.0 1.0 PA A:AGS901 4.3 47.2 1.0 O2G A:AGS901 4.4 47.2 1.0 NH1 B:ARG129 4.4 40.6 1.0 O2A A:AGS901 4.5 47.2 1.0 N A:THR360 4.5 45.0 1.0 CA A:THR360 4.6 45.0 1.0 OE2 A:GLU425 4.6 49.5 1.0 NH2 B:ARG157 4.6 36.5 1.0 NH2 B:ARG128 4.7 36.8 1.0 O2B A:AGS901 4.7 47.2 1.0 CG2 A:ILE454 4.8 47.8 1.0

Magnesium binding site 2 out of 4 in the Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Open Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) and Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Open Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) and Primer-Template Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:24.2 occ:1.00 OG1 B:THR56 2.1 26.8 1.0 O3G B:AGS401 2.1 28.7 1.0 O1B B:AGS401 2.6 28.7 1.0 PG B:AGS401 3.1 28.7 1.0 S1G B:AGS401 3.2 28.7 1.0 CB B:THR56 3.4 26.8 1.0 PB B:AGS401 3.7 28.7 1.0 O3B B:AGS401 3.8 28.7 1.0 OE2 B:GLU115 4.0 25.7 1.0 N B:THR56 4.0 26.8 1.0 CA B:THR56 4.2 26.8 1.0 OD1 B:ASP114 4.4 24.8 1.0 O1A B:AGS401 4.4 28.7 1.0 O2G B:AGS401 4.4 28.7 1.0 CG2 B:THR56 4.4 26.8 1.0 O3A B:AGS401 4.6 28.7 1.0 NH2 C:ARG160 4.7 18.2 1.0 CB B:LYS55 4.7 22.6 1.0 O2B B:AGS401 4.8 28.7 1.0 PA B:AGS401 4.9 28.7 1.0 CE B:LYS55 4.9 22.6 1.0 O2A B:AGS401 4.9 28.7 1.0 C B:LYS55 5.0 22.6 1.0 CG B:ASP114 5.0 24.8 1.0

Magnesium binding site 3 out of 4 in the Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Open Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) and Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Open Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) and Primer-Template Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:22.0 occ:1.00 OG1 C:THR60 2.1 21.4 1.0 O3G C:AGS401 2.2 43.2 1.0 O1B C:AGS401 2.7 43.2 1.0 CB C:THR60 3.3 21.4 1.0 PG C:AGS401 3.4 43.2 1.0 OD2 C:ASP117 3.5 18.3 1.0 NH2 D:ARG183 3.5 16.1 1.0 OD1 C:ASP117 3.7 18.3 1.0 S1G C:AGS401 3.7 43.2 1.0 PB C:AGS401 3.9 43.2 1.0 OE1 D:GLU158 3.9 24.4 1.0 CG C:ASP117 4.0 18.3 1.0 CG2 C:THR60 4.0 21.4 1.0 O1A C:AGS401 4.0 43.2 1.0 O3B C:AGS401 4.1 43.2 1.0 OE2 C:GLU118 4.2 18.3 1.0 NH2 C:ARG206 4.3 21.3 1.0 CA C:THR60 4.5 21.4 1.0 N C:THR60 4.5 21.4 1.0 O2G C:AGS401 4.6 43.2 1.0 CD2 C:LEU146 4.6 15.1 1.0 O3A C:AGS401 4.6 43.2 1.0 OE2 D:GLU158 4.6 24.4 1.0 CD D:GLU158 4.7 24.4 1.0 CZ D:ARG183 4.7 16.1 1.0 CD D:ARG155 4.7 16.4 1.0 NH1 D:ARG155 4.7 16.4 1.0 CG C:GLU118 4.8 18.3 1.0 PA C:AGS401 4.8 43.2 1.0 CD C:GLU118 4.9 18.3 1.0 O2A C:AGS401 5.0 43.2 1.0

Magnesium binding site 4 out of 4 in the Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Open Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) and Primer-Template Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Open Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) and Primer-Template Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:26.3 occ:1.00 O3G D:AGS401 2.1 43.2 1.0 O2B D:AGS401 2.2 43.2 1.0 OG1 D:THR72 2.2 24.2 1.0 PG D:AGS401 3.3 43.2 1.0 CB D:THR72 3.4 24.2 1.0 OD1 D:ASP140 3.5 22.9 1.0 PB D:AGS401 3.6 43.2 1.0 S1G D:AGS401 3.7 43.2 1.0 OD2 D:ASP140 3.8 22.9 1.0 NH2 E:ARG184 3.8 27.4 1.0 O3B D:AGS401 4.0 43.2 1.0 OE2 D:GLU141 4.0 22.9 1.0 O2A D:AGS401 4.0 43.2 1.0 CG D:ASP140 4.1 22.9 1.0 N D:THR72 4.2 24.2 1.0 CG2 D:THR72 4.3 24.2 1.0 CA D:THR72 4.3 24.2 1.0 O1B D:AGS401 4.4 43.2 1.0 CG2 D:ILE169 4.6 18.6 1.0 O3A D:AGS401 4.6 43.2 1.0 O2G D:AGS401 4.6 43.2 1.0 PA D:AGS401 4.6 43.2 1.0 O1A D:AGS401 4.7 43.2 1.0 OE1 E:GLU159 4.8 39.4 1.0 CZ E:ARG184 4.9 27.4 1.0 CD D:GLU141 5.0 22.9 1.0

C.Gaubitz, X.Liu, J.Pajak, N.P.Stone, J.A.Hayes, G.Demo, B.A.Kelch Phd. Cryo-Em Structures Reveal High-Resolution Mechanism of A Dna Polymerase Sliding Clamp Loader. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35179493
DOI: 10.7554/ELIFE.74175