Magnesium in PDB 7thj: Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) in An Autoinhibited Conformation

The binding sites of Magnesium atom in the Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) in An Autoinhibited Conformation (pdb code 7thj). 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 Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) in An Autoinhibited Conformation, PDB code: 7thj:
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 Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) in An Autoinhibited Conformation


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 Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) in An Autoinhibited Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:30.6 occ:1.00 OG1 A:THR360 2.1 45.6 1.0 O1B A:AGS901 2.2 45.6 1.0 O3G A:AGS901 2.3 45.6 1.0 OD2 A:ASP424 3.2 43.9 1.0 CB A:THR360 3.2 45.6 1.0 OD1 A:ASP424 3.5 43.9 1.0 PB A:AGS901 3.6 45.6 1.0 CG A:ASP424 3.7 43.9 1.0 PG A:AGS901 3.7 45.6 1.0 CG2 A:THR360 4.0 45.6 1.0 O3B A:AGS901 4.1 45.6 1.0 O1A A:AGS901 4.2 45.6 1.0 O3A A:AGS901 4.4 45.6 1.0 CA A:THR360 4.4 45.6 1.0 O2G A:AGS901 4.4 45.6 1.0 N A:THR360 4.5 45.6 1.0 O2B A:AGS901 4.6 45.6 1.0 NH1 B:ARG129 4.6 37.4 1.0 NH2 B:ARG128 4.6 45.6 1.0 NH2 B:ARG157 4.7 35.0 1.0 PA A:AGS901 4.8 45.6 1.0 CG2 A:ILE454 4.9 45.6 1.0 OE1 B:GLU132 5.0 32.3 1.0

Magnesium binding site 2 out of 4 in the Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) in An Autoinhibited Conformation


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 Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) in An Autoinhibited Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:35.1 occ:1.00 OG1 B:THR56 2.0 41.1 1.0 O3G B:AGS401 2.1 45.6 1.0 O1B B:AGS401 2.1 45.6 1.0 CB B:THR56 3.0 41.1 1.0 PB B:AGS401 3.5 45.6 1.0 PG B:AGS401 3.5 45.6 1.0 CG2 B:THR56 3.9 41.1 1.0 O3B B:AGS401 3.9 45.6 1.0 OD2 B:ASP114 4.1 35.4 1.0 CA B:THR56 4.2 41.1 1.0 N B:THR56 4.2 41.1 1.0 O3A B:AGS401 4.3 45.6 1.0 O1A B:AGS401 4.3 45.6 1.0 S1G B:AGS401 4.3 45.6 1.0 NH2 C:ARG131 4.5 47.0 1.0 NH1 C:ARG132 4.6 44.2 1.0 O2B B:AGS401 4.6 45.6 1.0 O2G B:AGS401 4.6 45.6 1.0 PA B:AGS401 4.7 45.6 1.0 CG B:ASP114 4.7 35.4 1.0 O2A B:AGS401 4.8 45.6 1.0 NH1 C:ARG131 5.0 47.0 1.0

Magnesium binding site 3 out of 4 in the Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) in An Autoinhibited Conformation


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 Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) in An Autoinhibited Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:56.6 occ:1.00 OG1 C:THR60 2.1 53.6 1.0 O1A C:AGS401 2.1 72.6 1.0 O3G C:AGS401 2.1 72.6 1.0 O1B C:AGS401 2.2 72.6 1.0 CB C:THR60 2.7 53.6 1.0 PA C:AGS401 3.0 72.6 1.0 PB C:AGS401 3.2 72.6 1.0 O3A C:AGS401 3.3 72.6 1.0 O2A C:AGS401 3.4 72.6 1.0 PG C:AGS401 3.4 72.6 1.0 NH2 C:ARG206 3.6 76.2 1.0 CG2 C:THR60 3.6 53.6 1.0 O3B C:AGS401 3.8 72.6 1.0 CA C:THR60 3.9 53.6 1.0 N C:THR60 3.9 53.6 1.0 OD2 C:ASP117 4.2 70.9 1.0 S1G C:AGS401 4.4 72.6 1.0 O5' C:AGS401 4.4 72.6 1.0 O2B C:AGS401 4.5 72.6 1.0 O2G C:AGS401 4.6 72.6 1.0 C C:THR60 4.9 53.6 1.0 CZ C:ARG206 4.9 76.2 1.0 C5' C:AGS401 4.9 72.6 1.0 N C:SER61 5.0 52.1 1.0

Magnesium binding site 4 out of 4 in the Structure of the Yeast Clamp Loader (Replication Factor C Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) in An Autoinhibited Conformation


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 Sliding Clamp (Proliferating Cell Nuclear Antigen Pcna) in An Autoinhibited Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:81.2 occ:1.00 O3G D:AGS401 2.2 132.3 1.0 OG1 D:THR72 2.3 106.5 1.0 O2A D:AGS401 2.4 132.3 1.0 O2B D:AGS401 2.4 132.3 1.0 PG D:AGS401 3.4 132.3 1.0 PB D:AGS401 3.6 132.3 1.0 CB D:THR72 3.6 106.5 1.0 O3B D:AGS401 3.7 132.3 1.0 PA D:AGS401 3.7 132.3 1.0 O3A D:AGS401 4.2 132.3 1.0 S1G D:AGS401 4.2 132.3 1.0 N D:THR72 4.3 106.5 1.0 O1A D:AGS401 4.3 132.3 1.0 CG2 D:THR72 4.5 106.5 1.0 CA D:THR72 4.6 106.5 1.0 O2G D:AGS401 4.7 132.3 1.0 O1B D:AGS401 4.8 132.3 1.0 CB D:LYS71 4.8 117.0 1.0 OD2 D:ASP140 4.9 131.1 1.0 O5' D:AGS401 4.9 132.3 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