Magnesium in PDB 6vvo: Structure of the Human Clamp Loader (Replication Factor C, Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna)

The binding sites of Magnesium atom in the Structure of the Human Clamp Loader (Replication Factor C, Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) (pdb code 6vvo). 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 Human Clamp Loader (Replication Factor C, Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna), PDB code: 6vvo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Human Clamp Loader (Replication Factor C, Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna)


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 Human Clamp Loader (Replication Factor C, Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:41.6 occ:1.00 O1B A:AGS1202 1.9 42.2 1.0 OG1 A:THR658 2.0 39.3 1.0 O3G A:AGS1202 2.0 42.2 1.0 CB A:THR658 3.1 39.3 1.0 PB A:AGS1202 3.3 42.2 1.0 PG A:AGS1202 3.5 42.2 1.0 OD2 A:ASP720 3.8 43.4 1.0 O3B A:AGS1202 3.8 42.2 1.0 O1A A:AGS1202 4.0 42.2 1.0 OD1 A:ASP720 4.0 43.4 1.0 CG2 A:THR658 4.1 39.3 1.0 CA A:THR658 4.2 39.3 1.0 N A:THR658 4.2 39.3 1.0 O3A A:AGS1202 4.3 42.2 1.0 O2B A:AGS1202 4.3 42.2 1.0 CG A:ASP720 4.3 43.4 1.0 OE1 B:GLU159 4.4 35.3 1.0 O2G A:AGS1202 4.4 42.2 1.0 NH1 B:ARG156 4.4 36.7 1.0 PA A:AGS1202 4.6 42.2 1.0 S1G A:AGS1202 4.7 42.2 1.0 OE2 B:GLU159 4.7 35.3 1.0 OE2 A:GLU721 4.8 44.5 1.0 NH2 B:ARG155 4.8 38.7 1.0 NH1 B:ARG184 4.9 41.5 1.0 CD B:GLU159 4.9 35.3 1.0 O2A A:AGS1202 5.0 42.2 1.0

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


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 Human Clamp Loader (Replication Factor C, Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:43.9 occ:1.00 OG1 B:THR83 1.9 40.2 1.0 O3G B:AGS402 2.0 47.0 1.0 O1B B:AGS402 2.1 47.0 1.0 CB B:THR83 3.0 40.2 1.0 NH2 C:ARG139 3.4 45.4 1.0 PB B:AGS402 3.5 47.0 1.0 PG B:AGS402 3.5 47.0 1.0 CG2 B:THR83 3.9 40.2 1.0 O3B B:AGS402 3.9 47.0 1.0 N B:THR83 4.1 40.2 1.0 CA B:THR83 4.1 40.2 1.0 O1A B:AGS402 4.1 47.0 1.0 O2B B:AGS402 4.3 47.0 1.0 O2G B:AGS402 4.4 47.0 1.0 CZ C:ARG139 4.6 45.4 1.0 O3A B:AGS402 4.6 47.0 1.0 NH1 C:ARG140 4.6 43.8 1.0 PA B:AGS402 4.7 47.0 1.0 S1G B:AGS402 4.7 47.0 1.0 OD1 B:ASP141 4.8 38.2 1.0 OE2 B:GLU142 4.9 40.9 1.0 CG B:ASP141 4.9 38.2 1.0 OD2 B:ASP141 4.9 38.2 1.0 NH1 C:ARG139 5.0 45.4 1.0

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


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 Human Clamp Loader (Replication Factor C, Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:61.1 occ:1.00 O3G C:AGS402 1.9 68.8 1.0 O1B C:AGS402 2.0 68.8 1.0 CG2 C:THR67 2.4 58.7 1.0 OG1 C:THR67 2.7 58.7 1.0 CB C:THR67 3.1 58.7 1.0 PB C:AGS402 3.3 68.8 1.0 PG C:AGS402 3.4 68.8 1.0 OD2 C:ASP125 3.6 59.6 1.0 O3B C:AGS402 3.7 68.8 1.0 O1A C:AGS402 3.8 68.8 1.0 O2G C:AGS402 4.2 68.8 1.0 O2B C:AGS402 4.3 68.8 1.0 CA C:THR67 4.4 58.7 1.0 O3A C:AGS402 4.4 68.8 1.0 N C:THR67 4.4 58.7 1.0 PA C:AGS402 4.5 68.8 1.0 CG C:ASP125 4.5 59.6 1.0 OD1 C:ASP125 4.6 59.6 1.0 S1G C:AGS402 4.7 68.8 1.0 O2A C:AGS402 4.9 68.8 1.0

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


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 Human Clamp Loader (Replication Factor C, Rfc) Bound to the Sliding Clamp (Proliferating Cell Nuclear Antigen, Pcna) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:78.4 occ:1.00 O2B D:AGS402 1.9 79.6 1.0 OG1 D:THR85 2.0 80.1 1.0 O3G D:AGS402 2.4 79.6 1.0 CB D:THR85 3.0 80.1 1.0 PB D:AGS402 3.1 79.6 1.0 O1B D:AGS402 3.4 79.6 1.0 OD2 D:ASP150 3.6 81.1 1.0 PG D:AGS402 3.6 79.6 1.0 N D:THR85 3.8 80.1 1.0 O3B D:AGS402 3.9 79.6 1.0 O2A D:AGS402 3.9 79.6 1.0 CA D:THR85 4.1 80.1 1.0 CG2 D:THR85 4.1 80.1 1.0 O3A D:AGS402 4.3 79.6 1.0 O1A D:AGS402 4.3 79.6 1.0 PA D:AGS402 4.4 79.6 1.0 S1G D:AGS402 4.5 79.6 1.0 CG D:ASP150 4.5 81.1 1.0 OD1 D:ASP150 4.8 81.1 1.0 CB D:LYS84 4.9 77.4 1.0 O2G D:AGS402 4.9 79.6 1.0 C D:LYS84 5.0 77.4 1.0

C.Gaubitz, X.Liu, J.Magrino, N.P.Stone, J.Landeck, M.Hedglin, B.A.Kelch. Structure of the Human Clamp Loader Bound to the Sliding Clamp: A Further Twist on Aaa+ Mechanism Biorxiv 2020.
DOI: 10.1101/2020.02.18.953257