Magnesium in PDB 8umy: Atomic Model of the Human CTF18-Rfc-Pcna-Dna Ternary Complex with Narrow Pcna Opening State II (State 6)

The binding sites of Magnesium atom in the Atomic Model of the Human CTF18-Rfc-Pcna-Dna Ternary Complex with Narrow Pcna Opening State II (State 6) (pdb code 8umy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Atomic Model of the Human CTF18-Rfc-Pcna-Dna Ternary Complex with Narrow Pcna Opening State II (State 6), PDB code: 8umy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Atomic Model of the Human CTF18-Rfc-Pcna-Dna Ternary Complex with Narrow Pcna Opening State II (State 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atomic Model of the Human CTF18-Rfc-Pcna-Dna Ternary Complex with Narrow Pcna Opening State II (State 6) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:68.0 occ:1.00 OG1 A:THR381 2.1 64.5 1.0 O3G A:AGS1202 2.2 63.6 1.0 O3A A:AGS1202 3.0 62.4 1.0 O1B A:AGS1202 3.3 66.3 1.0 CB A:THR381 3.3 58.4 1.0 OD1 A:ASP435 3.5 78.1 1.0 PB A:AGS1202 3.6 43.0 1.0 PG A:AGS1202 3.6 53.9 1.0 NH2 B:ARG184 3.9 40.2 1.0 CG2 A:THR381 4.0 63.3 1.0 OE1 B:GLU159 4.1 72.5 1.0 CG A:ASP435 4.1 77.3 1.0 O3B A:AGS1202 4.1 62.1 1.0 PA A:AGS1202 4.2 56.4 1.0 O2A A:AGS1202 4.3 64.1 1.0 NH1 B:ARG156 4.3 64.2 1.0 OD2 A:ASP435 4.4 74.9 1.0 O2G A:AGS1202 4.4 61.9 1.0 NH2 B:ARG155 4.5 60.5 1.0 CA A:THR381 4.5 55.8 1.0 N A:THR381 4.5 60.2 1.0 OE2 A:GLU436 4.6 73.8 1.0 O1A A:AGS1202 4.8 64.0 1.0 OE2 B:GLU159 4.8 65.3 1.0 CD B:GLU159 4.9 70.9 1.0 NH2 A:ARG550 4.9 52.5 1.0 S1G A:AGS1202 5.0 75.2 1.0

Magnesium binding site 2 out of 4 in the Atomic Model of the Human CTF18-Rfc-Pcna-Dna Ternary Complex with Narrow Pcna Opening State II (State 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Atomic Model of the Human CTF18-Rfc-Pcna-Dna Ternary Complex with Narrow Pcna Opening State II (State 6) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:62.6 occ:1.00 OG1 B:THR83 2.1 59.0 1.0 O2G B:AGS402 2.1 50.3 1.0 O1B B:AGS402 2.5 39.7 1.0 CB B:THR83 3.3 52.2 1.0 OD2 B:ASP141 3.4 71.5 1.0 NH2 C:ARG168 3.6 51.5 1.0 PG B:AGS402 3.6 52.8 1.0 OD1 B:ASP141 3.7 62.4 1.0 CG2 B:THR83 3.8 54.2 1.0 PB B:AGS402 3.8 35.2 1.0 CG B:ASP141 4.0 68.5 1.0 OE2 B:GLU142 4.1 71.0 1.0 O1A B:AGS402 4.2 50.5 1.0 O3B B:AGS402 4.2 47.9 1.0 NH2 C:ARG139 4.3 51.8 1.0 OE1 C:GLU143 4.4 60.4 1.0 O3G B:AGS402 4.5 62.4 1.0 CA B:THR83 4.5 43.0 1.0 O3A B:AGS402 4.5 57.5 1.0 CG B:GLU142 4.6 70.4 1.0 NH2 B:ARG230 4.6 54.7 1.0 N B:THR83 4.6 45.8 1.0 S1G B:AGS402 4.8 56.3 1.0 CZ C:ARG168 4.8 46.4 1.0 CD B:GLU142 4.8 67.9 1.0 PA B:AGS402 4.8 41.5 1.0 NH1 C:ARG140 4.9 59.1 1.0 CD C:ARG140 5.0 57.1 1.0

Magnesium binding site 3 out of 4 in the Atomic Model of the Human CTF18-Rfc-Pcna-Dna Ternary Complex with Narrow Pcna Opening State II (State 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Atomic Model of the Human CTF18-Rfc-Pcna-Dna Ternary Complex with Narrow Pcna Opening State II (State 6) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:36.4 occ:1.00 OG1 C:THR67 2.1 59.2 1.0 O3G C:AGS402 2.1 38.0 1.0 O1B C:AGS402 2.9 43.5 1.0 CB C:THR67 3.3 46.8 1.0 OD2 C:ASP125 3.3 61.1 1.0 NH2 D:ARG193 3.4 46.7 1.0 PG C:AGS402 3.6 40.1 1.0 OE1 D:GLU168 3.8 62.5 1.0 OD1 C:ASP125 3.8 69.0 1.0 CG2 C:THR67 3.9 43.6 1.0 O1A C:AGS402 4.0 48.9 1.0 CG C:ASP125 4.0 60.8 1.0 OE2 C:GLU126 4.1 56.3 1.0 OE2 D:GLU168 4.1 66.2 1.0 PB C:AGS402 4.2 28.0 1.0 NH2 C:ARG214 4.3 53.2 1.0 O3B C:AGS402 4.3 48.3 1.0 CD D:GLU168 4.4 61.1 1.0 CA C:THR67 4.5 42.7 1.0 S1G C:AGS402 4.5 40.5 1.0 O2G C:AGS402 4.5 51.2 1.0 N C:THR67 4.6 34.8 1.0 CZ D:ARG193 4.7 38.5 1.0 NH2 D:ARG164 4.7 40.2 1.0 NE D:ARG165 4.9 53.7 1.0 PA C:AGS402 4.9 19.6 1.0

Magnesium binding site 4 out of 4 in the Atomic Model of the Human CTF18-Rfc-Pcna-Dna Ternary Complex with Narrow Pcna Opening State II (State 6)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Atomic Model of the Human CTF18-Rfc-Pcna-Dna Ternary Complex with Narrow Pcna Opening State II (State 6) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:52.6 occ:1.00 O2G D:AGS402 2.1 80.9 1.0 OG1 D:THR85 2.1 66.2 1.0 O2B D:AGS402 2.6 75.6 1.0 CB D:THR85 3.3 58.7 1.0 OD2 D:ASP150 3.4 54.4 1.0 NH2 E:ARG178 3.5 52.0 1.0 PG D:AGS402 3.6 55.0 1.0 OD1 D:ASP150 3.6 66.2 1.0 CG D:ASP150 3.9 57.8 1.0 PB D:AGS402 4.0 54.2 1.0 OE2 D:GLU151 4.0 63.0 1.0 CG2 D:THR85 4.0 60.1 1.0 O2A D:AGS402 4.1 73.1 1.0 O3B D:AGS402 4.2 72.5 1.0 NH2 E:ARG149 4.4 45.6 1.0 O3G D:AGS402 4.4 79.4 1.0 CA D:THR85 4.5 55.8 1.0 N D:THR85 4.5 53.0 1.0 CD E:ARG150 4.6 57.5 1.0 OE1 E:GLU153 4.7 71.0 1.0 O1B D:AGS402 4.8 69.2 1.0 S1G D:AGS402 4.8 56.0 1.0 CZ E:ARG178 4.8 51.6 1.0 CG2 D:ILE179 4.8 45.9 1.0 NH1 E:ARG150 4.8 59.3 1.0 PA D:AGS402 5.0 42.2 1.0

F.Wang, Q.He, H.Li. Cryo-Em Reveals A Nearly Complete Pcna Loading Process and Unique Features of the Human Alternative Clamp Loader CTF18-Rfc Proc.Natl.Acad.Sci.Usa 2024.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2319727121