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Magnesium in PDB 7tfh: Atomic Model of the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Atomic Model of the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End (pdb code 7tfh). 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 S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End, PDB code: 7tfh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7tfh

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Magnesium binding site 1 out of 4 in the Atomic Model of the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End


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 S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:46.7
occ:1.00
OG1 A:THR360 2.1 48.5 1.0
O3G A:AGS901 2.1 45.2 1.0
O1B A:AGS901 2.7 45.2 1.0
OD1 A:ASP424 3.1 64.8 1.0
CB A:THR360 3.3 48.5 1.0
PG A:AGS901 3.6 45.2 1.0
CG A:ASP424 3.8 64.8 1.0
PB A:AGS901 4.0 45.2 1.0
CG2 A:THR360 4.1 48.5 1.0
O3B A:AGS901 4.3 45.2 1.0
OE2 A:GLU425 4.3 65.5 1.0
CG2 A:ILE454 4.3 58.8 1.0
O2G A:AGS901 4.4 45.2 1.0
CA A:THR360 4.4 48.5 1.0
NH2 B:ARG128 4.4 47.6 1.0
CB A:ASP424 4.4 64.8 1.0
N A:THR360 4.4 48.5 1.0
OD2 A:ASP424 4.5 64.8 1.0
OE1 B:GLU132 4.6 45.6 1.0
O1A A:AGS901 4.8 45.2 1.0
S1G A:AGS901 4.8 45.2 1.0
O2B A:AGS901 4.8 45.2 1.0
CD A:GLU425 4.9 65.5 1.0
OE2 B:GLU132 4.9 45.6 1.0

Magnesium binding site 2 out of 4 in 7tfh

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Magnesium binding site 2 out of 4 in the Atomic Model of the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End


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 S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:35.2
occ:1.00
O2G B:AGS401 2.1 30.1 1.0
O1B B:AGS401 2.2 30.1 1.0
CG2 B:THR56 2.7 33.5 1.0
CB B:THR56 3.0 33.5 1.0
PG B:AGS401 3.6 30.1 1.0
PB B:AGS401 3.6 30.1 1.0
OD2 B:ASP114 3.9 43.2 1.0
OG1 B:THR56 3.9 33.5 1.0
NH1 C:ARG132 4.0 41.9 1.0
OD1 B:ASP114 4.0 43.2 1.0
O1A B:AGS401 4.0 30.1 1.0
OE2 C:GLU135 4.0 40.2 1.0
O3B B:AGS401 4.1 30.1 1.0
N B:THR56 4.2 33.5 1.0
CA B:THR56 4.2 33.5 1.0
NH2 C:ARG160 4.3 34.8 1.0
O3A B:AGS401 4.3 30.1 1.0
CG B:ASP114 4.4 43.2 1.0
O3G B:AGS401 4.5 30.1 1.0
OE1 C:GLU135 4.6 40.2 1.0
PA B:AGS401 4.6 30.1 1.0
S1G B:AGS401 4.7 30.1 1.0
O2B B:AGS401 4.7 30.1 1.0
CD C:GLU135 4.8 40.2 1.0
O2A B:AGS401 4.9 30.1 1.0

Magnesium binding site 3 out of 4 in 7tfh

Go back to Magnesium Binding Sites List in 7tfh
Magnesium binding site 3 out of 4 in the Atomic Model of the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End


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 S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:41.1
occ:1.00
O2G C:AGS401 2.1 53.9 1.0
CG2 C:THR60 2.5 35.4 1.0
CB C:THR60 2.8 35.4 1.0
O1B C:AGS401 2.9 53.9 1.0
PG C:AGS401 3.6 53.9 1.0
O3A C:AGS401 3.6 53.9 1.0
PB C:AGS401 3.7 53.9 1.0
OD1 C:ASP117 3.7 40.2 1.0
OG1 C:THR60 3.7 35.4 1.0
N C:THR60 4.0 35.4 1.0
NH2 D:ARG183 4.0 33.3 1.0
CA C:THR60 4.0 35.4 1.0
OD2 C:ASP117 4.0 40.2 1.0
OE1 D:GLU158 4.1 40.2 1.0
O3B C:AGS401 4.2 53.9 1.0
O3G C:AGS401 4.2 53.9 1.0
CG C:ASP117 4.3 40.2 1.0
OE2 D:GLU158 4.6 40.2 1.0
CD D:GLU158 4.8 40.2 1.0
PA C:AGS401 4.8 53.9 1.0
O2A C:AGS401 4.8 53.9 1.0
CD D:ARG155 4.9 41.3 1.0
S1G C:AGS401 4.9 53.9 1.0
CD1 C:LEU146 5.0 33.2 1.0

Magnesium binding site 4 out of 4 in 7tfh

Go back to Magnesium Binding Sites List in 7tfh
Magnesium binding site 4 out of 4 in the Atomic Model of the S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End


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 S. Cerevisiae Clamp-Clamp Loader Complex Pcna-Rfc Bound to Two Dna Molecules, One at the 5'-Recessed End and the Other at the 3'-Recessed End within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:34.0
occ:1.00
OG1 D:THR72 2.1 26.7 1.0
O3G D:AGS401 2.1 26.0 1.0
O2B D:AGS401 2.5 26.0 1.0
CB D:THR72 3.3 26.7 1.0
PG D:AGS401 3.6 26.0 1.0
OD2 D:ASP140 3.7 40.9 1.0
OD1 D:ASP140 3.8 40.9 1.0
PB D:AGS401 3.9 26.0 1.0
O2A D:AGS401 4.1 26.0 1.0
CG D:ASP140 4.1 40.9 1.0
CG2 D:THR72 4.2 26.7 1.0
OE1 E:GLU159 4.2 46.7 1.0
O3B D:AGS401 4.2 26.0 1.0
N D:THR72 4.2 26.7 1.0
CA D:THR72 4.3 26.7 1.0
O1B D:AGS401 4.4 26.0 1.0
OE2 E:GLU159 4.4 46.7 1.0
O2G D:AGS401 4.5 26.0 1.0
S1G D:AGS401 4.6 26.0 1.0
NH2 E:ARG155 4.7 47.5 1.0
CD E:GLU159 4.7 46.7 1.0
CG2 D:ILE169 4.8 33.2 1.0
NH2 E:ARG184 4.8 36.4 1.0
NH1 E:ARG156 5.0 50.4 1.0
O3A D:AGS401 5.0 26.0 1.0

Reference:

F.Zheng, R.Georgescu, N.Y.Yao, H.Li, M.E.O'donnell. Cryo-Em Structures Reveal That Rfc Recognizes Both the 3'- and 5'-Dna Ends to Load Pcna Onto Gaps For Dna Repair. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35829698
DOI: 10.7554/ELIFE.77469
Page generated: Thu Oct 3 09:07:24 2024

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