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Magnesium in PDB 9c53: Cryo-Em Structure of the Strand Displacement Complex (III) of Yeast Mitochondrial Dna Polymerase Gamma (MIP1) with Downstream Dna

Enzymatic activity of Cryo-Em Structure of the Strand Displacement Complex (III) of Yeast Mitochondrial Dna Polymerase Gamma (MIP1) with Downstream Dna

All present enzymatic activity of Cryo-Em Structure of the Strand Displacement Complex (III) of Yeast Mitochondrial Dna Polymerase Gamma (MIP1) with Downstream Dna:
2.7.7.7;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Strand Displacement Complex (III) of Yeast Mitochondrial Dna Polymerase Gamma (MIP1) with Downstream Dna (pdb code 9c53). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Cryo-Em Structure of the Strand Displacement Complex (III) of Yeast Mitochondrial Dna Polymerase Gamma (MIP1) with Downstream Dna, PDB code: 9c53:

Magnesium binding site 1 out of 1 in 9c53

Go back to Magnesium Binding Sites List in 9c53
Magnesium binding site 1 out of 1 in the Cryo-Em Structure of the Strand Displacement Complex (III) of Yeast Mitochondrial Dna Polymerase Gamma (MIP1) with Downstream Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Strand Displacement Complex (III) of Yeast Mitochondrial Dna Polymerase Gamma (MIP1) with Downstream Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:30.0
occ:1.00
O A:VAL694 2.0 89.7 1.0
OD2 A:ASP892 2.1 84.4 1.0
O2G A:DTP1301 2.2 20.0 1.0
OD1 A:ASP693 2.5 92.5 1.0
O1B A:DTP1301 2.5 20.0 1.0
O1A A:DTP1301 2.8 20.0 1.0
CG A:ASP892 3.1 84.4 1.0
C A:VAL694 3.1 89.7 1.0
OD1 A:ASP892 3.4 84.4 1.0
CG A:ASP693 3.6 92.5 1.0
PG A:DTP1301 3.6 20.0 1.0
PB A:DTP1301 3.7 20.0 1.0
N A:VAL694 3.8 89.7 1.0
PA A:DTP1301 3.9 20.0 1.0
CA A:VAL694 3.9 89.7 1.0
O3B A:DTP1301 3.9 20.0 1.0
N A:ASP695 4.1 80.6 1.0
O3A A:DTP1301 4.1 20.0 1.0
O5' A:DTP1301 4.2 20.0 1.0
OD2 A:ASP693 4.2 92.5 1.0
CB A:VAL694 4.3 89.7 1.0
CA A:ASP695 4.3 80.6 1.0
CB A:ASP892 4.3 84.4 1.0
C A:ASP693 4.4 92.5 1.0
O3G A:DTP1301 4.4 20.0 1.0
O1G A:DTP1301 4.6 20.0 1.0
CB A:ASP693 4.6 92.5 1.0
N A:SER696 4.8 81.8 1.0
O A:ASP892 4.8 84.4 1.0
C A:ASP695 4.9 80.6 1.0

Reference:

A.R.Nayak, V.Sokolova, S.Sillamaa, K.Herbine, J.Sedman, D.Temiakov. Structural Basis For Intrinsic Strand Displacement Activity of Mitochondrial Dna Polymerase Nat Commun V. 16 2417 2025.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-025-57594-Z
Page generated: Fri Aug 15 23:37:47 2025

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