Atomistry » Magnesium » PDB 9bz9-9c87 » 9c51
Atomistry »
  Magnesium »
    PDB 9bz9-9c87 »
      9c51 »

Magnesium in PDB 9c51: Cryo-Em Structure of the Strand Displacement Complex (IV) of Yeast Mitochondrial Dna Polymerase Gamma (MIP1) with Downstream Dna

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

All present enzymatic activity of Cryo-Em Structure of the Strand Displacement Complex (IV) 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 (IV) of Yeast Mitochondrial Dna Polymerase Gamma (MIP1) with Downstream Dna (pdb code 9c51). 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 (IV) of Yeast Mitochondrial Dna Polymerase Gamma (MIP1) with Downstream Dna, PDB code: 9c51:

Magnesium binding site 1 out of 1 in 9c51

Go back to Magnesium Binding Sites List in 9c51
Magnesium binding site 1 out of 1 in the Cryo-Em Structure of the Strand Displacement Complex (IV) 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 (IV) 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 2.1 89.7 1.0
O2G A:DTP1301 2.2 20.0 1.0
O1A A:DTP1301 2.4 20.0 1.0
OD2 A:ASP892 2.4 84.4 1.0
OD2 A:ASP693 2.6 92.5 1.0
O1B A:DTP1301 2.7 20.0 1.0
C A:VAL694 3.3 89.7 1.0
CG A:ASP693 3.4 92.5 1.0
CG A:ASP892 3.5 84.4 1.0
PG A:DTP1301 3.5 20.0 1.0
OD1 A:ASP693 3.6 92.5 1.0
PB A:DTP1301 3.8 20.0 1.0
PA A:DTP1301 3.8 20.0 1.0
N A:VAL694 3.9 89.7 1.0
OD1 A:ASP892 4.0 84.4 1.0
O3B A:DTP1301 4.0 20.0 1.0
CA A:VAL694 4.1 89.7 1.0
O3G A:DTP1301 4.2 20.0 1.0
O3A A:DTP1301 4.3 20.0 1.0
N A:ASP695 4.3 80.6 1.0
N A:SER696 4.4 81.8 1.0
CA A:ASP695 4.5 80.6 1.0
C A:ASP693 4.5 92.5 1.0
C5' A:DTP1301 4.6 20.0 1.0
CB A:VAL694 4.6 89.7 1.0
O1G A:DTP1301 4.6 20.0 1.0
O5' A:DTP1301 4.6 20.0 1.0
CB A:ASP693 4.7 92.5 1.0
CB A:ASP892 4.8 84.4 1.0
O2A A:DTP1301 4.8 20.0 1.0
C A:ASP695 4.8 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 23:37:41 2025

Last articles

Mn in 2QGI
Mn in 2QEY
Mn in 2QF1
Mn in 2QCS
Mn in 2PYO
Mn in 2QEW
Mn in 2QB0
Mn in 2QB5
Mn in 2QB6
Mn in 2Q96
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy