Magnesium in PDB 8d9d: Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template

Enzymatic activity of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template

All present enzymatic activity of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template:
2.7.7.102; 2.7.7.7;

Other elements in 8d9d:

The structure of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Zinc (Zn) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template (pdb code 8d9d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template, PDB code: 8d9d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8d9d

Go back to Magnesium Binding Sites List in 8d9d
Magnesium binding site 1 out of 2 in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:59.7
occ:1.00
OD1 C:ASP1004 2.2 63.1 1.0
O C:PHE861 2.5 53.6 1.0
OD2 C:ASP860 2.5 59.4 1.0
O2B C:DTP1504 2.7 75.5 1.0
CG C:ASP860 3.0 59.4 1.0
OD1 C:ASP860 3.1 59.4 1.0
O3G C:DTP1504 3.2 75.5 1.0
O1A C:DTP1504 3.2 75.5 1.0
CG C:ASP1004 3.4 63.1 1.0
O3B C:DTP1504 3.5 75.5 1.0
PB C:DTP1504 3.5 75.5 1.0
O3A C:DTP1504 3.6 75.5 1.0
C C:PHE861 3.6 53.6 1.0
N C:PHE861 3.9 53.6 1.0
PA C:DTP1504 4.0 75.5 1.0
PG C:DTP1504 4.0 75.5 1.0
CB C:ASP1004 4.2 63.1 1.0
CB C:ASP860 4.2 59.4 1.0
CA C:PHE861 4.3 53.6 1.0
OD2 C:ASP1004 4.4 63.1 1.0
C C:ASP860 4.6 59.4 1.0
N C:ASN862 4.7 58.7 1.0
CB C:PHE861 4.8 53.6 1.0
C5' C:DTP1504 4.8 75.5 1.0
CA C:ASP860 4.8 59.4 1.0
O5' C:DTP1504 4.9 75.5 1.0
O1B C:DTP1504 4.9 75.5 1.0
CA C:ASN862 5.0 58.7 1.0

Magnesium binding site 2 out of 2 in 8d9d

Go back to Magnesium Binding Sites List in 8d9d
Magnesium binding site 2 out of 2 in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:72.0
occ:1.00
O1G E:GTP1 2.8 76.2 1.0
O1A E:GTP1 2.8 76.2 1.0
O2B E:GTP1 3.3 76.2 1.0
PA E:GTP1 4.1 76.2 1.0
PG E:GTP1 4.1 76.2 1.0
O3A E:GTP1 4.2 76.2 1.0
PB E:GTP1 4.3 76.2 1.0
O3G E:GTP1 4.6 76.2 1.0
O3B E:GTP1 4.7 76.2 1.0
N7 E:GTP1 4.8 76.2 1.0
O5' E:GTP1 4.9 76.2 1.0

Reference:

Q.He, A.G.Baranovskiy, L.M.Morstadt, A.E.Lisova, N.D.Babayeva, B.L.Lusk, C.Lim, T.H.Tahirov. Structures of Human Primosome Elongation Complexes Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-00971-3
Page generated: Thu Oct 3 23:42:36 2024

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