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: Tue Apr 25 23:24:59 2023

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy