Magnesium in PDB 6as7: Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Dna-Primed Dna Template and Dctp

Enzymatic activity of Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Dna-Primed Dna Template and Dctp

All present enzymatic activity of Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Dna-Primed Dna Template and Dctp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Dna-Primed Dna Template and Dctp, PDB code: 6as7 was solved by T.H.Tahirov, A.G.Baranovskiy, N.D.Babayeva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.20 / 2.95
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 151.807, 151.807, 113.299, 90.00, 90.00, 90.00
R / Rfree (%) 25.9 / 30.1

Other elements in 6as7:

The structure of Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Dna-Primed Dna Template and Dctp also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Dna-Primed Dna Template and Dctp (pdb code 6as7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Dna-Primed Dna Template and Dctp, PDB code: 6as7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6as7

Go back to Magnesium Binding Sites List in 6as7
Magnesium binding site 1 out of 2 in the Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Dna-Primed Dna Template and Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Dna-Primed Dna Template and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:45.0
occ:1.00
 O1G A:DCP1301 1.8 0.4 1.0
O A:PHE861 1.9 37.7 1.0
O1B A:DCP1301 2.0 0.8 1.0
OD1 A:ASP1004 2.2 38.4 1.0
OD2 A:ASP860 2.5 66.7 1.0
O1A A:DCP1301 2.5 0.7 1.0
PG A:DCP1301 3.1 0.8 1.0
C A:PHE861 3.1 35.9 1.0
MG A:MG1303 3.3 52.0 1.0
CG A:ASP1004 3.3 32.9 1.0
PB A:DCP1301 3.3 0.5 1.0
CG A:ASP860 3.5 60.1 1.0
O2G A:DCP1301 3.6 0.7 1.0
N A:PHE861 3.7 28.6 1.0
O3B A:DCP1301 3.7 0.1 1.0
PA A:DCP1301 3.8 0.7 1.0
CA A:PHE861 3.8 30.4 1.0
OD2 A:ASP1004 4.0 38.1 1.0
O3A A:DCP1301 4.1 0.4 1.0
C A:ASP860 4.1 31.0 1.0
OD1 A:ASP860 4.2 68.1 1.0
N A:ASN862 4.2 43.4 1.0
CB A:PHE861 4.2 26.0 1.0
O3G A:DCP1301 4.2 0.2 1.0
N A:SER863 4.3 26.5 1.0
CB A:ASP1004 4.3 29.9 1.0
C5' A:DCP1301 4.4 98.1 1.0
CB A:ASP860 4.5 47.2 1.0
O2B A:DCP1301 4.5 0.8 1.0
CA A:ASN862 4.5 46.7 1.0
O A:ASP860 4.5 31.5 1.0
O A:ASP1004 4.6 38.3 1.0
N A:LEU864 4.7 16.0 1.0
O5' A:DCP1301 4.7 0.0 1.0
C A:ASN862 4.8 41.8 1.0
CA A:ASP860 4.8 33.3 1.0
CB A:LEU864 4.8 15.7 1.0
O2A A:DCP1301 4.9 0.6 1.0

Magnesium binding site 2 out of 2 in 6as7

Go back to Magnesium Binding Sites List in 6as7
Magnesium binding site 2 out of 2 in the Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Dna-Primed Dna Template and Dctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Dna-Primed Dna Template and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:52.0
occ:1.00
 OD2 A:ASP1004 1.8 38.1 1.0
O1A A:DCP1301 1.9 0.7 1.0
OD1 A:ASP1004 2.4 38.4 1.0
CG A:ASP1004 2.4 32.9 1.0
OD2 A:ASP860 2.8 66.7 1.0
OD1 A:ASP860 2.9 68.1 1.0
PA A:DCP1301 3.0 0.7 1.0
CG A:ASP860 3.2 60.1 1.0
MG A:MG1302 3.3 45.0 1.0
O5' A:DCP1301 3.4 0.0 1.0
O2A A:DCP1301 3.5 0.6 1.0
C5' A:DCP1301 3.6 98.1 1.0
CB A:ASP1004 3.9 29.9 1.0
O1G A:DCP1301 4.0 0.4 1.0
O1B A:DCP1301 4.1 0.8 1.0
C A:ASP1004 4.2 33.9 1.0
C2' B:DC11 4.3 27.3 1.0
CB A:SER1005 4.4 25.5 1.0
N A:SER1005 4.4 29.0 1.0
C3' B:DC11 4.4 29.6 1.0
O A:ASP1004 4.4 38.3 1.0
O3A A:DCP1301 4.5 0.4 1.0
CA A:ASP1004 4.5 32.2 1.0
O A:ASP1002 4.6 15.9 1.0
N A:ASP1004 4.6 33.7 1.0
CB A:ASP860 4.7 47.2 1.0
OG A:SER1005 4.8 28.6 1.0
CA A:SER1005 4.8 24.7 1.0
PB A:DCP1301 4.9 0.5 1.0
C4' B:DC11 5.0 24.2 1.0

Reference:

A.G.Baranovskiy, V.N.Duong, N.D.Babayeva, Y.Zhang, Y.I.Pavlov, K.S.Anderson, T.H.Tahirov. Activity and Fidelity of Human Dna Polymerase Alpha Depend on Primer Structure. J. Biol. Chem. V. 293 6824 2018.
ISSN: ESSN 1083-351X
PubMed: 29555682
DOI: 10.1074/JBC.RA117.001074
Page generated: Mon Dec 14 22:21:20 2020

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