Atomistry » Zinc » PDB 4q8v-4qhj » 4qcl
Atomistry »
  Zinc »
    PDB 4q8v-4qhj »
      4qcl »

Zinc in PDB 4qcl: Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Rna-Primed Dna Template and Dctp

Enzymatic activity of Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Rna-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 Rna-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 Rna-Primed Dna Template and Dctp, PDB code: 4qcl was solved by A.G.Baranovskiy, Y.Suwa, N.D.Babayeva, J.Gu, T.H.Tahirov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.51 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.763, 140.763, 181.315, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 23.9

Other elements in 4qcl:

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

Magnesium (Mg) 1 atom
Potassium (K) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Rna-Primed Dna Template and Dctp (pdb code 4qcl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Rna-Primed Dna Template and Dctp, PDB code: 4qcl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4qcl

Go back to Zinc Binding Sites List in 4qcl
Zinc binding site 1 out of 3 in the Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Rna-Primed Dna Template and Dctp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Rna-Primed Dna Template and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:34.7
occ:1.00
O A:HOH1601 1.9 25.2 1.0
OD2 A:ASP1004 1.9 17.0 1.0
OD1 A:ASP860 2.0 40.7 1.0
O1A A:DCP1301 2.4 30.3 1.0
O A:HOH1516 2.5 37.2 1.0
CG A:ASP1004 2.8 25.0 1.0
CG A:ASP860 2.9 42.4 1.0
OD1 A:ASP1004 3.1 26.0 1.0
OD2 A:ASP860 3.1 34.7 1.0
PA A:DCP1301 3.5 26.4 1.0
MG A:MG1302 3.5 21.8 1.0
O2A A:DCP1301 3.8 19.8 1.0
C3' B:DC11 3.9 18.9 1.0
O A:HOH1448 3.9 37.5 1.0
O A:HOH1444 3.9 33.1 1.0
O5' A:DCP1301 3.9 26.2 1.0
O A:HOH1575 4.2 51.9 1.0
C5' A:DCP1301 4.2 19.6 1.0
CB A:ASP1004 4.3 26.2 1.0
CB A:ASP860 4.3 39.2 1.0
CB A:SER1005 4.3 33.2 1.0
O A:ASP1004 4.3 43.1 1.0
C A:ASP1004 4.3 34.0 1.0
O A:ASP1002 4.4 30.8 1.0
O3G A:DCP1301 4.4 40.8 1.0
O B:HOH614 4.5 35.4 1.0
O2B A:DCP1301 4.6 29.5 1.0
N A:SER1005 4.7 33.7 1.0
CA A:ASP1004 4.7 36.2 1.0
N A:ASP1004 4.7 30.3 1.0
OG A:SER1005 4.8 33.2 1.0
C4' B:DC11 4.8 18.9 1.0
C2' B:DC11 4.9 22.8 1.0
O3A A:DCP1301 5.0 40.7 1.0

Zinc binding site 2 out of 3 in 4qcl

Go back to Zinc Binding Sites List in 4qcl
Zinc binding site 2 out of 3 in the Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Rna-Primed Dna Template and Dctp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Rna-Primed Dna Template and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1304

b:30.7
occ:0.50
OE1 A:GLU500 2.0 44.5 1.0
NE2 A:HIS342 2.0 19.2 1.0
CE1 A:HIS342 2.9 29.9 1.0
CD A:GLU500 2.9 39.9 1.0
CD2 A:HIS342 3.0 34.6 1.0
CG A:GLU500 3.4 43.6 1.0
OE2 A:GLU500 3.9 45.1 1.0
ND1 A:HIS342 4.0 21.1 1.0
CG A:HIS342 4.1 27.5 1.0
CD1 A:ILE529 4.6 37.0 1.0
CB A:GLU500 4.8 33.2 1.0

Zinc binding site 3 out of 3 in 4qcl

Go back to Zinc Binding Sites List in 4qcl
Zinc binding site 3 out of 3 in the Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Rna-Primed Dna Template and Dctp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Core of Human Dna Polymerase Alpha in Ternary Complex with An Rna-Primed Dna Template and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:72.7
occ:1.00
N7 B:G6 2.3 23.7 1.0
O B:HOH610 2.8 61.6 1.0
O B:HOH615 3.1 50.5 1.0
C8 B:G6 3.2 23.2 1.0
C5 B:G6 3.3 26.2 1.0
O6 B:G6 3.7 27.4 1.0
C6 B:G6 3.9 30.3 1.0
N9 B:G6 4.4 34.3 1.0
OP2 B:G6 4.4 40.7 1.0
N7 B:A7 4.5 26.4 1.0
C4 B:G6 4.5 26.6 1.0
O B:HOH607 4.5 52.8 1.0
N7 B:G5 4.6 35.1 1.0
C5 B:G5 4.8 35.0 1.0
O6 B:G5 4.9 37.4 1.0
C6 B:G5 4.9 36.0 1.0

Reference:

A.G.Baranovskiy, N.D.Babayeva, Y.Suwa, J.Gu, T.H.Tahirov. Crystal Structure of Human Dna Polymerase Alpha Catalytic Core in Complex with Dna/Rna and Dcp To Be Published.
Page generated: Sun Oct 27 06:27:14 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy