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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: Wed Dec 16 05:43:17 2020

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