Zinc in PDB 7n2m: Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site

Enzymatic activity of Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site

All present enzymatic activity of Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site, PDB code: 7n2m 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) 44.51 / 2.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.285, 140.285, 181.066, 90, 90, 120
R / Rfree (%) 19.5 / 22.8

Other elements in 7n2m:

The structure of Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site (pdb code 7n2m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site, PDB code: 7n2m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7n2m

Go back to Zinc Binding Sites List in 7n2m
Zinc binding site 1 out of 4 in the Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site


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 Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:38.4
occ:1.00
 OD2 A:ASP1004 2.1 13.2 1.0
OD1 A:ASP860 2.1 30.6 1.0
O1A A:DCP1301 2.4 18.1 1.0
CG A:ASP1004 3.0 22.5 1.0
CG A:ASP860 3.1 41.4 1.0
OD1 A:ASP1004 3.2 20.7 1.0
PA A:DCP1301 3.4 26.2 1.0
OD2 A:ASP860 3.5 43.5 1.0
O2A A:DCP1301 3.7 21.3 1.0
MG A:MG1302 3.7 1.8 1.0
O5' A:DCP1301 3.9 12.3 1.0
O B:HOH608 3.9 45.0 1.0
C5' A:DCP1301 4.1 18.7 1.0
C3' B:C11 4.1 33.1 1.0
O A:HOH1455 4.2 33.4 1.0
O3G A:DCP1301 4.3 26.5 1.0
CB A:ASP860 4.3 35.7 1.0
O A:ASP1002 4.4 35.3 1.0
CB A:ASP1004 4.4 18.4 1.0
CB A:SER1005 4.5 27.6 1.0
C5' B:C11 4.5 20.2 1.0
O1B A:DCP1301 4.6 16.4 1.0
C A:ASP1004 4.6 25.9 1.0
OG A:SER1005 4.6 31.5 1.0
O A:ASP1004 4.7 29.2 1.0
C4' B:C11 4.8 26.2 1.0
N A:SER1005 4.9 24.4 1.0
N A:ASP1004 4.9 28.1 1.0
O3A A:DCP1301 4.9 23.4 1.0
CA A:ASP1004 4.9 24.1 1.0

Zinc binding site 2 out of 4 in 7n2m

Go back to Zinc Binding Sites List in 7n2m
Zinc binding site 2 out of 4 in the Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site


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 Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1304

b:28.7
occ:0.50
 NE2 A:HIS342 1.9 10.2 1.0
OE1 A:GLU500 1.9 35.7 1.0
CE1 A:HIS342 2.7 24.9 1.0
CD A:GLU500 2.8 33.5 1.0
CD2 A:HIS342 3.1 17.1 1.0
CG A:GLU500 3.5 32.2 1.0
OE2 A:GLU500 3.8 38.9 1.0
ND1 A:HIS342 3.9 26.2 1.0
CG A:HIS342 4.1 16.3 1.0
CD1 A:ILE529 4.7 33.6 1.0
CB A:GLU500 4.9 20.9 1.0

Zinc binding site 3 out of 4 in 7n2m

Go back to Zinc Binding Sites List in 7n2m
Zinc binding site 3 out of 4 in the Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site


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 Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:47.6
occ:1.00
 N7 B:G6 2.1 26.6 1.0
C8 B:G6 3.0 27.1 1.0
C5 B:G6 3.1 33.8 1.0
O6 B:G6 3.5 35.0 1.0
C6 B:G6 3.6 34.1 1.0
N9 B:G6 4.2 29.2 1.0
C4 B:G6 4.2 27.1 1.0
OP2 B:G6 4.3 45.6 1.0
N7 B:A7 4.3 19.0 1.0
O B:HOH603 4.5 54.8 1.0
N7 B:G5 4.7 38.5 1.0
C5 B:G5 4.8 37.9 1.0
C6 B:G5 4.9 36.5 1.0
C8 B:A7 4.9 21.3 1.0
O6 B:G5 5.0 38.4 1.0
N1 B:G6 5.0 30.6 1.0

Zinc binding site 4 out of 4 in 7n2m

Go back to Zinc Binding Sites List in 7n2m
Zinc binding site 4 out of 4 in the Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Dna Polymerase Alpha Catalytic Core in Complex with Dctp and Template/Primer Having T-C Mismatch at the Post- Insertion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:57.9
occ:0.50
 N7 C:DG119 2.7 46.5 1.0
O6 C:DG119 3.6 56.6 1.0
C5 C:DG119 3.7 47.5 1.0
C8 C:DG119 3.7 53.4 1.0
C6 C:DG119 4.0 51.2 1.0
N7 C:DA118 4.2 33.4 1.0
O6 C:DG120 4.4 69.4 1.0
C8 C:DA118 4.5 36.9 1.0
C4 C:DG119 4.8 48.1 1.0
N9 C:DG119 4.9 56.5 1.0
C5 C:DA118 4.9 27.9 1.0
N4 B:C2 5.0 73.8 1.0

Reference:

A.G.Baranovskiy, N.D.Babayeva, A.E.Lisova, L.M.Morstadt, T.H.Tahirov. Structural and Functional Insight Into Mismatch Extension By Human Dna Polymerase Alpha. Proc.Natl.Acad.Sci.Usa V. 119 44119 2022.
ISSN: ESSN 1091-6490
PubMed: 35467978
DOI: 10.1073/PNAS.2111744119
Page generated: Sat Apr 8 00:57:24 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy