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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: Wed Oct 30 07:38:39 2024

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