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Calcium in PDB 6g0a: The Crystal Structure of the POL2 Catalytic Domain of Dna Polymerase Epsilon Carrying A P301R Substitution.

Enzymatic activity of The Crystal Structure of the POL2 Catalytic Domain of Dna Polymerase Epsilon Carrying A P301R Substitution.

All present enzymatic activity of The Crystal Structure of the POL2 Catalytic Domain of Dna Polymerase Epsilon Carrying A P301R Substitution.:
2.7.7.7;

Protein crystallography data

The structure of The Crystal Structure of the POL2 Catalytic Domain of Dna Polymerase Epsilon Carrying A P301R Substitution., PDB code: 6g0a was solved by V.Parkash, E.Johansson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.62
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.895, 67.252, 151.639, 90.00, 111.50, 90.00
R / Rfree (%) 22.4 / 26.5

Other elements in 6g0a:

The structure of The Crystal Structure of the POL2 Catalytic Domain of Dna Polymerase Epsilon Carrying A P301R Substitution. also contains other interesting chemical elements:

Iron (Fe) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of the POL2 Catalytic Domain of Dna Polymerase Epsilon Carrying A P301R Substitution. (pdb code 6g0a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Crystal Structure of the POL2 Catalytic Domain of Dna Polymerase Epsilon Carrying A P301R Substitution., PDB code: 6g0a:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6g0a

Go back to Calcium Binding Sites List in 6g0a
Calcium binding site 1 out of 2 in the The Crystal Structure of the POL2 Catalytic Domain of Dna Polymerase Epsilon Carrying A P301R Substitution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of the POL2 Catalytic Domain of Dna Polymerase Epsilon Carrying A P301R Substitution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1302

b:40.9
occ:1.00
OD2 A:ASP877 2.2 38.2 1.0
O2B A:DTP1301 2.2 33.5 1.0
O3G A:DTP1301 2.2 39.0 1.0
OD1 A:ASP640 2.3 41.3 1.0
O A:VAL641 2.3 37.0 1.0
O1A A:DTP1301 2.4 34.0 1.0
CG A:ASP877 3.2 37.4 1.0
PB A:DTP1301 3.2 32.8 1.0
CG A:ASP640 3.3 41.6 1.0
C A:VAL641 3.5 37.5 1.0
PG A:DTP1301 3.5 36.0 1.0
PA A:DTP1301 3.6 31.2 1.0
O3A A:DTP1301 3.6 38.3 1.0
OD2 A:ASP640 3.7 49.7 1.0
OD1 A:ASP877 3.7 40.4 1.0
O3B A:DTP1301 3.8 33.0 1.0
N A:VAL641 4.1 37.6 1.0
N A:SER643 4.3 35.5 1.0
CA A:VAL641 4.4 36.3 1.0
O1G A:DTP1301 4.4 42.1 1.0
N A:ALA642 4.4 36.1 1.0
CB A:ASP877 4.4 36.6 1.0
C5' A:DTP1301 4.4 30.2 1.0
CA A:ALA642 4.5 37.5 1.0
CB A:ASP640 4.5 38.4 1.0
O5' A:DTP1301 4.5 27.7 1.0
O1B A:DTP1301 4.6 36.5 1.0
C A:ASP640 4.6 39.6 1.0
O2G A:DTP1301 4.6 37.6 1.0
N A:MET644 4.6 34.8 1.0
O2A A:DTP1301 4.7 36.9 1.0
C A:ALA642 4.8 37.3 1.0
CB A:VAL641 4.9 36.3 1.0
CB A:MET644 5.0 36.6 1.0

Calcium binding site 2 out of 2 in 6g0a

Go back to Calcium Binding Sites List in 6g0a
Calcium binding site 2 out of 2 in the The Crystal Structure of the POL2 Catalytic Domain of Dna Polymerase Epsilon Carrying A P301R Substitution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of the POL2 Catalytic Domain of Dna Polymerase Epsilon Carrying A P301R Substitution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1303

b:68.1
occ:0.80
OE2 A:GLU292 2.4 66.7 1.0
O A:HOH1412 2.5 65.0 1.0
O A:HOH1411 2.6 55.1 1.0
OD2 A:ASP290 2.7 63.6 1.0
OD2 A:ASP477 2.8 61.0 1.0
OD1 A:ASP290 3.3 60.7 1.0
CG A:ASP290 3.4 60.6 1.0
CD A:GLU292 3.6 64.9 1.0
CG A:ASP477 3.9 61.1 1.0
OE1 A:GLU292 4.1 62.6 1.0
OH A:TYR473 4.1 66.4 1.0
CB A:ASP477 4.4 57.9 1.0
O A:ILE291 4.5 60.1 1.0
CG A:GLU292 4.8 64.8 1.0
CB A:ASP290 4.8 56.5 1.0
CZ A:TYR473 4.9 65.9 1.0
OD1 A:ASP477 5.0 60.6 1.0

Reference:

V.Parkash, Y.Kulkarni, J.Ter Beek, P.V.Shcherbakova, S.C.L.Kamerlin, E.Johansson. Structural Consequence of the Most Frequently Recurring Cancer-Associated Substitution in Dna Polymerase Epsilon. Nat Commun V. 10 373 2019.
ISSN: ESSN 2041-1723
PubMed: 30670696
DOI: 10.1038/S41467-018-08114-9
Page generated: Tue Jul 16 07:59:19 2024

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