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Calcium in PDB 6i8a: 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: 6i8a 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) 19.96 / 2.65
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.466, 70.257, 159.335, 90.00, 112.85, 90.00
R / Rfree (%) 22.9 / 27.9

Other elements in 6i8a:

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) 2 atoms

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 6i8a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 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: 6i8a:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6i8a

Go back to Calcium Binding Sites List in 6i8a
Calcium binding site 1 out of 4 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:63.5
occ:1.00
 OD1 A:ASP640 1.8 67.6 1.0
O3G A:DTP1301 2.1 61.6 1.0
OD2 A:ASP877 2.2 63.1 1.0
O2B A:DTP1301 2.2 57.8 1.0
O2A A:DTP1301 2.3 55.4 1.0
O A:VAL641 2.5 59.7 1.0
CG A:ASP640 2.8 63.0 1.0
PB A:DTP1301 3.2 56.6 1.0
CG A:ASP877 3.3 63.4 1.0
OD2 A:ASP640 3.3 65.4 1.0
PG A:DTP1301 3.4 54.9 1.0
PA A:DTP1301 3.4 56.9 1.0
O3A A:DTP1301 3.4 63.6 1.0
C A:VAL641 3.7 60.1 1.0
OD1 A:ASP877 3.8 63.7 1.0
O3B A:DTP1301 3.8 59.2 1.0
CB A:ASP640 4.1 57.7 1.0
O2G A:DTP1301 4.1 63.0 1.0
N A:VAL641 4.3 61.7 1.0
N A:SER643 4.4 54.1 1.0
O1A A:DTP1301 4.4 58.2 1.0
O1G A:DTP1301 4.5 62.6 1.0
CB A:ASP877 4.5 60.8 1.0
O1B A:DTP1301 4.5 56.3 1.0
CA A:VAL641 4.5 61.1 1.0
C A:ASP640 4.5 64.8 1.0
O5' A:DTP1301 4.6 52.2 1.0
N A:ALA642 4.6 61.3 1.0
C5' A:DTP1301 4.6 56.7 1.0
CA A:ALA642 4.6 58.6 1.0
CA A:ASP640 4.8 61.7 1.0
N A:MET644 4.8 58.1 1.0
C A:ALA642 4.9 57.8 1.0

Calcium binding site 2 out of 4 in 6i8a

Go back to Calcium Binding Sites List in 6i8a
Calcium binding site 2 out of 4 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:86.2
occ:0.80
 OE2 A:GLU292 2.3 85.6 1.0
O A:HOH1402 2.4 76.9 1.0
OD2 A:ASP477 2.4 80.4 1.0
OD2 A:ASP290 2.4 85.0 1.0
OD1 A:ASP290 3.0 82.8 1.0
CG A:ASP290 3.1 82.9 1.0
CG A:ASP477 3.4 82.1 1.0
CD A:GLU292 3.5 87.3 1.0
CB A:ASP477 3.8 77.4 1.0
OH A:TYR473 3.8 89.9 1.0
OE1 A:GLU292 4.1 85.7 1.0
O A:ILE291 4.5 82.7 1.0
OD1 A:ASP477 4.6 82.2 1.0
CZ A:TYR473 4.6 87.1 1.0
CB A:ASP290 4.6 80.7 1.0
CG A:GLU292 4.7 84.7 1.0
CE2 A:TYR473 4.7 86.6 1.0

Calcium binding site 3 out of 4 in 6i8a

Go back to Calcium Binding Sites List in 6i8a
Calcium binding site 3 out of 4 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 3 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
B:Ca1302

b:55.4
occ:1.00
 OD2 B:ASP877 2.1 62.8 1.0
OD2 B:ASP640 2.2 68.2 1.0
O1G B:DTP1301 2.3 60.7 1.0
O1B B:DTP1301 2.3 56.7 1.0
O B:VAL641 2.4 66.3 1.0
O1A B:DTP1301 2.5 52.8 1.0
CG B:ASP640 2.9 66.7 1.0
OD1 B:ASP640 3.0 70.0 1.0
CG B:ASP877 3.2 63.5 1.0
PB B:DTP1301 3.3 55.5 1.0
O3A B:DTP1301 3.5 61.6 1.0
PA B:DTP1301 3.6 52.5 1.0
C B:VAL641 3.6 61.4 1.0
PG B:DTP1301 3.6 60.0 1.0
OD1 B:ASP877 3.6 63.5 1.0
O3B B:DTP1301 3.9 55.8 1.0
N B:VAL641 4.1 65.9 1.0
N B:SER643 4.3 57.5 1.0
CB B:ASP640 4.3 65.9 1.0
O3G B:DTP1301 4.4 67.1 1.0
CA B:VAL641 4.4 64.1 1.0
CB B:ASP877 4.5 63.1 1.0
N B:ALA642 4.5 65.2 1.0
CA B:ALA642 4.5 62.9 1.0
C B:ASP640 4.5 66.8 1.0
C5' B:DTP1301 4.5 52.0 1.0
CG2 B:VAL641 4.5 65.0 1.0
O2B B:DTP1301 4.6 55.1 1.0
O5' B:DTP1301 4.6 52.5 1.0
O2A B:DTP1301 4.6 52.8 1.0
O2G B:DTP1301 4.6 61.9 1.0
C B:ALA642 4.8 61.0 1.0
N B:MET644 4.9 59.7 1.0
CA B:ASP640 4.9 67.5 1.0
O B:ASP877 5.0 66.6 1.0

Calcium binding site 4 out of 4 in 6i8a

Go back to Calcium Binding Sites List in 6i8a
Calcium binding site 4 out of 4 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 4 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
B:Ca1303

b:90.0
occ:0.80
 OD2 B:ASP477 2.3 82.2 1.0
OE1 B:GLU292 2.6 91.3 1.0
OD2 B:ASP290 2.6 87.8 1.0
O B:HOH1403 2.7 75.2 1.0
O B:HOH1401 2.8 86.3 1.0
OD1 B:ASP290 3.1 85.1 1.0
CG B:ASP290 3.2 84.5 1.0
CG B:ASP477 3.5 83.7 1.0
CD B:GLU292 3.9 92.0 1.0
CB B:ASP477 4.1 79.0 1.0
OH B:TYR473 4.2 84.0 1.0
OD1 B:ASP477 4.4 82.4 1.0
OE2 B:GLU292 4.6 91.6 1.0
O B:ILE291 4.7 87.1 1.0
CB B:ASP290 4.7 80.2 1.0
CG B:GLU292 4.8 89.2 1.0
CZ B:TYR473 4.8 85.6 1.0
CE2 B:TYR473 4.9 87.0 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 09:20:50 2024

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