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Calcium in PDB 6fwk: The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide

Enzymatic activity of The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide

All present enzymatic activity of The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide:
2.7.7.7;

Protein crystallography data

The structure of The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide, PDB code: 6fwk 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) 19.99 / 2.50
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 153.961, 70.342, 158.965, 90.00, 112.82, 90.00
R / Rfree (%) 22.3 / 26.3

Other elements in 6fwk:

The structure of The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide 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 POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide (pdb code 6fwk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide, PDB code: 6fwk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6fwk

Go back to Calcium Binding Sites List in 6fwk
Calcium binding site 1 out of 5 in the The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide


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 POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1302

b:60.4
occ:1.00
 O2A A:DTP1301 1.9 50.3 1.0
O2B A:DTP1301 2.0 54.1 1.0
O3G A:DTP1301 2.0 56.1 1.0
OD1 A:ASP640 2.1 60.5 1.0
OD2 A:ASP877 2.2 61.6 1.0
O A:VAL641 2.3 53.6 1.0
CG A:ASP877 3.1 60.5 1.0
PB A:DTP1301 3.2 54.7 1.0
PA A:DTP1301 3.3 52.1 1.0
CG A:ASP640 3.3 59.6 1.0
OD1 A:ASP877 3.3 67.8 1.0
PG A:DTP1301 3.3 61.4 1.0
C A:VAL641 3.5 55.2 1.0
O3A A:DTP1301 3.6 64.3 1.0
O3B A:DTP1301 3.6 54.2 1.0
OD2 A:ASP640 3.7 70.7 1.0
O2G A:DTP1301 4.0 61.7 1.0
C5' A:DTP1301 4.0 51.0 1.0
N A:VAL641 4.1 56.4 1.0
O5' A:DTP1301 4.2 45.9 1.0
N A:GLY644 4.3 53.5 1.0
CA A:VAL641 4.3 52.2 1.0
O1A A:DTP1301 4.3 50.1 1.0
N A:SER643 4.4 54.8 1.0
O1B A:DTP1301 4.5 60.6 1.0
O1G A:DTP1301 4.5 67.0 1.0
C A:ASP640 4.5 59.7 1.0
CB A:ASP877 4.5 52.4 1.0
CB A:ASP640 4.5 53.5 1.0
N A:ALA642 4.5 53.3 1.0
CA A:ALA642 4.7 54.5 1.0
CB A:VAL641 4.7 55.0 1.0
C A:ALA642 4.9 56.6 1.0
CA A:GLY644 4.9 51.8 1.0
CA A:ASP640 4.9 56.5 1.0
O A:ASP640 5.0 54.4 1.0

Calcium binding site 2 out of 5 in 6fwk

Go back to Calcium Binding Sites List in 6fwk
Calcium binding site 2 out of 5 in the The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide


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 POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1303

b:82.7
occ:0.75
 O A:HOH1401 2.4 81.3 1.0
OD1 A:ASP290 2.5 72.2 1.0
OE1 A:GLU292 2.6 83.2 1.0
OD2 A:ASP290 2.6 77.3 1.0
O A:HOH1405 2.7 60.3 1.0
OD2 A:ASP477 2.7 76.4 1.0
O A:HOH1403 2.7 77.7 1.0
CG A:ASP290 2.8 75.0 1.0
CD A:GLU292 3.7 82.9 1.0
CG A:ASP477 3.8 75.4 1.0
O A:ILE291 4.0 76.5 1.0
OE2 A:GLU292 4.2 80.2 1.0
CB A:ASP477 4.2 66.0 1.0
CB A:ASP290 4.2 68.7 1.0
OH A:TYR473 4.3 89.8 1.0
CG A:GLU292 4.8 77.7 1.0
OD1 A:ASP477 4.8 78.2 1.0
CE2 A:TYR473 4.9 85.6 1.0
CZ A:TYR473 4.9 87.2 1.0

Calcium binding site 3 out of 5 in 6fwk

Go back to Calcium Binding Sites List in 6fwk
Calcium binding site 3 out of 5 in the The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide


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 POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1302

b:59.0
occ:1.00
 O1B B:DTP1301 2.1 56.0 1.0
O1A B:DTP1301 2.2 54.9 1.0
O B:VAL641 2.3 60.2 1.0
O1G B:DTP1301 2.3 62.0 1.0
OD1 B:ASP640 2.4 69.3 1.0
OD2 B:ASP877 2.4 57.1 1.0
CG B:ASP640 3.0 65.3 1.0
CG B:ASP877 3.1 58.9 1.0
OD2 B:ASP640 3.2 72.4 1.0
OD1 B:ASP877 3.2 64.7 1.0
PB B:DTP1301 3.4 52.5 1.0
C B:VAL641 3.5 59.2 1.0
PA B:DTP1301 3.6 47.2 1.0
PG B:DTP1301 3.6 65.3 1.0
O3B B:DTP1301 3.9 55.3 1.0
N B:VAL641 3.9 56.7 1.0
O3A B:DTP1301 3.9 63.4 1.0
O3G B:DTP1301 4.2 63.8 1.0
C5' B:DTP1301 4.2 52.2 1.0
CA B:VAL641 4.2 56.6 1.0
CB B:ASP640 4.3 56.4 1.0
C B:ASP640 4.4 60.9 1.0
O5' B:DTP1301 4.4 46.3 1.0
N B:ALA642 4.5 56.4 1.0
CB B:ASP877 4.5 56.1 1.0
N B:GLY644 4.5 59.6 1.0
N B:SER643 4.6 55.2 1.0
O2A B:DTP1301 4.7 52.2 1.0
O2B B:DTP1301 4.7 57.4 1.0
CA B:ALA642 4.7 60.1 1.0
O B:ASP877 4.7 58.8 1.0
CB B:VAL641 4.7 53.9 1.0
CA B:ASP640 4.8 59.3 1.0
O2G B:DTP1301 4.8 61.6 1.0
O B:ASP640 4.9 64.7 1.0
C B:ALA642 5.0 59.8 1.0
CA B:GLY644 5.0 50.0 1.0

Calcium binding site 4 out of 5 in 6fwk

Go back to Calcium Binding Sites List in 6fwk
Calcium binding site 4 out of 5 in the The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide


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 POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1303

b:86.8
occ:0.87
 OD2 B:ASP477 2.2 77.8 1.0
OE2 B:GLU292 2.5 88.9 1.0
OD2 B:ASP290 2.5 84.7 1.0
OD1 B:ASP290 2.7 81.9 1.0
CG B:ASP290 2.8 78.0 1.0
O B:HOH1404 3.0 74.3 1.0
O B:HOH1405 3.1 77.3 1.0
CG B:ASP477 3.1 76.8 1.0
CB B:ASP477 3.4 72.6 1.0
CD B:GLU292 3.6 85.2 1.0
OH B:TYR473 4.1 85.7 1.0
CA B:CA1304 4.1 90.9 0.7
CG B:GLU292 4.2 80.2 1.0
CB B:ASP290 4.2 70.3 1.0
OD1 B:ASP477 4.3 79.3 1.0
CE2 B:TYR473 4.3 82.6 1.0
O B:ILE291 4.4 72.5 1.0
CZ B:TYR473 4.4 82.6 1.0
OE1 B:GLU292 4.6 85.5 1.0
CA B:ASP477 4.9 69.5 1.0

Calcium binding site 5 out of 5 in 6fwk

Go back to Calcium Binding Sites List in 6fwk
Calcium binding site 5 out of 5 in the The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Crystal Structure of POL2CORE-M644G in Complex with Dna and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1304

b:90.9
occ:0.71
 OD1 B:ASP290 2.5 81.9 1.0
OD2 B:ASP383 2.6 70.4 1.0
O B:HOH1404 2.6 74.3 1.0
OD1 B:ASP383 2.8 73.1 1.0
CG B:ASP383 3.0 72.7 1.0
O B:HOH1406 3.1 69.0 1.0
CG B:ASP290 3.5 78.0 1.0
O B:HOH1405 3.6 77.3 1.0
O B:ILE291 3.7 72.5 1.0
CD2 B:PHE382 3.9 72.3 1.0
O B:HOH1403 4.1 63.7 1.0
CA B:CA1303 4.1 86.8 0.9
OD2 B:ASP290 4.1 84.7 1.0
O B:PHE377 4.2 63.9 1.0
CE2 B:PHE382 4.2 74.5 1.0
N B:ILE291 4.3 66.0 1.0
CB B:ASP383 4.5 68.4 1.0
CB B:ASP290 4.6 70.3 1.0
CA B:ASP290 4.7 66.4 1.0
C B:ILE291 4.7 73.0 1.0
CG1 B:ILE291 4.7 66.5 1.0
OE2 B:GLU292 4.9 88.9 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: Wed Jul 9 14:18:30 2025

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