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Calcium in PDB 8b76: The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site

Enzymatic activity of The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site

All present enzymatic activity of The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site:
2.7.7.7;

Protein crystallography data

The structure of The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site, PDB code: 8b76 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) 86.83 / 2.60
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.16, 69.88, 159.05, 90, 112.63, 90
R / Rfree (%) 22 / 24.7

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site (pdb code 8b76). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site, PDB code: 8b76:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8b76

Go back to Calcium Binding Sites List in 8b76
Calcium binding site 1 out of 6 in the The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site


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 M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1201

b:85.3
occ:1.00
 OD2 A:ASP640 2.3 67.2 1.0
O A:HOH1309 3.1 47.3 1.0
O1G A:TTP1204 3.2 50.7 1.0
O3G A:TTP1204 3.3 45.3 1.0
CG A:ASP640 3.5 53.5 1.0
PG A:TTP1204 3.7 42.5 1.0
O2G A:TTP1204 4.3 44.5 1.0
NZ A:LYS785 4.4 59.2 1.0
OD1 A:ASP640 4.4 53.5 1.0
CB A:ASP640 4.4 40.1 1.0
CA A:CA1203 4.5 48.6 1.0
CE A:LYS785 4.7 64.5 1.0

Calcium binding site 2 out of 6 in 8b76

Go back to Calcium Binding Sites List in 8b76
Calcium binding site 2 out of 6 in the The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site


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 M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1202

b:81.4
occ:1.00
 OXT A:ACT1205 2.1 91.3 1.0
OE1 A:GLU292 2.2 82.6 1.0
OD1 A:ASP290 2.4 68.0 1.0
OD2 A:ASP477 2.4 71.8 1.0
O A:HOH1315 2.5 83.6 1.0
C A:ACT1205 2.7 82.5 1.0
O A:ACT1205 2.7 83.9 1.0
CG A:ASP290 3.0 75.9 1.0
OD2 A:ASP290 3.1 84.0 1.0
CD A:GLU292 3.2 82.7 1.0
CG A:ASP477 3.5 65.4 1.0
OE2 A:GLU292 3.6 87.9 1.0
CB A:ASP477 4.0 58.9 1.0
CH3 A:ACT1205 4.2 66.8 1.0
O A:ILE291 4.3 76.6 1.0
CB A:ASP290 4.4 68.7 1.0
OH A:TYR473 4.4 90.8 1.0
CG A:GLU292 4.5 73.1 1.0
OD1 A:ASP477 4.6 59.4 1.0
CE2 A:TYR473 4.7 83.2 1.0
CZ A:TYR473 5.0 81.9 1.0

Calcium binding site 3 out of 6 in 8b76

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Calcium binding site 3 out of 6 in the The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site


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 M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1203

b:48.6
occ:1.00
 O1G A:TTP1204 2.0 50.7 1.0
OD1 A:ASP640 2.1 53.5 1.0
O1B A:TTP1204 2.1 47.6 1.0
OD2 A:ASP877 2.2 39.4 1.0
O1A A:TTP1204 2.3 46.9 1.0
O A:VAL641 2.3 49.7 1.0
CG A:ASP640 2.9 53.5 1.0
OD2 A:ASP640 3.1 67.2 1.0
CG A:ASP877 3.1 48.7 1.0
PB A:TTP1204 3.3 35.2 1.0
PG A:TTP1204 3.3 42.5 1.0
OD1 A:ASP877 3.4 64.2 1.0
C A:VAL641 3.5 45.4 1.0
PA A:TTP1204 3.5 37.2 1.0
O3B A:TTP1204 3.6 42.2 1.0
O3A A:TTP1204 3.7 59.0 1.0
N A:VAL641 4.1 40.8 1.0
O2G A:TTP1204 4.1 44.5 1.0
C5' A:TTP1204 4.2 37.3 1.0
CB A:ASP640 4.3 40.1 1.0
N A:SER643 4.3 41.6 1.0
O A:HOH1309 4.3 47.3 1.0
CA A:VAL641 4.4 46.3 1.0
N A:GLY644 4.4 43.2 1.0
N A:ALA642 4.4 46.1 1.0
O3G A:TTP1204 4.4 45.3 1.0
O5' A:TTP1204 4.4 38.4 1.0
CA A:ALA642 4.5 44.2 1.0
C A:ASP640 4.5 49.5 1.0
CB A:ASP877 4.5 37.4 1.0
CA A:CA1201 4.5 85.3 1.0
O2A A:TTP1204 4.6 39.6 1.0
O2B A:TTP1204 4.6 46.6 1.0
C A:ALA642 4.7 47.2 1.0
CA A:ASP640 4.9 50.5 1.0
CB A:VAL641 4.9 44.1 1.0
O A:ASP640 5.0 45.6 1.0

Calcium binding site 4 out of 6 in 8b76

Go back to Calcium Binding Sites List in 8b76
Calcium binding site 4 out of 6 in the The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site


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 M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1301

b:46.6
occ:1.00
 OD1 B:ASP640 2.0 59.9 1.0
O1B B:TTP1304 2.1 40.3 1.0
O1G B:TTP1304 2.1 53.1 1.0
OD2 B:ASP877 2.2 45.7 1.0
O1A B:TTP1304 2.2 44.9 1.0
O B:VAL641 2.3 56.1 1.0
CG B:ASP640 3.0 63.4 1.0
CG B:ASP877 3.1 54.0 1.0
PB B:TTP1304 3.2 38.0 1.0
OD1 B:ASP877 3.3 56.7 1.0
PA B:TTP1304 3.4 50.8 1.0
OD2 B:ASP640 3.4 66.7 1.0
PG B:TTP1304 3.4 48.1 1.0
O3A B:TTP1304 3.5 57.2 1.0
C B:VAL641 3.6 50.6 1.0
O3B B:TTP1304 3.7 40.5 1.0
C5' B:TTP1304 4.0 40.9 1.0
N B:VAL641 4.2 43.9 1.0
O5' B:TTP1304 4.2 34.5 1.0
N B:GLY644 4.2 41.4 1.0
O2G B:TTP1304 4.3 58.1 1.0
CB B:ASP640 4.3 48.5 1.0
CA B:VAL641 4.4 49.1 1.0
O3G B:TTP1304 4.4 46.9 1.0
N B:SER643 4.4 40.6 1.0
CB B:ASP877 4.4 48.3 1.0
N B:ALA642 4.5 50.2 1.0
O2B B:TTP1304 4.5 45.4 1.0
O2A B:TTP1304 4.6 40.3 1.0
CA B:ALA642 4.6 52.0 1.0
C B:ASP640 4.6 49.6 1.0
CA B:CA1302 4.7 84.1 1.0
CA B:GLY644 4.8 40.6 1.0
C B:ALA642 4.8 48.1 1.0
CB B:VAL641 4.8 41.3 1.0

Calcium binding site 5 out of 6 in 8b76

Go back to Calcium Binding Sites List in 8b76
Calcium binding site 5 out of 6 in the The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site


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 M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1302

b:84.1
occ:1.00
 OD2 B:ASP640 2.0 66.7 1.0
CG B:ASP640 3.2 63.4 1.0
O1G B:TTP1304 3.3 53.1 1.0
O3G B:TTP1304 3.5 46.9 1.0
PG B:TTP1304 3.7 48.1 1.0
OD1 B:ASP640 4.0 59.9 1.0
O2G B:TTP1304 4.1 58.1 1.0
CB B:ASP640 4.1 48.5 1.0
NZ B:LYS785 4.2 60.0 1.0
OE1 B:GLU945 4.6 74.1 1.0
CA B:CA1301 4.7 46.6 1.0
CE B:LYS785 4.8 69.5 1.0
O B:ASP640 4.8 52.4 1.0
O B:VAL641 5.0 56.1 1.0

Calcium binding site 6 out of 6 in 8b76

Go back to Calcium Binding Sites List in 8b76
Calcium binding site 6 out of 6 in the The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Crystal Structure of M644G Variant of Dna Pol Epsilon Containing Dttp in the Polymerase Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1303

b:72.3
occ:1.00
 OD2 B:ASP290 2.1 75.6 1.0
OXT B:ACT1305 2.1 85.2 1.0
OE2 B:GLU292 2.3 66.7 1.0
OD2 B:ASP477 2.4 57.8 1.0
OD1 B:ASP290 2.5 74.1 1.0
O B:HOH1402 2.6 71.4 1.0
CG B:ASP290 2.6 64.8 1.0
O B:HOH1406 2.6 65.8 1.0
C B:ACT1305 3.0 84.1 1.0
O B:ACT1305 3.3 72.7 1.0
CD B:GLU292 3.4 74.1 1.0
CG B:ASP477 3.5 64.3 1.0
CB B:ASP477 3.8 61.7 1.0
OE1 B:GLU292 3.9 74.8 1.0
CB B:ASP290 4.1 60.1 1.0
O B:ILE291 4.1 61.9 1.0
CH3 B:ACT1305 4.4 76.6 1.0
CG B:GLU292 4.5 68.7 1.0
OD1 B:ASP477 4.6 68.0 1.0
OH B:TYR473 4.7 79.7 1.0

Reference:

V.Parkash, Y.Kulkarni, G.O.Bylund, P.Osterman, S.C.L.Kamerlin, E.Johansson. A Sensor Complements the Steric Gate When Dna Polymerase Epsilon Discriminates Ribonucleotides. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37819038
DOI: 10.1093/NAR/GKAD817
Page generated: Thu Dec 28 01:34:31 2023

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