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Calcium in PDB 7r3y: The Crystal Structure of the V426L Variant of POL2CORE in Complex with Dna and An Incoming Nucleotide

Enzymatic activity of The Crystal Structure of the V426L Variant of POL2CORE in Complex with Dna and An Incoming Nucleotide

All present enzymatic activity of The Crystal Structure of the V426L Variant of POL2CORE in Complex with Dna and An Incoming Nucleotide:
2.7.7.7;

Protein crystallography data

The structure of The Crystal Structure of the V426L Variant of POL2CORE in Complex with Dna and An Incoming Nucleotide, PDB code: 7r3y was solved by S.R.Barbari, A.K.Beach, J.G.Markgren, V.Parkash, E.Johansson, P.V.Shcherbakova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.84 / 2.60
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.4, 70.1, 159.5, 90, 113.1, 90
R / Rfree (%) 22 / 27

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of the V426L Variant of POL2CORE in Complex with Dna and An Incoming Nucleotide (pdb code 7r3y). 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 V426L Variant of POL2CORE in Complex with Dna and An Incoming Nucleotide, PDB code: 7r3y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7r3y

Go back to Calcium Binding Sites List in 7r3y
Calcium binding site 1 out of 4 in the The Crystal Structure of the V426L Variant of POL2CORE 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 the V426L Variant of POL2CORE in Complex with Dna and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1302

b:74.8
occ:1.00
 O3G A:DTP1301 1.9 75.0 1.0
OD2 A:ASP877 2.1 77.5 1.0
OD1 A:ASP640 2.1 76.8 1.0
O1A A:DTP1301 2.2 60.0 1.0
O1B A:DTP1301 2.2 68.5 1.0
O A:VAL641 2.3 63.5 1.0
CG A:ASP640 3.1 76.2 1.0
CG A:ASP877 3.2 71.8 1.0
PG A:DTP1301 3.3 65.5 1.0
PB A:DTP1301 3.3 61.2 1.0
PA A:DTP1301 3.4 59.7 1.0
C A:VAL641 3.5 64.8 1.0
OD2 A:ASP640 3.6 83.2 1.0
O3B A:DTP1301 3.6 67.0 1.0
O3A A:DTP1301 3.6 85.1 1.0
OD1 A:ASP877 3.7 76.7 1.0
C5' A:DTP1301 4.1 55.0 1.0
O1G A:DTP1301 4.1 68.7 1.0
N A:VAL641 4.2 68.2 1.0
O5' A:DTP1301 4.3 55.9 1.0
CB A:ASP640 4.3 59.3 1.0
N A:SER643 4.3 54.5 1.0
CB A:ASP877 4.3 69.1 1.0
O2G A:DTP1301 4.3 64.8 1.0
CA A:VAL641 4.4 69.6 1.0
N A:ALA642 4.5 68.5 1.0
CA A:ALA642 4.5 63.0 1.0
C A:ASP640 4.5 73.4 1.0
O2A A:DTP1301 4.6 69.3 1.0
N A:MET644 4.7 63.4 1.0
O2B A:DTP1301 4.7 61.8 1.0
C A:ALA642 4.7 60.7 1.0
CA A:ASP640 4.9 68.6 1.0
CB A:VAL641 4.9 68.0 1.0
CB A:MET644 5.0 58.1 1.0
O A:ASP640 5.0 68.1 1.0

Calcium binding site 2 out of 4 in 7r3y

Go back to Calcium Binding Sites List in 7r3y
Calcium binding site 2 out of 4 in the The Crystal Structure of the V426L Variant of POL2CORE 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 the V426L Variant of POL2CORE in Complex with Dna and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1303

b:134.9
occ:1.00
 OE1 A:GLU292 2.1 116.5 1.0
OD2 A:ASP290 2.3 103.6 1.0
O A:HOH1402 2.5 99.1 1.0
CD A:GLU292 2.6 118.5 1.0
OE2 A:GLU292 2.6 121.2 1.0
OD1 A:ASP290 2.6 101.2 1.0
CG A:ASP290 2.8 99.0 1.0
OD2 A:ASP477 2.9 104.2 1.0
O A:ILE291 3.7 99.6 1.0
CG A:GLU292 3.9 110.7 1.0
CG A:ASP477 4.0 100.6 1.0
CB A:ASP290 4.3 93.0 1.0
OH A:TYR473 4.5 113.6 1.0
C A:ILE291 4.5 97.2 1.0
CB A:ASP477 4.5 95.1 1.0
N A:ILE291 4.8 85.5 1.0
CB A:GLU292 4.9 98.4 1.0
CE2 A:TYR473 4.9 108.0 1.0
CA A:GLU292 5.0 101.6 1.0

Calcium binding site 3 out of 4 in 7r3y

Go back to Calcium Binding Sites List in 7r3y
Calcium binding site 3 out of 4 in the The Crystal Structure of the V426L Variant of POL2CORE 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 the V426L Variant of POL2CORE in Complex with Dna and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1302

b:64.4
occ:1.00
 OD2 B:ASP877 2.0 76.1 1.0
O3G B:DTP1301 2.0 72.5 1.0
O B:VAL641 2.1 73.6 1.0
O1A B:DTP1301 2.1 65.7 1.0
OD1 B:ASP640 2.2 79.8 1.0
O1B B:DTP1301 2.4 64.5 1.0
CG B:ASP640 3.0 73.5 1.0
OD2 B:ASP640 3.1 78.2 1.0
CG B:ASP877 3.1 74.6 1.0
C B:VAL641 3.3 62.9 1.0
PG B:DTP1301 3.4 63.7 1.0
PA B:DTP1301 3.5 73.7 1.0
PB B:DTP1301 3.5 76.2 1.0
OD1 B:ASP877 3.7 75.6 1.0
O3B B:DTP1301 3.8 67.3 1.0
O3A B:DTP1301 3.8 76.7 1.0
N B:VAL641 4.0 68.9 1.0
C5' B:DTP1301 4.2 53.9 1.0
N B:ALA642 4.2 74.5 1.0
O1G B:DTP1301 4.2 79.8 1.0
CA B:ALA642 4.2 69.7 1.0
CA B:VAL641 4.2 73.0 1.0
CG2 B:VAL641 4.3 75.1 1.0
CB B:ASP877 4.3 68.8 1.0
O5' B:DTP1301 4.4 64.7 1.0
N B:SER643 4.4 60.2 1.0
CB B:ASP640 4.4 63.1 1.0
C B:ASP640 4.4 77.7 1.0
O2G B:DTP1301 4.5 64.8 1.0
O2A B:DTP1301 4.6 64.4 1.0
C B:ALA642 4.6 65.8 1.0
O2B B:DTP1301 4.9 72.7 1.0
N B:MET644 4.9 69.0 1.0
CA B:ASP640 4.9 70.8 1.0
O B:ASP640 4.9 78.2 1.0
CB B:VAL641 5.0 71.1 1.0

Calcium binding site 4 out of 4 in 7r3y

Go back to Calcium Binding Sites List in 7r3y
Calcium binding site 4 out of 4 in the The Crystal Structure of the V426L Variant of POL2CORE 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 the V426L Variant of POL2CORE in Complex with Dna and An Incoming Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1303

b:111.1
occ:1.00
 OD2 B:ASP290 2.3 111.3 1.0
OD2 B:ASP477 2.5 90.9 1.0
O B:HOH1405 2.6 81.9 1.0
OE2 B:GLU292 2.9 111.3 1.0
CG B:ASP290 2.9 110.2 1.0
OD1 B:ASP290 2.9 110.2 1.0
CG B:ASP477 3.6 93.3 1.0
CD B:GLU292 4.1 113.4 1.0
CB B:ASP477 4.2 102.2 1.0
CB B:ASP290 4.4 94.7 1.0
OH B:TYR473 4.5 94.3 1.0
O B:ILE291 4.7 103.2 1.0
OD1 B:ASP477 4.7 97.2 1.0
OE1 B:GLU292 4.8 107.7 1.0

Reference:

S.R.Barbari, A.K.Beach, J.G.Markgren, V.Parkash, E.A.Moore, E.Johansson, P.V.Shcherbakova. Enhanced Polymerase Activity Permits Efficient Synthesis By Cancer-Associated Dna Polymerase ε Variants at Low Dntp Levels. Nucleic Acids Res. V. 50 8023 2022.
ISSN: ESSN 1362-4962
PubMed: 35822874
DOI: 10.1093/NAR/GKAC602
Page generated: Thu Jul 10 00:41:10 2025

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