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Calcium in PDB 3sq1: RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da, PDB code: 3sq1 was solved by S.Xia, W.H.Konigsberg, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.54 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.101, 120.470, 130.561, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.3

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da (pdb code 3sq1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da, PDB code: 3sq1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3sq1

Go back to Calcium Binding Sites List in 3sq1
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:28.4
occ:1.00
 OD1 A:ASP623 2.2 29.9 1.0
O1G A:DUP902 2.2 21.3 1.0
O2B A:DUP902 2.3 21.7 1.0
O A:LEU412 2.3 16.6 1.0
O A:HOH1397 2.4 24.6 1.0
OD1 A:ASP411 2.4 31.1 1.0
OD2 A:ASP411 2.8 34.2 1.0
CG A:ASP411 2.9 27.1 1.0
O2A A:DUP902 3.1 32.8 1.0
PB A:DUP902 3.3 23.7 1.0
PG A:DUP902 3.4 25.4 1.0
CG A:ASP623 3.4 22.8 1.0
C A:LEU412 3.5 17.0 1.0
O3B A:DUP902 3.7 25.4 1.0
CA A:CA906 3.7 74.2 1.0
N3A A:DUP902 3.8 27.3 1.0
O2G A:DUP902 4.0 24.8 1.0
PA A:DUP902 4.1 31.7 1.0
OD2 A:ASP623 4.1 23.4 1.0
CA A:CA905 4.1 45.7 1.0
N A:LEU412 4.1 17.1 1.0
N A:SER414 4.2 14.3 1.0
CA A:LEU412 4.4 16.6 1.0
CB A:ASP411 4.4 22.7 1.0
CB A:ASP623 4.4 19.8 1.0
O A:HOH1502 4.5 46.5 1.0
N A:THR413 4.5 16.2 1.0
O3G A:DUP902 4.5 99.0 1.0
C5' A:DUP902 4.5 20.6 1.0
CA A:THR413 4.6 16.8 1.0
C A:THR413 4.6 15.9 1.0
C A:ASP411 4.6 17.8 1.0
O1B A:DUP902 4.6 24.9 1.0
N A:LEU415 4.7 12.9 1.0
O5' A:DUP902 4.8 25.3 1.0
CB A:LEU412 4.9 15.0 1.0
CA A:SER414 4.9 15.1 1.0
CA A:ASP411 5.0 19.5 1.0

Calcium binding site 2 out of 5 in 3sq1

Go back to Calcium Binding Sites List in 3sq1
Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:57.5
occ:1.00
 OD1 A:ASP684 2.4 31.0 1.0
O A:HOH1519 2.5 37.3 1.0
OE1 A:GLU660 3.1 31.5 1.0
CG A:ASP684 3.5 29.9 1.0
CD A:GLU660 3.9 30.0 1.0
OD2 A:ASP684 4.2 34.3 1.0
OD1 A:ASP664 4.3 37.2 1.0
O A:MET683 4.3 25.6 1.0
OD2 A:ASP664 4.4 32.7 1.0
CB A:GLU660 4.4 26.7 1.0
CG A:GLU660 4.4 26.8 1.0
CB A:ASP684 4.6 26.0 1.0
OE2 A:GLU660 4.7 30.3 1.0
CA A:ASP684 4.8 23.9 1.0
CG A:ASP664 4.8 31.2 1.0
C A:MET683 4.9 23.6 1.0

Calcium binding site 3 out of 5 in 3sq1

Go back to Calcium Binding Sites List in 3sq1
Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:45.7
occ:1.00
 O A:HOH1397 2.4 24.6 1.0
O A:HOH1275 2.4 36.7 1.0
O2A A:DUP902 2.6 32.8 1.0
OD2 A:ASP623 2.7 23.4 1.0
O A:HOH1465 2.8 34.0 1.0
OD2 A:ASP411 2.9 34.2 1.0
CG A:ASP623 3.5 22.8 1.0
OD1 A:ASP623 3.5 29.9 1.0
C3' P:DOC115 3.7 18.4 1.0
CG A:ASP411 3.9 27.1 1.0
PA A:DUP902 3.9 31.7 1.0
CA A:CA903 4.1 28.4 1.0
CB A:SER624 4.1 20.4 1.0
O A:HOH1197 4.1 18.6 1.0
O A:HOH1502 4.3 46.5 1.0
O1A A:DUP902 4.3 31.1 1.0
OG A:SER624 4.4 25.7 1.0
OD1 A:ASP411 4.5 31.1 1.0
O5' P:DOC115 4.5 23.0 1.0
C5' P:DOC115 4.5 21.5 1.0
O P:HOH300 4.6 23.4 1.0
C4' P:DOC115 4.7 18.7 1.0
O5' A:DUP902 4.7 25.3 1.0
C5' A:DUP902 4.9 20.6 1.0
O A:ASP621 4.9 14.2 1.0
CB A:ASP411 4.9 22.7 1.0
C2' P:DOC115 4.9 18.6 1.0
CB A:ASP623 4.9 19.8 1.0
N A:SER624 4.9 17.0 1.0
N3A A:DUP902 5.0 27.3 1.0
OE2 A:GLU686 5.0 35.7 1.0
O1G A:DUP902 5.0 21.3 1.0

Calcium binding site 4 out of 5 in 3sq1

Go back to Calcium Binding Sites List in 3sq1
Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:74.2
occ:1.00
 O A:HOH1373 2.3 13.2 0.5
O A:HOH1373 2.4 7.7 0.5
OD1 A:ASP411 2.5 31.1 1.0
O A:HOH1387 2.9 27.0 1.0
O1G A:DUP902 3.0 21.3 1.0
O A:HOH1631 3.2 40.3 1.0
O2G A:DUP902 3.4 24.8 1.0
PG A:DUP902 3.5 25.4 1.0
CG A:ASP411 3.7 27.1 1.0
CA A:CA903 3.7 28.4 1.0
NZ A:LYS486 3.9 29.5 1.0
O A:HOH1125 3.9 30.3 1.0
O3G A:DUP902 4.0 99.0 1.0
O A:LEU412 4.0 16.6 1.0
OE1 A:GLU716 4.1 42.0 1.0
O A:HOH1397 4.2 24.6 1.0
O A:HOH1502 4.3 46.5 1.0
OE1 A:GLU686 4.3 31.8 1.0
CB A:ASP411 4.3 22.7 1.0
CA A:THR413 4.3 16.8 1.0
C A:LEU412 4.5 17.0 1.0
OD2 A:ASP411 4.6 34.2 1.0
CD A:GLU716 4.6 37.5 1.0
O A:ASP411 4.7 20.8 1.0
N A:THR413 4.7 16.2 1.0
OG1 A:THR413 4.8 21.4 1.0
C A:ASP411 4.9 17.8 1.0
O3B A:DUP902 4.9 25.4 1.0
OE2 A:GLU716 4.9 39.2 1.0
N A:SER414 5.0 14.3 1.0

Calcium binding site 5 out of 5 in 3sq1

Go back to Calcium Binding Sites List in 3sq1
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of RB69 Dna Polymerase Ternary Complex with Dupcpp Opposite Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:40.7
occ:1.00
 O A:LYS531 2.3 39.8 1.0
O A:ASN505 2.3 42.2 1.0
O A:HOH1655 2.4 17.8 1.0
OD1 A:ASN507 2.4 44.5 1.0
O A:HOH1209 2.6 18.4 1.0
C A:LYS531 3.3 39.1 1.0
CG A:ASN507 3.5 46.4 1.0
C A:ASN505 3.6 43.5 1.0
CA A:LYS531 4.0 38.3 1.0
CB A:ASN505 4.1 44.6 1.0
ND2 A:ASN507 4.1 45.6 1.0
O A:HOH1656 4.2 28.1 1.0
N A:LYS532 4.3 38.8 1.0
N A:ASN507 4.4 45.8 1.0
CA A:ASN505 4.4 43.8 1.0
C A:PRO506 4.5 45.7 1.0
CA A:PRO506 4.5 44.1 1.0
N A:PRO506 4.5 43.6 1.0
CA A:LYS532 4.6 39.1 1.0
CB A:LYS531 4.6 40.1 1.0
O A:ALA502 4.6 33.3 1.0
CB A:ASN507 4.8 46.9 1.0
O A:LEU533 4.8 36.1 1.0
CA A:ASN507 5.0 47.2 1.0
C A:LYS532 5.0 37.9 1.0

Reference:

S.Xia, M.Wang, G.Blaha, W.H.Konigsberg, J.Wang. Structural Insights Into Complete Metal Ion Coordination From Ternary Complexes of B Family RB69 Dna Polymerase. Biochemistry V. 50 9114 2011.
ISSN: ISSN 0006-2960
PubMed: 21923197
DOI: 10.1021/BI201260H
Page generated: Tue Jul 8 16:42:35 2025

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