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Calcium in PDB 3uiq: RB69 Dna Polymerase Ternary Complex Containing Dupnpp

Enzymatic activity of RB69 Dna Polymerase Ternary Complex Containing Dupnpp

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex Containing Dupnpp:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Ternary Complex Containing Dupnpp, PDB code: 3uiq 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) 49.23 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.243, 120.204, 130.213, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex Containing Dupnpp (pdb code 3uiq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the RB69 Dna Polymerase Ternary Complex Containing Dupnpp, PDB code: 3uiq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3uiq

Go back to Calcium Binding Sites List in 3uiq
Calcium binding site 1 out of 6 in the RB69 Dna Polymerase Ternary Complex Containing Dupnpp


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 Containing Dupnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:51.3
occ:1.00
 O1G A:DUP904 2.2 45.4 1.0
O2B A:DUP904 2.2 36.4 1.0
O A:LEU412 2.3 25.8 1.0
OD1 A:ASP411 2.4 44.7 1.0
OD1 A:ASP623 2.5 40.5 1.0
OD2 A:ASP411 3.0 48.1 1.0
CG A:ASP411 3.0 40.1 1.0
PG A:DUP904 3.0 50.5 1.0
O3G A:DUP904 3.2 45.9 1.0
PB A:DUP904 3.3 48.1 1.0
CA A:CA907 3.3 49.9 1.0
C A:LEU412 3.4 27.7 1.0
O3B A:DUP904 3.5 46.4 1.0
N3A A:DUP904 3.7 42.5 1.0
O A:HOH1229 3.7 58.1 1.0
CG A:ASP623 3.7 32.8 1.0
N A:SER414 4.0 25.2 1.0
O2A A:DUP904 4.1 42.6 1.0
N A:LEU412 4.2 26.7 1.0
N A:THR413 4.3 26.5 1.0
O2G A:DUP904 4.3 63.4 1.0
CA A:THR413 4.3 26.7 1.0
CA A:LEU412 4.4 27.4 1.0
C A:THR413 4.4 26.5 1.0
CB A:ASP411 4.4 32.5 1.0
OD2 A:ASP623 4.5 31.8 1.0
PA A:DUP904 4.6 41.2 1.0
C A:ASP411 4.6 27.9 1.0
CB A:ASP623 4.6 26.9 1.0
O1B A:DUP904 4.6 43.0 1.0
O A:HOH1038 4.7 42.7 1.0
CA A:SER414 4.7 25.5 1.0
N A:LEU415 4.8 21.4 1.0
CA A:CA908 4.8 90.3 1.0

Calcium binding site 2 out of 6 in 3uiq

Go back to Calcium Binding Sites List in 3uiq
Calcium binding site 2 out of 6 in the RB69 Dna Polymerase Ternary Complex Containing Dupnpp


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 Containing Dupnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:66.6
occ:1.00
 O A:HOH1156 2.4 44.9 1.0
OD1 A:ASP684 2.4 39.4 1.0
OE1 A:GLU660 3.0 43.0 1.0
CG A:ASP684 3.6 41.0 1.0
CD A:GLU660 3.7 37.8 1.0
CB A:GLU660 4.3 36.4 1.0
O A:MET683 4.3 35.6 1.0
CG A:GLU660 4.3 35.1 1.0
OD2 A:ASP684 4.4 45.2 1.0
OD1 A:ASP664 4.4 45.9 1.0
OD2 A:ASP664 4.5 42.7 1.0
OE2 A:GLU660 4.5 36.0 1.0
CB A:ASP684 4.6 36.1 1.0
CA A:ASP684 4.7 34.0 1.0
C A:MET683 4.9 33.1 1.0
CG A:ASP664 4.9 43.4 1.0

Calcium binding site 3 out of 6 in 3uiq

Go back to Calcium Binding Sites List in 3uiq
Calcium binding site 3 out of 6 in the RB69 Dna Polymerase Ternary Complex Containing Dupnpp


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 Containing Dupnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:49.9
occ:1.00
 O2A A:DUP904 2.2 42.6 1.0
O A:HOH1231 2.3 46.0 1.0
OD2 A:ASP411 2.4 48.1 1.0
O A:HOH1230 2.5 40.0 1.0
OD1 A:ASP623 2.7 40.5 1.0
OD2 A:ASP623 2.8 31.8 1.0
O A:HOH1229 2.8 58.1 1.0
CG A:ASP623 3.1 32.8 1.0
CA A:CA905 3.3 51.3 1.0
CG A:ASP411 3.4 40.1 1.0
O1G A:DUP904 3.5 45.4 1.0
PA A:DUP904 3.5 41.2 1.0
O3' P:DC115 3.8 30.7 1.0
OD1 A:ASP411 3.8 44.7 1.0
N3A A:DUP904 3.8 42.5 1.0
O2B A:DUP904 4.3 36.4 1.0
C3' P:DC115 4.4 28.7 1.0
O1A A:DUP904 4.5 42.0 1.0
O5' A:DUP904 4.5 30.9 1.0
CB A:ASP411 4.6 32.5 1.0
OE1 A:GLU686 4.6 42.1 1.0
CB A:ASP623 4.6 26.9 1.0
C5' A:DUP904 4.7 23.8 1.0
PB A:DUP904 4.7 48.1 1.0
O A:HOH1218 4.9 48.4 1.0
CB A:SER624 4.9 26.6 1.0
PG A:DUP904 4.9 50.5 1.0

Calcium binding site 4 out of 6 in 3uiq

Go back to Calcium Binding Sites List in 3uiq
Calcium binding site 4 out of 6 in the RB69 Dna Polymerase Ternary Complex Containing Dupnpp


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 Containing Dupnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:90.3
occ:1.00
 O A:HOH1038 2.4 42.7 1.0
OD1 A:ASP411 3.1 44.7 1.0
OE1 A:GLU716 3.5 54.3 1.0
O A:ASP411 3.9 27.8 1.0
CG A:ASP411 4.0 40.1 1.0
CB A:ASP411 4.1 32.5 1.0
CD A:GLU716 4.3 49.2 1.0
NZ A:LYS486 4.5 41.1 1.0
C A:ASP411 4.5 27.9 1.0
OG1 A:THR413 4.6 33.0 1.0
OE1 A:GLU686 4.6 42.1 1.0
CB A:ASP684 4.7 36.1 1.0
O3G A:DUP904 4.7 45.9 1.0
CG A:GLU716 4.7 45.7 1.0
CA A:CA905 4.8 51.3 1.0
O A:LEU412 4.9 25.8 1.0
OD2 A:ASP684 4.9 45.2 1.0
CA A:THR413 4.9 26.7 1.0
CA A:ASP411 4.9 28.9 1.0
O A:ASP684 5.0 29.5 1.0
C A:LEU412 5.0 27.7 1.0
O A:HOH1229 5.0 58.1 1.0
N A:THR413 5.0 26.5 1.0

Calcium binding site 5 out of 6 in 3uiq

Go back to Calcium Binding Sites List in 3uiq
Calcium binding site 5 out of 6 in the RB69 Dna Polymerase Ternary Complex Containing Dupnpp


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 Containing Dupnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:51.3
occ:1.00
 O A:LYS531 2.2 55.2 1.0
OD1 A:ASN507 2.2 66.1 1.0
O A:ASN505 2.4 59.9 1.0
O A:HOH1132 2.4 34.1 1.0
O A:HOH1346 2.4 22.2 1.0
C A:LYS531 3.2 54.3 1.0
CG A:ASN507 3.4 67.2 1.0
C A:ASN505 3.6 60.9 1.0
N A:ASN507 4.0 64.8 1.0
ND2 A:ASN507 4.0 67.5 1.0
N A:LYS532 4.0 54.2 1.0
CA A:LYS531 4.0 53.0 1.0
CA A:LYS532 4.2 54.8 1.0
CB A:ASN505 4.3 62.5 1.0
CA A:PRO506 4.3 61.8 1.0
C A:PRO506 4.4 63.7 1.0
N A:PRO506 4.4 61.3 1.0
O A:LEU533 4.5 50.6 1.0
C A:LYS532 4.5 53.5 1.0
CB A:ASN507 4.6 66.8 1.0
CA A:ASN505 4.6 61.4 1.0
N A:LEU533 4.6 51.6 1.0
CA A:ASN507 4.7 66.4 1.0
CB A:LYS531 4.8 54.4 1.0
O A:ALA502 4.8 48.9 1.0
O A:ILE530 4.8 47.3 1.0

Calcium binding site 6 out of 6 in 3uiq

Go back to Calcium Binding Sites List in 3uiq
Calcium binding site 6 out of 6 in the RB69 Dna Polymerase Ternary Complex Containing Dupnpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of RB69 Dna Polymerase Ternary Complex Containing Dupnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:30.0
occ:1.00
 O A:HOH1338 2.3 28.4 1.0
O A:HOH1408 2.4 30.0 1.0
O A:HOH1409 2.5 30.0 1.0
OE1 A:GLU116 2.6 33.5 1.0
OE2 A:GLU116 2.6 34.8 1.0
O A:HOH1235 2.6 48.2 1.0
CD A:GLU116 2.9 32.8 1.0
OD2 A:ASP114 4.2 40.8 1.0
O A:HOH1234 4.2 33.4 1.0
O A:HOH1233 4.3 37.3 1.0
CG A:GLU116 4.5 26.7 1.0
O A:ILE115 4.6 23.9 1.0
CD1 A:ILE309 4.8 48.2 1.0

Reference:

S.Xia, S.H.Eom, W.H.Konigsberg, J.Wang. Bidentate and Tridentate Metal-Ion Coordination States Within Ternary Complexes of RB69 Dna Polymerase. Protein Sci. V. 21 447 2012.
ISSN: ISSN 0961-8368
PubMed: 22238207
DOI: 10.1002/PRO.2026
Page generated: Tue Jul 8 17:15:09 2025

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