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Calcium in PDB 3qev: RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt

Enzymatic activity of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt

All present enzymatic activity of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt, PDB code: 3qev 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) 45.50 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.018, 119.553, 130.369, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt (pdb code 3qev). 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 (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt, PDB code: 3qev:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3qev

Go back to Calcium Binding Sites List in 3qev
Calcium binding site 1 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt


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 (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:19.1
occ:1.00
 OD1 A:ASP623 2.3 27.2 1.0
O1G A:DCP904 2.3 18.2 1.0
O2B A:DCP904 2.3 15.0 1.0
O A:LEU412 2.3 17.8 1.0
OD2 A:ASP411 2.4 30.0 1.0
O2A A:DCP904 2.5 21.6 1.0
OD1 A:ASP411 2.6 33.2 1.0
CG A:ASP411 2.8 25.1 1.0
PB A:DCP904 3.3 17.6 1.0
CG A:ASP623 3.3 21.8 1.0
C A:LEU412 3.5 18.1 1.0
PG A:DCP904 3.5 19.3 1.0
PA A:DCP904 3.6 19.8 1.0
CA A:CA906 3.7 40.4 1.0
O3A A:DCP904 3.7 19.5 1.0
OD2 A:ASP623 3.8 22.8 1.0
O3B A:DCP904 3.8 19.0 1.0
O A:HOH1280 3.9 33.9 1.0
N A:LEU412 4.1 16.6 1.0
O2G A:DCP904 4.2 17.6 1.0
CB A:ASP411 4.3 23.3 1.0
CA A:LEU412 4.3 17.1 1.0
C5' A:DCP904 4.3 15.5 1.0
N A:SER414 4.4 16.4 1.0
O A:HOH1641 4.4 45.2 1.0
N A:THR413 4.5 17.5 1.0
O5' A:DCP904 4.5 17.6 1.0
C A:ASP411 4.5 18.6 1.0
CB A:ASP623 4.6 19.0 1.0
CA A:THR413 4.6 17.8 1.0
N A:LEU415 4.7 13.2 1.0
O3G A:DCP904 4.7 19.8 1.0
C A:THR413 4.7 17.4 1.0
O1B A:DCP904 4.7 21.2 1.0
O1A A:DCP904 4.8 18.8 1.0
CB A:LEU412 4.8 17.6 1.0
CA A:ASP411 4.9 20.4 1.0

Calcium binding site 2 out of 6 in 3qev

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Calcium binding site 2 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt


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 (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:40.4
occ:1.00
 O A:HOH1171 2.2 33.7 1.0
OD2 A:ASP411 2.4 30.0 1.0
O2A A:DCP904 2.5 21.6 1.0
OD2 A:ASP623 2.6 22.8 1.0
O A:HOH1462 3.2 36.6 1.0
CG A:ASP623 3.5 21.8 1.0
CG A:ASP411 3.6 25.1 1.0
OD1 A:ASP623 3.7 27.2 1.0
CA A:CA905 3.7 19.1 1.0
PA A:DCP904 3.8 19.8 1.0
C3' P:DOC115 3.9 22.5 1.0
O A:HOH1280 3.9 33.9 1.0
CB A:SER624 4.0 22.3 1.0
O1A A:DCP904 4.2 18.8 1.0
O A:HOH1099 4.3 28.2 1.0
OD1 A:ASP411 4.4 33.2 1.0
CB A:ASP411 4.4 23.3 1.0
O5' A:DCP904 4.4 17.6 1.0
OG A:SER624 4.5 25.8 1.0
C5' A:DCP904 4.6 15.5 1.0
N A:SER624 4.7 18.1 1.0
O A:ASP621 4.7 15.9 1.0
C5' P:DOC115 4.7 25.8 1.0
C A:ASP623 4.7 18.9 1.0
CA A:SER624 4.8 19.4 1.0
O5' P:DOC115 4.9 24.6 1.0
C4' P:DOC115 4.9 20.8 1.0
CB A:ASP623 4.9 19.0 1.0
O P:HOH516 4.9 33.8 1.0
O A:ASP623 4.9 18.6 1.0
O1G A:DCP904 4.9 18.2 1.0

Calcium binding site 3 out of 6 in 3qev

Go back to Calcium Binding Sites List in 3qev
Calcium binding site 3 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt


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 (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:30.0
occ:1.00
 OD1 A:ASN507 2.2 35.2 1.0
O A:LYS531 2.3 33.5 1.0
O A:ASN505 2.3 34.4 1.0
O A:HOH1163 2.4 38.2 1.0
O A:HOH968 2.4 26.2 1.0
O A:HOH1113 2.6 29.6 1.0
C A:LYS531 3.3 33.2 1.0
CG A:ASN507 3.4 36.8 1.0
C A:ASN505 3.6 35.3 1.0
ND2 A:ASN507 4.0 34.6 1.0
CA A:LYS531 4.0 31.4 1.0
N A:ASN507 4.1 35.5 1.0
N A:LYS532 4.2 32.9 1.0
CB A:ASN505 4.2 38.5 1.0
C A:PRO506 4.3 35.4 1.0
CA A:PRO506 4.4 34.5 1.0
CA A:LYS532 4.4 33.4 1.0
N A:PRO506 4.4 34.2 1.0
CA A:ASN505 4.5 37.0 1.0
CB A:ASN507 4.5 35.7 1.0
O A:LEU533 4.5 29.1 1.0
O A:HOH1120 4.5 32.2 1.0
O A:ALA502 4.7 29.6 1.0
CB A:LYS531 4.7 33.1 1.0
CA A:ASN507 4.7 35.2 1.0
C A:LYS532 4.8 33.0 1.0
N A:LEU533 4.9 30.9 1.0
O A:ILE530 4.9 27.8 1.0
O A:PRO506 4.9 35.7 1.0

Calcium binding site 4 out of 6 in 3qev

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Calcium binding site 4 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt


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 (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:77.0
occ:1.00
 O A:HOH1398 2.4 53.4 1.0
O A:HOH1353 2.4 40.2 1.0
O A:HOH1641 2.6 45.2 1.0
OE1 A:GLU716 2.7 42.4 1.0
O A:HOH1306 2.8 40.1 1.0
CD A:GLU716 3.6 37.5 1.0
OD1 A:ASP411 4.0 33.2 1.0
O A:HOH1135 4.1 25.2 1.0
CG A:GLU716 4.1 32.7 1.0
NZ A:LYS486 4.2 27.1 1.0
OG1 A:THR413 4.5 22.1 1.0
O A:ASP411 4.5 19.9 1.0
OE1 A:GLU686 4.5 37.4 1.0
OE2 A:GLU716 4.6 38.2 1.0
CB A:ASP684 4.7 27.8 1.0
O A:HOH1487 4.7 41.8 1.0
CG A:ASP411 4.9 25.1 1.0
OD2 A:ASP684 4.9 38.4 1.0
CB A:ASP411 4.9 23.3 1.0
O A:HOH1537 5.0 43.4 1.0

Calcium binding site 5 out of 6 in 3qev

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Calcium binding site 5 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt


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 (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:41.2
occ:1.00
 O A:HOH1088 2.2 29.9 1.0
O A:HOH1234 2.4 35.7 1.0
O A:HOH932 2.5 25.2 1.0
OE2 A:GLU116 2.6 26.3 1.0
OE1 A:GLU116 2.6 26.3 1.0
CD A:GLU116 2.9 26.2 1.0
O A:HOH1431 4.1 33.6 1.0
OD2 A:ASP114 4.1 31.8 1.0
O A:HOH1677 4.3 38.1 1.0
O A:HOH1360 4.4 39.3 1.0
CG A:GLU116 4.5 20.2 1.0
O A:ILE115 4.5 17.7 1.0
CD1 A:ILE309 4.8 41.4 1.0

Calcium binding site 6 out of 6 in 3qev

Go back to Calcium Binding Sites List in 3qev
Calcium binding site 6 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt


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 (L561A/S565G/Y567A) Ternary Complex with Dctp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca1

b:55.5
occ:1.00
 O T:HOH545 2.4 38.7 1.0
O T:HOH564 2.6 37.3 1.0
O T:HOH562 2.6 35.3 1.0
O T:HOH563 2.6 47.1 1.0
O6 T:DG12 4.6 25.3 1.0
N7 T:DG12 4.6 25.9 1.0
O4 T:DT13 4.6 29.0 1.0
N7 P:DG105 4.6 49.5 1.0
C8 P:DG105 4.8 51.3 1.0
O6 P:DG106 4.8 36.3 1.0
N6 P:DA107 4.9 30.8 1.0
N7 P:DG106 4.9 39.2 1.0

Reference:

S.Xia, W.H.Konigsberg, J.Wang. Hydrogen-Bonding Capability of Difluorotoluene Nucleoside in Replication Complexes To Be Published.
Page generated: Tue Jul 8 15:57:38 2025

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