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

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

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

Protein crystallography data

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp Opposite Dt, PDB code: 3qet 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) 50.00 / 2.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.381, 118.508, 130.117, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.7

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 3qet

Go back to Calcium Binding Sites List in 3qet
Calcium binding site 1 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp 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 Dttp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:34.7
occ:1.00
 OD1 A:ASP623 2.2 38.3 1.0
O1G A:TTP904 2.3 34.9 1.0
OD1 A:ASP411 2.3 47.3 1.0
O A:LEU412 2.3 37.5 1.0
O2A A:TTP904 2.3 33.8 1.0
O2B A:TTP904 2.4 27.9 1.0
CG A:ASP411 3.0 42.5 1.0
OD2 A:ASP411 3.1 51.7 1.0
CG A:ASP623 3.3 37.4 1.0
PB A:TTP904 3.4 32.8 1.0
C A:LEU412 3.5 34.5 1.0
PG A:TTP904 3.5 35.6 1.0
PA A:TTP904 3.5 33.3 1.0
CA A:CA906 3.6 68.5 1.0
OD2 A:ASP623 3.6 39.0 1.0
O3A A:TTP904 3.7 34.7 1.0
O3B A:TTP904 3.9 34.3 1.0
N A:LEU412 4.0 35.7 1.0
O2G A:TTP904 4.2 33.7 1.0
CA A:LEU412 4.3 35.6 1.0
N A:SER414 4.3 31.1 1.0
C5' A:TTP904 4.4 31.9 1.0
CB A:ASP411 4.4 38.8 1.0
O5' A:TTP904 4.5 35.1 1.0
N A:THR413 4.5 33.2 1.0
CB A:ASP623 4.6 34.7 1.0
C A:ASP411 4.6 36.0 1.0
O1A A:TTP904 4.6 33.1 1.0
N A:LEU415 4.6 29.7 1.0
O3G A:TTP904 4.7 32.2 1.0
C A:THR413 4.7 33.3 1.0
CA A:THR413 4.7 35.4 1.0
O1B A:TTP904 4.8 34.3 1.0
CB A:LEU412 4.8 33.9 1.0
CB A:LEU415 4.9 30.5 1.0
CA A:ASP411 4.9 36.3 1.0

Calcium binding site 2 out of 6 in 3qet

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Calcium binding site 2 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp 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 Dttp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:68.5
occ:1.00
 OD2 A:ASP411 2.3 51.7 1.0
O A:HOH1101 2.4 44.2 1.0
O2A A:TTP904 2.4 33.8 1.0
OD2 A:ASP623 2.6 39.0 1.0
O A:HOH1047 2.7 56.4 1.0
CG A:ASP411 3.5 42.5 1.0
PA A:TTP904 3.5 33.3 1.0
C3' P:DOC115 3.6 42.1 1.0
CG A:ASP623 3.6 37.4 1.0
CA A:CA905 3.6 34.7 1.0
O1A A:TTP904 3.8 33.1 1.0
OD1 A:ASP623 3.8 38.3 1.0
OD1 A:ASP411 4.0 47.3 1.0
O5' A:TTP904 4.3 35.1 1.0
CB A:SER624 4.3 37.2 1.0
C5' P:DOC115 4.3 47.2 1.0
O P:HOH201 4.4 40.2 1.0
C4' P:DOC115 4.5 42.4 1.0
C5' A:TTP904 4.6 31.9 1.0
O A:ASP621 4.7 30.5 1.0
CB A:ASP411 4.7 38.8 1.0
OG A:SER624 4.8 40.5 1.0
O1G A:TTP904 4.8 34.9 1.0
O5' P:DOC115 4.8 45.8 1.0
N A:SER624 4.8 34.9 1.0
O P:HOH205 4.9 52.0 1.0
C2' P:DOC115 4.9 41.5 1.0
O3A A:TTP904 4.9 34.7 1.0
C A:ASP623 4.9 35.6 1.0
CB A:ASP623 5.0 34.7 1.0

Calcium binding site 3 out of 6 in 3qet

Go back to Calcium Binding Sites List in 3qet
Calcium binding site 3 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp 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 Dttp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:61.8
occ:1.00
 O A:HOH1301 2.2 56.6 1.0
O A:LYS531 2.2 58.0 1.0
OD1 A:ASN507 2.3 60.0 1.0
O A:ASN505 2.3 61.0 1.0
O A:HOH932 2.4 53.6 1.0
O A:HOH1017 2.6 54.2 1.0
O A:HOH1062 2.7 55.6 1.0
C A:LYS531 3.2 57.5 1.0
CG A:ASN507 3.5 61.6 1.0
C A:ASN505 3.6 61.6 1.0
CA A:LYS531 4.0 56.3 1.0
N A:LYS532 4.1 57.6 1.0
ND2 A:ASN507 4.1 61.0 1.0
C A:PRO506 4.3 62.7 1.0
CB A:ASN505 4.3 65.3 1.0
N A:ASN507 4.3 62.4 1.0
CA A:LYS532 4.3 59.1 1.0
CA A:PRO506 4.3 61.6 1.0
N A:PRO506 4.4 60.9 1.0
O A:LEU533 4.5 55.4 1.0
CA A:ASN505 4.5 64.0 1.0
O A:ALA502 4.6 53.8 1.0
CB A:ASN507 4.7 61.9 1.0
O A:PRO506 4.7 64.9 1.0
C A:LYS532 4.7 58.7 1.0
CB A:LYS531 4.7 58.0 1.0
N A:LEU533 4.8 56.7 1.0
O A:ILE530 4.8 51.5 1.0
CA A:ASN507 4.9 62.9 1.0

Calcium binding site 4 out of 6 in 3qet

Go back to Calcium Binding Sites List in 3qet
Calcium binding site 4 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp 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 Dttp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:79.3
occ:1.00
 OE1 A:GLU716 3.0 58.6 1.0
O A:HOH1076 3.8 50.5 1.0
CD A:GLU716 3.8 56.3 1.0
NZ A:LYS486 4.1 44.6 1.0
CG A:GLU716 4.2 52.2 1.0
O A:ASP411 4.3 36.0 1.0
OD1 A:ASP411 4.3 47.3 1.0
CB A:ASP684 4.5 46.1 1.0
O A:HOH1163 4.5 50.9 1.0
CB A:ASP411 4.7 38.8 1.0
OE2 A:GLU716 4.7 58.4 1.0
OG1 A:THR413 4.7 39.5 1.0
OE1 A:GLU686 4.8 56.3 1.0
O A:ASP684 4.8 38.8 1.0
OD2 A:ASP684 4.8 56.6 1.0
CG A:GLU686 4.9 49.8 1.0
CG A:ASP411 4.9 42.5 1.0
C A:ASP411 5.0 36.0 1.0

Calcium binding site 5 out of 6 in 3qet

Go back to Calcium Binding Sites List in 3qet
Calcium binding site 5 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp 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 Dttp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:57.9
occ:1.00
 O A:HOH1178 2.4 49.6 1.0
OE1 A:GLU116 2.6 44.4 1.0
OE2 A:GLU116 2.7 45.4 1.0
O A:HOH1179 2.8 60.4 1.0
CD A:GLU116 3.0 40.8 1.0
CG A:GLU116 4.5 41.7 1.0
O A:ILE115 4.6 36.6 1.0
OD2 A:ASP114 4.8 52.9 1.0
O A:HOH1053 4.8 61.0 1.0

Calcium binding site 6 out of 6 in 3qet

Go back to Calcium Binding Sites List in 3qet
Calcium binding site 6 out of 6 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dttp 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 Dttp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:98.7
occ:1.00
 OD1 A:ASP861 2.5 77.4 1.0
O A:LEU857 2.6 69.3 1.0
OD1 A:ASP860 3.3 75.9 1.0
OD2 A:ASP860 3.3 71.0 1.0
CG A:ASP861 3.6 73.3 1.0
CG A:ASP860 3.7 71.9 1.0
C A:LEU857 3.8 67.5 1.0
CA A:ILE858 4.3 61.5 1.0
OD2 A:ASP861 4.3 75.7 1.0
N A:ILE858 4.5 64.2 1.0
CB A:ASP861 4.6 68.0 1.0
CA A:LEU857 4.9 69.6 1.0
CG2 A:ILE858 5.0 59.4 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 15:57:06 2025

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