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

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

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

Protein crystallography data

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp Opposite Dt, PDB code: 3qew 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) 36.00 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.861, 120.342, 130.631, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.5

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 3qew

Go back to Calcium Binding Sites List in 3qew
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp 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 Ddtp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:20.1
occ:1.00
 OD1 A:ASP623 2.2 34.0 1.0
O1G A:DTP904 2.2 17.5 1.0
O2B A:DTP904 2.3 16.0 1.0
OD2 A:ASP411 2.3 27.8 1.0
O A:LEU412 2.3 15.6 1.0
O A:HOH1379 2.7 36.2 1.0
OD1 A:ASP411 2.8 32.2 1.0
CG A:ASP411 2.9 28.6 1.0
O2A A:DTP904 3.0 27.6 1.0
PB A:DTP904 3.4 18.3 1.0
CG A:ASP623 3.4 26.0 1.0
C A:LEU412 3.5 17.9 1.0
PG A:DTP904 3.5 21.0 1.0
O3A A:DTP904 3.7 24.4 1.0
O3B A:DTP904 3.8 18.2 1.0
CA A:CA906 3.9 32.8 1.0
PA A:DTP904 3.9 22.9 1.0
OD2 A:ASP623 4.1 23.6 1.0
N A:LEU412 4.1 17.2 1.0
O A:HOH1474 4.2 49.5 1.0
O2G A:DTP904 4.2 19.6 1.0
CB A:ASP411 4.3 24.9 1.0
CA A:LEU412 4.3 15.5 1.0
N A:SER414 4.4 14.6 1.0
CB A:ASP623 4.4 22.9 1.0
N A:THR413 4.4 17.0 1.0
O A:HOH1353 4.5 39.0 1.0
CA A:THR413 4.6 17.9 1.0
C A:ASP411 4.6 18.8 1.0
O3G A:DTP904 4.6 20.3 1.0
C5' A:DTP904 4.6 16.4 1.0
C A:THR413 4.7 16.2 1.0
O1B A:DTP904 4.8 21.4 1.0
N A:LEU415 4.8 14.1 1.0
O5' A:DTP904 4.8 18.6 1.0
CA A:ASP411 4.9 21.5 1.0
CB A:LEU412 4.9 14.8 1.0
O A:ASP623 4.9 19.1 1.0

Calcium binding site 2 out of 5 in 3qew

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp 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 Ddtp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:32.8
occ:1.00
 O A:HOH1377 2.3 31.7 1.0
O2A A:DTP904 2.4 27.6 1.0
O A:HOH1396 2.5 35.6 1.0
OD2 A:ASP623 2.6 23.6 1.0
O A:HOH1379 2.6 36.2 1.0
OD2 A:ASP411 3.1 27.8 1.0
CG A:ASP623 3.3 26.0 1.0
OD1 A:ASP623 3.3 34.0 1.0
C3' P:DOC115 3.8 21.2 1.0
PA A:DTP904 3.8 22.9 1.0
CA A:CA905 3.9 20.1 1.0
CB A:SER624 3.9 23.8 1.0
OG A:SER624 4.1 30.6 1.0
CG A:ASP411 4.2 28.6 1.0
O A:HOH1271 4.3 27.5 1.0
O1A A:DTP904 4.4 22.5 1.0
O A:HOH1353 4.5 39.0 1.0
O5' A:DTP904 4.6 18.6 1.0
N A:SER624 4.6 19.7 1.0
O A:ASP621 4.7 15.3 1.0
C5' P:DOC115 4.7 26.8 1.0
O5' P:DOC115 4.7 26.3 1.0
C5' A:DTP904 4.7 16.4 1.0
CB A:ASP623 4.7 22.9 1.0
O P:HOH511 4.7 30.3 1.0
C A:ASP623 4.8 19.7 1.0
C4' P:DOC115 4.8 21.2 1.0
CA A:SER624 4.9 20.9 1.0
O3A A:DTP904 4.9 24.4 1.0
C2' P:DOC115 5.0 22.7 1.0
OE2 A:GLU686 5.0 42.0 1.0
OD1 A:ASP411 5.0 32.2 1.0
CB A:ASP411 5.0 24.9 1.0

Calcium binding site 3 out of 5 in 3qew

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Calcium binding site 3 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp 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 Ddtp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:36.2
occ:1.00
 OD1 A:ASN507 2.2 44.6 1.0
O A:HOH1409 2.2 42.7 1.0
O A:LYS531 2.3 39.3 1.0
O A:ASN505 2.4 41.7 1.0
O A:HOH1338 2.4 30.6 1.0
O A:HOH1372 2.5 30.3 1.0
O A:HOH1509 2.6 42.0 1.0
C A:LYS531 3.3 38.4 1.0
CG A:ASN507 3.4 45.3 1.0
C A:ASN505 3.6 42.5 1.0
ND2 A:ASN507 4.0 42.8 1.0
CA A:LYS531 4.1 37.8 1.0
N A:LYS532 4.2 38.1 1.0
N A:ASN507 4.2 45.1 1.0
CB A:ASN505 4.3 42.3 0.5
CB A:ASN505 4.3 42.8 0.5
C A:PRO506 4.3 44.3 1.0
CA A:PRO506 4.3 43.0 1.0
CA A:LYS532 4.4 38.8 1.0
O A:HOH1426 4.4 36.5 1.0
N A:PRO506 4.5 42.6 1.0
CA A:ASN505 4.6 42.7 0.5
CA A:ASN505 4.6 42.8 0.5
CB A:ASN507 4.6 45.5 1.0
O A:LEU533 4.6 34.2 1.0
O A:ALA502 4.6 33.3 1.0
C A:LYS532 4.7 38.0 1.0
CB A:LYS531 4.8 39.8 1.0
CA A:ASN507 4.8 46.6 1.0
N A:LEU533 4.8 35.5 1.0
O A:ILE530 4.9 31.7 1.0
O A:PRO506 4.9 44.9 1.0

Calcium binding site 4 out of 5 in 3qew

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp 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 Ddtp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:62.1
occ:1.00
 O A:HOH1474 2.3 49.5 1.0
O A:HOH1068 2.6 30.2 1.0
O A:HOH1369 2.6 34.5 1.0
O A:HOH1711 3.0 49.0 1.0
OD1 A:ASP411 3.2 32.2 1.0
OE1 A:GLU716 3.5 39.6 1.0
NZ A:LYS486 4.1 28.8 1.0
O A:HOH1104 4.2 23.6 1.0
CG A:ASP411 4.2 28.6 1.0
OE1 A:GLU686 4.3 38.5 1.0
CD A:GLU716 4.4 37.2 1.0
CB A:ASP411 4.4 24.9 1.0
CG A:GLU716 4.5 33.3 1.0
O A:ASP411 4.7 21.0 1.0
OG1 A:THR413 4.8 23.9 1.0
O1G A:DTP904 4.8 17.5 1.0
CD A:GLU686 5.0 39.2 1.0

Calcium binding site 5 out of 5 in 3qew

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Calcium binding site 5 out of 5 in the RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Ddtp 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 Ddtp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:41.7
occ:1.00
 O A:HOH1561 2.3 32.2 1.0
O A:HOH1562 2.5 24.6 1.0
OE2 A:GLU116 2.6 27.4 1.0
OE1 A:GLU116 2.6 27.6 1.0
CD A:GLU116 3.0 26.2 1.0
OD2 A:ASP114 4.1 37.1 1.0
O A:HOH1505 4.3 30.5 1.0
O A:HOH1387 4.4 34.2 1.0
CG A:GLU116 4.5 19.8 1.0
O A:ILE115 4.6 18.1 1.0
OD1 A:ASP114 4.9 34.4 1.0
CG A:ASP114 4.9 31.5 1.0
CD1 A:ILE309 4.9 43.4 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 15:57:43 2025

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