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

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

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

Protein crystallography data

The structure of RB69 Dna Polymerase (L561A/S565G/Y567A) Ternary Complex with Dgtp Opposite Dt, PDB code: 3qex 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) 30.00 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.991, 120.211, 130.361, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.6

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 3qex

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

b:22.3
occ:1.00
 OD1 A:ASP623 2.1 34.7 1.0
O1G A:DGT904 2.2 21.0 1.0
O A:LEU412 2.3 16.7 1.0
O2B A:DGT904 2.3 18.0 1.0
OD2 A:ASP411 2.4 30.2 1.0
OD1 A:ASP411 2.6 30.8 1.0
O A:HOH1207 2.6 31.9 1.0
CG A:ASP411 2.8 28.1 1.0
PB A:DGT904 3.3 19.8 1.0
CG A:ASP623 3.4 24.8 1.0
O2A A:DGT904 3.5 33.8 1.0
C A:LEU412 3.5 18.8 1.0
PG A:DGT904 3.5 21.8 1.0
O3A A:DGT904 3.5 26.4 1.0
O3B A:DGT904 3.8 20.6 1.0
CA A:CA906 4.0 36.3 1.0
PA A:DGT904 4.1 29.9 1.0
N A:LEU412 4.1 18.0 1.0
OD2 A:ASP623 4.1 26.2 1.0
O2G A:DGT904 4.2 21.7 1.0
CB A:ASP411 4.3 26.1 1.0
N A:SER414 4.3 16.0 1.0
CA A:LEU412 4.3 18.2 1.0
CB A:ASP623 4.3 21.5 1.0
N A:THR413 4.4 17.5 1.0
CA A:THR413 4.5 17.7 1.0
C A:ASP411 4.5 20.3 1.0
C A:THR413 4.6 17.3 1.0
O3G A:DGT904 4.6 22.2 1.0
C5' A:DGT904 4.7 19.4 1.0
O1B A:DGT904 4.7 20.0 1.0
N A:LEU415 4.8 14.5 1.0
CA A:ASP411 4.9 22.1 1.0
O5' A:DGT904 4.9 22.8 1.0
CB A:LEU412 4.9 17.6 1.0

Calcium binding site 2 out of 5 in 3qex

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

b:36.3
occ:1.00
 O2A A:DGT904 2.3 33.8 1.0
O A:HOH1145 2.4 33.1 1.0
O A:HOH1207 2.5 31.9 1.0
OD2 A:ASP623 2.6 26.2 1.0
O A:HOH1181 2.6 34.4 1.0
OD2 A:ASP411 3.2 30.2 1.0
OD1 A:ASP623 3.3 34.7 1.0
CG A:ASP623 3.3 24.8 1.0
C3' P:DOC115 3.7 20.1 1.0
PA A:DGT904 3.8 29.9 1.0
CB A:SER624 4.0 22.0 1.0
CA A:CA905 4.0 22.3 1.0
CG A:ASP411 4.3 28.1 1.0
O A:HOH1136 4.3 26.2 1.0
OG A:SER624 4.3 29.7 1.0
O1A A:DGT904 4.4 28.1 1.0
O5' P:DOC115 4.6 24.5 1.0
C5' P:DOC115 4.6 23.9 1.0
O P:HOH511 4.6 26.6 1.0
C5' A:DGT904 4.6 19.4 1.0
O5' A:DGT904 4.7 22.8 1.0
O3A A:DGT904 4.7 26.4 1.0
C4' P:DOC115 4.7 19.6 1.0
O A:ASP621 4.7 15.2 1.0
N A:SER624 4.7 18.7 1.0
CB A:ASP623 4.7 21.5 1.0
C2' P:DOC115 4.9 22.8 1.0
OE2 A:GLU686 4.9 38.1 1.0
C A:ASP623 4.9 19.3 1.0
CA A:SER624 4.9 20.4 1.0

Calcium binding site 3 out of 5 in 3qex

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

b:37.1
occ:1.00
 OD1 A:ASN507 2.2 43.2 1.0
O A:LYS531 2.3 40.3 1.0
O A:ASN505 2.3 40.9 1.0
O A:HOH1270 2.4 40.8 1.0
O A:HOH1441 2.5 31.2 1.0
O A:HOH1006 2.5 29.4 1.0
C A:LYS531 3.3 39.1 1.0
CG A:ASN507 3.4 43.9 1.0
C A:ASN505 3.6 41.7 1.0
CA A:LYS531 4.1 38.0 1.0
ND2 A:ASN507 4.1 41.4 1.0
N A:LYS532 4.2 38.9 1.0
CB A:ASN505 4.2 43.8 1.0
N A:ASN507 4.2 43.7 1.0
C A:PRO506 4.3 43.0 1.0
CA A:PRO506 4.4 41.7 1.0
CA A:LYS532 4.4 38.8 1.0
N A:PRO506 4.4 41.1 1.0
CA A:ASN505 4.5 42.6 1.0
O A:HOH1299 4.6 38.1 1.0
O A:LEU533 4.6 36.0 1.0
CB A:ASN507 4.6 43.8 1.0
O A:ALA502 4.7 33.7 1.0
CB A:LYS531 4.7 39.1 1.0
C A:LYS532 4.7 38.0 1.0
CA A:ASN507 4.8 44.0 1.0
N A:LEU533 4.9 36.2 1.0
O A:PRO506 4.9 43.4 1.0
O A:ILE530 4.9 32.0 1.0

Calcium binding site 4 out of 5 in 3qex

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

b:51.9
occ:1.00
 O A:HOH1770 2.2 40.7 1.0
O A:HOH1172 2.3 34.6 1.0
O A:HOH1130 2.3 35.0 1.0
O A:HOH1702 2.5 51.6 1.0
O A:HOH1486 2.8 43.5 1.0
O A:HOH1490 3.1 48.9 1.0
OD1 A:ASP411 3.3 30.8 1.0
OE1 A:GLU716 4.1 35.2 1.0
CG A:ASP411 4.3 28.1 1.0
O A:HOH1168 4.3 26.0 1.0
NZ A:LYS486 4.4 28.5 1.0
O A:ASP411 4.4 20.4 1.0
CB A:ASP411 4.4 26.1 1.0
OE1 A:GLU686 4.5 35.1 1.0
OG1 A:THR413 4.6 23.8 1.0
O A:HOH1552 4.6 48.4 1.0
O1G A:DGT904 4.8 21.0 1.0
CB A:ASP684 4.9 28.9 1.0
CD A:GLU716 4.9 35.0 1.0
CG A:GLU716 5.0 32.0 1.0

Calcium binding site 5 out of 5 in 3qex

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

b:42.2
occ:1.00
 O A:HOH1743 2.2 30.7 1.0
O A:HOH1220 2.4 35.1 1.0
O A:HOH962 2.6 19.6 1.0
OE2 A:GLU116 2.6 25.1 1.0
OE1 A:GLU116 2.6 24.9 1.0
CD A:GLU116 2.9 25.4 1.0
OD2 A:ASP114 4.1 32.8 1.0
O A:HOH1328 4.2 30.8 1.0
CG A:GLU116 4.5 19.1 1.0
O A:HOH1396 4.5 48.4 1.0
O A:HOH1358 4.5 53.1 1.0
O A:ILE115 4.5 19.4 1.0
O A:HOH964 4.5 21.8 0.5
CD1 A:ILE309 4.8 43.1 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 15:57:44 2025

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