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Calcium in PDB 4j2b: RB69 Dna Polymerase L415G Ternary Complex

Enzymatic activity of RB69 Dna Polymerase L415G Ternary Complex

All present enzymatic activity of RB69 Dna Polymerase L415G Ternary Complex:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase L415G Ternary Complex, PDB code: 4j2b was solved by S Xia, J.Wang, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.52 / 2.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.590, 120.465, 130.865, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 22

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase L415G Ternary Complex (pdb code 4j2b). 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 L415G Ternary Complex, PDB code: 4j2b:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4j2b

Go back to Calcium Binding Sites List in 4j2b
Calcium binding site 1 out of 6 in the RB69 Dna Polymerase L415G Ternary Complex


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 L415G Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:22.1
occ:1.00
 O2B A:ATP1001 2.2 20.1 1.0
OD2 A:ASP411 2.2 29.8 1.0
O A:LEU412 2.3 19.4 1.0
O1G A:ATP1001 2.4 23.1 1.0
OD2 A:ASP623 2.4 20.0 1.0
O2A A:ATP1001 2.4 19.1 1.0
CG A:ASP623 3.1 23.9 1.0
OD1 A:ASP623 3.1 27.9 1.0
PB A:ATP1001 3.4 19.6 1.0
CG A:ASP411 3.4 35.9 1.0
C A:LEU412 3.5 22.7 1.0
PA A:ATP1001 3.6 19.3 1.0
PG A:ATP1001 3.6 24.8 1.0
O3A A:ATP1001 3.7 19.0 1.0
O3B A:ATP1001 3.9 22.1 1.0
N A:LEU412 3.9 22.7 1.0
CA A:CA1003 4.1 63.8 1.0
C5' A:ATP1001 4.1 19.2 1.0
O A:HOH1118 4.1 36.0 1.0
CB A:ASP411 4.1 34.7 1.0
CA A:LEU412 4.2 22.8 1.0
O2G A:ATP1001 4.2 21.4 1.0
O A:HOH1194 4.3 44.1 1.0
O5' A:ATP1001 4.3 19.4 1.0
C A:ASP411 4.4 27.0 1.0
OD1 A:ASP411 4.4 41.4 1.0
N A:GLY415 4.5 19.8 1.0
CB A:ASP623 4.5 21.7 1.0
CB A:LEU412 4.5 24.3 1.0
N A:THR413 4.5 21.5 1.0
N A:SER414 4.6 22.0 1.0
O1B A:ATP1001 4.7 21.6 1.0
CA A:THR413 4.8 21.8 1.0
O3G A:ATP1001 4.8 27.6 1.0
O1A A:ATP1001 4.9 19.5 1.0
C A:THR413 4.9 23.6 1.0
O A:ASP411 4.9 25.8 1.0
CA A:ASP411 4.9 28.5 1.0
O A:ASP623 5.0 18.5 1.0

Calcium binding site 2 out of 6 in 4j2b

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Calcium binding site 2 out of 6 in the RB69 Dna Polymerase L415G Ternary Complex


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 L415G Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:63.8
occ:1.00
 OD1 A:ASP623 2.8 27.9 1.0
O2A A:ATP1001 2.9 19.1 1.0
C3' P:DT115 3.5 21.4 1.0
OD2 A:ASP411 3.6 29.8 1.0
CB A:SER624 3.6 23.2 1.0
O A:HOH1152 3.6 22.7 1.0
OG A:SER624 3.9 23.4 1.0
CG A:ASP411 3.9 35.9 1.0
CG A:ASP623 4.0 23.9 1.0
CB A:ASP411 4.0 34.7 1.0
PA A:ATP1001 4.1 19.3 1.0
CA A:CA1002 4.1 22.1 1.0
O A:ASP621 4.1 18.4 1.0
O A:HOH1194 4.2 44.1 1.0
C5' P:DT115 4.4 23.2 1.0
O5' P:DT115 4.4 23.5 1.0
N A:SER624 4.4 21.6 1.0
C4' P:DT115 4.4 22.6 1.0
O1A A:ATP1001 4.5 19.5 1.0
CA A:SER624 4.6 21.6 1.0
OD2 A:ASP623 4.6 20.0 1.0
C A:ASP623 4.7 21.0 1.0
O5' A:ATP1001 4.7 19.4 1.0
C5' A:ATP1001 4.7 19.2 1.0
C2' P:DT115 4.7 21.8 1.0
OD1 A:ASP411 4.8 41.4 1.0
N A:ASP623 4.8 20.1 1.0
O P:HOH212 4.9 31.2 1.0

Calcium binding site 3 out of 6 in 4j2b

Go back to Calcium Binding Sites List in 4j2b
Calcium binding site 3 out of 6 in the RB69 Dna Polymerase L415G Ternary Complex


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 L415G Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:40.4
occ:1.00
 OD1 A:ASN507 2.1 41.2 1.0
O A:HOH1219 2.2 30.9 1.0
O A:LYS531 2.2 45.1 1.0
O A:ASN505 2.3 36.3 1.0
O A:HOH1197 2.6 32.7 1.0
CG A:ASN507 3.2 48.6 1.0
C A:LYS531 3.2 44.4 1.0
C A:ASN505 3.6 36.9 1.0
ND2 A:ASN507 3.8 49.4 1.0
CA A:LYS531 4.0 46.7 1.0
N A:ASN507 4.2 44.2 1.0
CB A:ASN505 4.2 44.8 1.0
N A:LYS532 4.2 38.4 1.0
O A:HOH1271 4.4 36.5 1.0
C A:PRO506 4.4 45.9 1.0
CA A:PRO506 4.4 40.7 1.0
N A:PRO506 4.5 38.4 1.0
CA A:LYS532 4.5 40.7 1.0
CB A:ASN507 4.5 47.3 1.0
CA A:ASN505 4.5 42.5 1.0
O A:LEU533 4.6 31.9 1.0
CB A:LYS531 4.6 48.2 1.0
O A:ALA502 4.6 37.9 1.0
CA A:ASN507 4.8 47.5 1.0
C A:LYS532 4.8 42.7 1.0
O A:ILE530 4.9 31.4 1.0
N A:LEU533 4.9 41.1 1.0
O A:HOH1575 5.0 48.8 1.0

Calcium binding site 4 out of 6 in 4j2b

Go back to Calcium Binding Sites List in 4j2b
Calcium binding site 4 out of 6 in the RB69 Dna Polymerase L415G Ternary Complex


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 L415G Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:64.0
occ:1.00
 O A:HOH1118 3.2 36.0 1.0
OE1 A:GLU716 3.3 44.7 1.0
NZ A:LYS486 4.1 33.6 1.0
OD1 A:ASP411 4.1 41.4 1.0
CD A:GLU716 4.2 42.0 1.0
O A:ASP411 4.4 25.8 1.0
OG1 A:THR413 4.4 27.3 1.0
O2G A:ATP1001 4.4 21.4 1.0
CB A:ASP684 4.5 46.3 1.0
O1G A:ATP1001 4.6 23.1 1.0
OD2 A:ASP684 4.6 57.8 1.0
CG A:GLU716 4.7 39.8 1.0
CG A:ASP411 4.7 35.9 1.0
OD2 A:ASP411 4.8 29.8 1.0
PG A:ATP1001 4.9 24.8 1.0
CA A:THR413 4.9 21.8 1.0

Calcium binding site 5 out of 6 in 4j2b

Go back to Calcium Binding Sites List in 4j2b
Calcium binding site 5 out of 6 in the RB69 Dna Polymerase L415G Ternary Complex


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 L415G Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:57.4
occ:1.00
 O A:HOH1352 2.4 37.3 1.0
O A:HOH1159 2.5 29.6 1.0
O A:HOH1406 2.6 55.3 1.0
O A:HOH1750 2.6 45.2 1.0
OE1 A:GLU116 2.6 30.2 1.0
OE2 A:GLU116 2.7 33.4 1.0
O A:HOH1749 2.7 44.4 1.0
CD A:GLU116 3.0 29.7 1.0
O A:HOH1434 4.2 32.2 1.0
OD2 A:ASP114 4.3 40.3 1.0
O A:HOH1667 4.4 39.1 1.0
O A:HOH1377 4.5 41.0 1.0
CG A:GLU116 4.6 25.4 1.0
O A:ILE115 4.7 24.8 1.0

Calcium binding site 6 out of 6 in 4j2b

Go back to Calcium Binding Sites List in 4j2b
Calcium binding site 6 out of 6 in the RB69 Dna Polymerase L415G Ternary Complex


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 L415G Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:71.1
occ:1.00
 O A:HOH1634 2.4 45.8 1.0
O A:LEU857 2.5 61.2 1.0
OD2 A:ASP861 2.8 45.7 1.0
OD1 A:ASP860 2.9 61.3 1.0
OD2 A:ASP860 3.2 54.6 1.0
CG A:ASP860 3.4 54.9 1.0
CG A:ASP861 3.6 46.3 1.0
C A:LEU857 3.7 60.1 1.0
OD1 A:ASP861 4.0 47.0 1.0
O A:HOH1250 4.4 47.9 1.0
CA A:ILE858 4.4 45.5 1.0
O A:HOH1270 4.5 39.8 1.0
N A:ILE858 4.5 49.9 1.0
CA A:LEU857 4.6 61.9 1.0
CB A:ASP861 4.6 39.0 1.0
N A:ASP861 4.7 36.4 1.0
CB A:ASP860 4.9 46.3 1.0

Reference:

S.Xia, M.Wood, M.J.Bradley, E.M.De La Cruz, W.H.Konigsberg. Alteration in the Cavity Size Adjacent to the Active Site of RB69 Dna Polymerase Changes Its Conformational Dynamics. Nucleic Acids Res. V. 41 9077 2013.
ISSN: ISSN 0305-1048
PubMed: 23921641
DOI: 10.1093/NAR/GKT674
Page generated: Tue Jul 8 23:03:59 2025

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