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Calcium in PDB 4j2d: RB69 Dna Polymerase L415K Ternary Complex

Enzymatic activity of RB69 Dna Polymerase L415K Ternary Complex

All present enzymatic activity of RB69 Dna Polymerase L415K Ternary Complex:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase L415K Ternary Complex, PDB code: 4j2d 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) 49.30 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.439, 119.806, 130.039, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.7

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase L415K Ternary Complex (pdb code 4j2d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the RB69 Dna Polymerase L415K Ternary Complex, PDB code: 4j2d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4j2d

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Calcium binding site 1 out of 9 in the RB69 Dna Polymerase L415K 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 L415K Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:13.7
occ:1.00
 O2B A:TTP1001 2.2 11.8 1.0
O1G A:TTP1001 2.3 12.2 1.0
O A:LEU412 2.3 13.8 1.0
OD2 A:ASP623 2.3 16.3 1.0
O2A A:TTP1001 2.4 14.3 1.0
OD2 A:ASP411 2.5 27.1 1.0
OD1 A:ASP411 2.5 24.2 1.0
CG A:ASP411 2.9 19.2 1.0
PB A:TTP1001 3.4 12.4 1.0
CG A:ASP623 3.4 18.4 1.0
C A:LEU412 3.5 14.7 1.0
PG A:TTP1001 3.5 12.5 1.0
PA A:TTP1001 3.6 13.8 1.0
O3A A:TTP1001 3.7 12.7 1.0
O3B A:TTP1001 3.8 12.4 1.0
O A:HOH1212 3.9 25.0 1.0
N A:LEU412 4.0 14.1 1.0
CA A:CA1003 4.0 47.4 1.0
OD1 A:ASP623 4.1 18.3 1.0
CA A:LEU412 4.2 14.3 1.0
O2G A:TTP1001 4.2 11.6 1.0
CB A:ASP623 4.3 16.8 1.0
C5' A:TTP1001 4.3 11.2 1.0
CB A:ASP411 4.3 18.2 1.0
O5' A:TTP1001 4.5 12.3 1.0
C A:ASP411 4.5 15.9 1.0
N A:SER414 4.5 14.8 1.0
N A:THR413 4.5 14.3 1.0
N A:LYS415 4.6 11.7 1.0
CB A:LEU412 4.7 13.9 1.0
CB A:LYS415 4.7 13.1 1.0
O3G A:TTP1001 4.7 12.4 1.0
O1B A:TTP1001 4.7 13.1 1.0
O A:HOH1433 4.7 37.8 1.0
CA A:THR413 4.8 14.5 1.0
C A:THR413 4.8 14.3 1.0
O1A A:TTP1001 4.8 12.1 1.0
CA A:ASP411 4.8 16.5 1.0

Calcium binding site 2 out of 9 in 4j2d

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Calcium binding site 2 out of 9 in the RB69 Dna Polymerase L415K 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 L415K Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:47.4
occ:1.00
 O A:HOH1219 2.5 18.7 1.0
O2A A:TTP1001 2.6 14.3 1.0
O P:HOH230 2.8 36.6 1.0
OD1 A:ASP411 2.9 24.2 1.0
OG A:SER624 3.2 23.3 1.0
O A:HOH1212 3.5 25.0 1.0
PA A:TTP1001 3.7 13.8 1.0
CG A:ASP411 3.7 19.2 1.0
O1A A:TTP1001 3.8 12.1 1.0
CA A:CA1002 4.0 13.7 1.0
O A:HOH1647 4.0 31.9 1.0
O A:HOH1468 4.1 31.6 1.0
C3' P:DT115 4.1 14.8 1.0
CB A:SER624 4.3 18.7 1.0
OD2 A:ASP411 4.3 27.1 1.0
O P:HOH217 4.4 21.6 1.0
O P:HOH208 4.6 18.9 1.0
O5' A:TTP1001 4.6 12.3 1.0
O1G A:TTP1001 4.6 12.2 1.0
CB A:ASP623 4.7 16.8 1.0
CB A:ASP411 4.7 18.2 1.0
N A:SER624 4.7 16.2 1.0
OD2 A:ASP623 4.7 16.3 1.0
CG A:ASP623 4.8 18.4 1.0
O5' P:DT115 4.9 15.2 1.0
O3A A:TTP1001 4.9 12.7 1.0
O A:HOH1166 4.9 20.0 1.0

Calcium binding site 3 out of 9 in 4j2d

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Calcium binding site 3 out of 9 in the RB69 Dna Polymerase L415K 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 L415K Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:29.8
occ:1.00
 OD1 A:ASN507 2.2 37.9 1.0
O A:LYS531 2.3 32.0 1.0
O A:HOH1531 2.3 34.6 1.0
O A:ASN505 2.3 32.2 1.0
O A:HOH1415 2.5 29.2 1.0
O A:HOH1261 2.5 29.2 1.0
O A:HOH1786 2.6 37.7 1.0
C A:LYS531 3.3 33.0 1.0
CG A:ASN507 3.4 38.0 1.0
C A:ASN505 3.5 33.5 1.0
CA A:LYS531 4.0 31.7 1.0
ND2 A:ASN507 4.0 36.7 1.0
N A:ASN507 4.1 35.8 1.0
N A:LYS532 4.2 32.4 1.0
CB A:ASN505 4.2 38.6 1.0
C A:PRO506 4.3 35.9 1.0
CA A:PRO506 4.3 34.2 1.0
CA A:LYS532 4.3 32.9 1.0
N A:PRO506 4.4 33.0 1.0
CA A:ASN505 4.5 36.1 1.0
CB A:ASN507 4.5 37.1 1.0
O A:LEU533 4.6 27.4 1.0
CB A:LYS531 4.7 36.3 1.0
O A:ALA502 4.7 28.3 1.0
O A:HOH1329 4.7 33.2 1.0
CA A:ASN507 4.7 37.1 1.0
C A:LYS532 4.8 32.2 1.0
O A:PRO506 4.9 38.5 1.0
O A:ILE530 4.9 26.6 1.0
N A:LEU533 4.9 29.9 1.0

Calcium binding site 4 out of 9 in 4j2d

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Calcium binding site 4 out of 9 in the RB69 Dna Polymerase L415K 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 L415K Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:62.7
occ:1.00
 O A:HOH1520 2.3 44.0 1.0
O A:HOH1433 2.4 37.8 1.0
O A:HOH1540 2.4 44.9 1.0
O A:HOH1697 2.7 43.3 1.0
OE1 A:GLU716 2.9 34.6 1.0
O A:HOH1434 2.9 34.9 1.0
OE1 A:GLU686 3.2 33.2 1.0
CD A:GLU716 3.5 31.0 1.0
O A:HOH1132 4.0 19.5 1.0
NZ A:LYS486 4.0 23.6 1.0
CG A:GLU716 4.1 27.9 1.0
OE2 A:GLU716 4.2 35.2 1.0
CA A:CA1009 4.2 60.3 1.0
OD2 A:ASP411 4.3 27.1 1.0
O A:HOH1807 4.3 39.9 1.0
CD A:GLU686 4.4 30.6 1.0
O A:ASP411 4.6 15.2 1.0
CB A:ASP684 4.8 22.3 1.0
OE2 A:GLU686 4.9 31.6 1.0
OG1 A:THR413 4.9 16.8 1.0
CB A:ASP411 5.0 18.2 1.0

Calcium binding site 5 out of 9 in 4j2d

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Calcium binding site 5 out of 9 in the RB69 Dna Polymerase L415K 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 L415K Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:39.2
occ:1.00
 O A:HOH1548 2.3 30.5 1.0
O A:HOH1552 2.4 34.1 1.0
O A:HOH1140 2.4 18.2 1.0
OE1 A:GLU116 2.6 24.1 1.0
O A:HOH1815 2.6 45.0 1.0
OE2 A:GLU116 2.7 24.3 1.0
CD A:GLU116 3.0 22.9 1.0
O A:HOH1429 4.2 29.3 1.0
OD2 A:ASP114 4.2 30.6 1.0
O A:HOH1814 4.2 31.6 1.0
O A:HOH1692 4.4 36.8 1.0
O A:HOH1596 4.4 39.8 1.0
CG A:GLU116 4.5 19.1 1.0
O A:ILE115 4.5 15.4 1.0
CD1 A:ILE309 4.9 40.6 1.0
O A:HOH1755 4.9 48.2 1.0

Calcium binding site 6 out of 9 in 4j2d

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Calcium binding site 6 out of 9 in the RB69 Dna Polymerase L415K 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 L415K Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:39.4
occ:1.00
 O A:HOH1775 2.3 30.6 1.0
O A:HOH1780 2.4 40.1 1.0
OD2 A:ASP861 2.5 39.0 1.0
O A:HOH1578 2.5 33.4 1.0
OD1 A:ASP860 2.5 33.5 1.0
O A:LEU857 2.6 44.5 1.0
OD2 A:ASP860 2.8 38.2 1.0
CG A:ASP860 3.0 35.7 1.0
CG A:ASP861 3.4 34.4 1.0
C A:LEU857 3.7 39.9 1.0
OD1 A:ASP861 3.9 35.2 1.0
O A:HOH1680 4.4 39.9 1.0
O A:HOH1547 4.4 35.3 1.0
CA A:ILE858 4.5 33.6 1.0
CB A:ASP861 4.5 31.6 1.0
N A:ASP861 4.5 28.6 1.0
N A:ILE858 4.5 35.4 1.0
CB A:ASP860 4.5 33.5 1.0
CA A:LEU857 4.6 40.9 1.0

Calcium binding site 7 out of 9 in 4j2d

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Calcium binding site 7 out of 9 in the RB69 Dna Polymerase L415K Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of RB69 Dna Polymerase L415K Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1008

b:42.9
occ:1.00
 O A:HOH1904 2.3 48.1 1.0
OD1 A:ASP684 2.3 27.1 1.0
O A:HOH1484 2.3 29.4 1.0
O A:HOH1485 2.4 34.5 1.0
OE1 A:GLU660 2.8 27.0 1.0
CG A:ASP684 3.5 26.0 1.0
CD A:GLU660 3.6 23.8 1.0
O A:HOH1706 3.9 32.9 1.0
OD2 A:ASP684 4.1 27.2 1.0
CB A:GLU660 4.3 21.3 1.0
CG A:GLU660 4.3 21.8 1.0
OE2 A:GLU660 4.4 23.3 1.0
OD2 A:ASP664 4.4 35.0 1.0
O A:MET683 4.5 23.0 1.0
CB A:ASP684 4.5 22.3 1.0
OD1 A:ASP664 4.6 30.3 1.0
CA A:ASP684 4.7 20.2 1.0
CG A:ASP664 5.0 28.7 1.0
C A:MET683 5.0 20.0 1.0

Calcium binding site 8 out of 9 in 4j2d

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Calcium binding site 8 out of 9 in the RB69 Dna Polymerase L415K Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of RB69 Dna Polymerase L415K Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1009

b:60.3
occ:1.00
 O A:HOH1212 2.3 25.0 1.0
O A:HOH1805 2.3 39.7 1.0
O A:HOH1433 2.3 37.8 1.0
OE2 A:GLU686 2.4 31.6 1.0
O A:HOH1320 2.5 22.8 1.0
OE2 A:GLU716 2.9 35.2 1.0
CD A:GLU686 3.2 30.6 1.0
OE1 A:GLU686 3.3 33.2 1.0
CD A:GLU716 3.6 31.0 1.0
NZ A:LYS486 3.8 23.6 1.0
O3G A:TTP1001 4.1 12.4 1.0
OD2 A:ASP411 4.1 27.1 1.0
O1G A:TTP1001 4.1 12.2 1.0
OE1 A:GLU716 4.2 34.6 1.0
CA A:CA1005 4.2 62.7 1.0
CG A:GLU716 4.5 27.9 1.0
PG A:TTP1001 4.6 12.5 1.0
CG A:GLU686 4.6 24.2 1.0
O A:HOH1806 4.7 35.3 1.0
CG A:ASP411 4.8 19.2 1.0

Calcium binding site 9 out of 9 in 4j2d

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Calcium binding site 9 out of 9 in the RB69 Dna Polymerase L415K Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of RB69 Dna Polymerase L415K Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1010

b:65.0
occ:1.00
 O A:HOH1839 2.4 36.9 1.0
O A:HOH1720 2.4 53.0 1.0
OD1 A:ASN232 2.4 29.4 1.0
O A:HOH1838 2.4 38.1 1.0
O A:HOH1528 2.6 35.2 1.0
CG A:ASN232 3.5 25.1 1.0
NZ A:LYS231 3.6 42.9 1.0
ND2 A:ASN232 4.1 27.3 1.0
CE A:LYS231 4.5 36.0 1.0
O A:HOH1408 4.7 32.6 1.0
CB A:ASN232 4.8 22.3 1.0
CA A:ASN232 4.9 20.8 1.0
O A:ASN228 4.9 16.7 1.0
O A:SER127 4.9 36.0 1.0

Reference:

S.Xia, J.Wang, W.H.Konigsberg. Role of L415 in the Replication of RB69 Dna Polymerase To Be Published.
Page generated: Tue Jul 8 23:04:22 2025

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