Atomistry » Calcium » PDB 4dtm-4ec5 » 4du1
Atomistry »
  Calcium »
    PDB 4dtm-4ec5 »
      4du1 »

Calcium in PDB 4du1: RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt, PDB code: 4du1 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) 49.10 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.983, 119.836, 129.949, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24.5

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt (pdb code 4du1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt, PDB code: 4du1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4du1

Go back to Calcium Binding Sites List in 4du1
Calcium binding site 1 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp 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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:30.4
occ:1.00
 O1G A:DTP1001 2.2 29.2 1.0
O A:LEU412 2.2 31.1 1.0
OD1 A:ASP623 2.3 41.3 1.0
O1B A:DTP1001 2.3 29.9 1.0
OD2 A:ASP411 2.3 38.3 1.0
OD1 A:ASP411 2.5 36.2 1.0
CG A:ASP411 2.7 35.1 1.0
O A:HOH1136 2.8 38.9 1.0
PB A:DTP1001 3.3 33.1 1.0
C A:LEU412 3.4 33.4 1.0
O3A A:DTP1001 3.4 34.7 1.0
CG A:ASP623 3.5 35.7 1.0
PG A:DTP1001 3.5 31.4 1.0
O1A A:DTP1001 3.7 39.2 1.0
O3B A:DTP1001 3.8 31.3 1.0
CA A:CA1003 3.9 38.7 1.0
O A:HOH1346 3.9 54.9 1.0
N A:LEU412 4.0 32.9 1.0
PA A:DTP1001 4.2 35.0 1.0
CB A:ASP411 4.2 34.4 1.0
CA A:LEU412 4.3 33.3 1.0
N A:SER414 4.3 30.7 1.0
N A:THR413 4.3 33.5 1.0
CB A:ASP623 4.3 32.4 1.0
O2G A:DTP1001 4.3 25.8 1.0
OD2 A:ASP623 4.3 35.8 1.0
CA A:THR413 4.4 33.4 1.0
C A:THR413 4.5 31.7 1.0
C A:ASP411 4.6 35.6 1.0
O3G A:DTP1001 4.6 31.7 1.0
OG A:SER624 4.7 45.0 1.0
O2B A:DTP1001 4.7 37.0 1.0
CB A:LEU412 4.8 32.5 1.0
C5' A:DTP1001 4.8 29.3 1.0
CA A:ASP411 4.9 34.9 1.0
N A:LEU415 4.9 27.4 1.0
O A:ASP623 4.9 28.6 1.0
O5' A:DTP1001 4.9 38.0 1.0

Calcium binding site 2 out of 7 in 4du1

Go back to Calcium Binding Sites List in 4du1
Calcium binding site 2 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp 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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:38.7
occ:1.00
 O A:HOH1171 2.2 26.4 1.0
O1A A:DTP1001 2.3 39.2 1.0
O A:HOH1136 2.4 38.9 1.0
O A:HOH1132 2.5 32.7 1.0
OD2 A:ASP623 2.5 35.8 1.0
OG A:SER624 2.7 45.0 1.0
OD1 A:ASP623 2.9 41.3 1.0
CG A:ASP623 3.1 35.7 1.0
OD2 A:ASP411 3.3 38.3 1.0
PA A:DTP1001 3.7 35.0 1.0
CB A:SER624 3.8 34.6 1.0
C3' P:2DT115 3.9 29.9 1.0
CA A:CA1002 3.9 30.4 1.0
CG A:ASP411 4.3 35.1 1.0
O3A A:DTP1001 4.4 34.7 1.0
CB A:ASP623 4.6 32.4 1.0
C5' P:2DT115 4.6 35.8 1.0
C5' A:DTP1001 4.6 29.3 1.0
O5' A:DTP1001 4.6 38.0 1.0
O2A A:DTP1001 4.7 43.4 1.0
N A:SER624 4.7 32.2 1.0
O5' P:2DT115 4.7 36.4 1.0
O A:ASP621 4.7 31.1 1.0
C A:ASP623 4.8 31.7 1.0
C4' P:2DT115 4.9 35.1 1.0
CA A:SER624 4.9 33.2 1.0
OE1 A:GLU686 5.0 55.5 1.0
OE2 A:GLU686 5.0 57.1 1.0
OD1 A:ASP411 5.0 36.2 1.0

Calcium binding site 3 out of 7 in 4du1

Go back to Calcium Binding Sites List in 4du1
Calcium binding site 3 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp 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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:51.1
occ:1.00
 OD1 A:ASN507 2.2 60.9 1.0
O A:HOH1255 2.2 37.3 1.0
O A:LYS531 2.2 55.2 1.0
O A:ASN505 2.4 56.8 1.0
O A:HOH1324 2.5 36.3 1.0
O A:HOH1301 2.6 44.9 1.0
C A:LYS531 3.2 55.1 1.0
CG A:ASN507 3.4 63.6 1.0
C A:ASN505 3.6 58.6 1.0
CA A:LYS531 4.0 54.5 1.0
ND2 A:ASN507 4.1 61.5 1.0
N A:LYS532 4.1 53.6 1.0
N A:ASN507 4.1 63.6 1.0
CA A:LYS532 4.3 53.9 1.0
CB A:ASN505 4.3 60.1 1.0
C A:PRO506 4.4 62.4 1.0
CA A:PRO506 4.4 60.7 1.0
N A:PRO506 4.5 59.2 1.0
O A:LEU533 4.5 48.6 1.0
CB A:ASN507 4.6 63.5 1.0
CA A:ASN505 4.6 59.4 1.0
C A:LYS532 4.7 52.5 1.0
N A:LEU533 4.7 50.8 1.0
CA A:ASN507 4.7 65.0 1.0
O A:ALA502 4.8 46.4 1.0
CB A:LYS531 4.8 54.4 1.0
O A:ILE530 4.8 50.6 1.0

Calcium binding site 4 out of 7 in 4du1

Go back to Calcium Binding Sites List in 4du1
Calcium binding site 4 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp 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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:76.8
occ:1.00
 O A:HOH1358 2.0 63.5 1.0
O A:HOH1346 2.1 54.9 1.0
O A:HOH1263 2.7 39.6 1.0
O A:HOH1404 2.8 46.0 1.0
OD1 A:ASP411 3.0 36.2 1.0
OE1 A:GLU716 3.3 45.7 1.0
CG A:ASP411 3.9 35.1 1.0
CD A:GLU716 4.0 48.3 1.0
CB A:ASP411 4.1 34.4 1.0
O A:HOH1286 4.1 30.0 1.0
NZ A:LYS486 4.1 30.1 1.0
OE1 A:GLU686 4.2 55.5 1.0
CG A:GLU716 4.4 46.6 1.0
O1G A:DTP1001 4.4 29.2 1.0
O A:ASP411 4.7 33.6 1.0
CD A:GLU686 4.8 56.1 1.0
CG A:GLU686 4.9 46.9 1.0
OG1 A:THR413 4.9 40.2 1.0
OE2 A:GLU716 4.9 47.2 1.0

Calcium binding site 5 out of 7 in 4du1

Go back to Calcium Binding Sites List in 4du1
Calcium binding site 5 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp 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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:78.3
occ:1.00
 O A:HOH1117 2.6 38.6 1.0
OE1 A:GLU116 2.8 42.5 1.0
OE2 A:GLU116 3.0 41.4 1.0
CD A:GLU116 3.3 40.9 1.0
OD2 A:ASP114 4.4 49.0 1.0
O A:HOH1259 4.6 42.5 1.0
O A:ILE115 4.8 30.4 1.0
CG A:GLU116 4.8 32.4 1.0
CD1 A:ILE309 4.9 49.6 1.0

Calcium binding site 6 out of 7 in 4du1

Go back to Calcium Binding Sites List in 4du1
Calcium binding site 6 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp 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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:74.3
occ:1.00
 O A:LEU857 2.6 60.1 1.0
OD1 A:ASP861 2.9 60.2 1.0
OD2 A:ASP860 2.9 62.6 1.0
OD1 A:ASP860 3.3 63.5 1.0
CG A:ASP860 3.5 60.7 1.0
CG A:ASP861 3.6 56.4 1.0
C A:LEU857 3.8 58.3 1.0
OD2 A:ASP861 3.9 57.6 1.0
CB A:ASP861 4.5 51.5 1.0
CA A:ILE858 4.6 51.7 1.0
N A:ILE858 4.7 53.9 1.0
CA A:LEU857 4.7 59.9 1.0
N A:ASP861 4.7 47.9 1.0
CB A:ASP860 5.0 55.2 1.0

Calcium binding site 7 out of 7 in 4du1

Go back to Calcium Binding Sites List in 4du1
Calcium binding site 7 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt


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 Ternary Complex with Datp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1008

b:74.8
occ:1.00
 OD1 A:ASP684 2.4 54.4 1.0
OE1 A:GLU660 2.9 47.2 1.0
CG A:ASP684 3.6 54.0 1.0
CD A:GLU660 3.7 43.4 1.0
CG A:GLU660 4.2 40.6 1.0
CB A:GLU660 4.2 41.1 1.0
OD2 A:ASP684 4.2 57.4 1.0
OD1 A:ASP664 4.3 53.1 1.0
OD2 A:ASP664 4.4 51.2 1.0
O A:MET683 4.5 38.8 1.0
OE2 A:GLU660 4.6 43.3 1.0
CB A:ASP684 4.7 46.5 1.0
CG A:ASP664 4.8 47.8 1.0
CA A:ASP684 4.8 44.4 1.0

Reference:

S.Xia, T.D.Christian, J.Wang, W.H.Konigsberg. Probing Minor Groove Hydrogen Bonding Interactions Between RB69 Dna Polymerase and Dna. Biochemistry V. 51 4343 2012.
ISSN: ISSN 0006-2960
PubMed: 22571765
DOI: 10.1021/BI300416Z
Page generated: Tue Jul 8 19:36:00 2025

Last articles

Mg in 7EWA
Mg in 7EW9
Mg in 7EV7
Mg in 7EVI
Mg in 7EUQ
Mg in 7EUN
Mg in 7EV3
Mg in 7EV2
Mg in 7EUL
Mg in 7EUK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy