Atomistry » Calcium » PDB 4dtm-4ec5 » 4du4
Atomistry »
  Calcium »
    PDB 4dtm-4ec5 »
      4du4 »

Calcium in PDB 4du4: RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand

Enzymatic activity of RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand, PDB code: 4du4 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) 46.20 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.143, 119.502, 130.540, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.9

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand (pdb code 4du4). 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 with 3- Deaza-Adenine at the N-3 Position of Primer Strand, PDB code: 4du4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4du4

Go back to Calcium Binding Sites List in 4du4
Calcium binding site 1 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand


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 with 3- Deaza-Adenine at the N-3 Position of Primer Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:47.9
occ:1.00
 O1G A:DTP1001 2.2 48.0 1.0
OD1 A:ASP623 2.2 56.5 1.0
O2B A:DTP1001 2.3 51.6 1.0
O A:LEU412 2.3 49.8 1.0
OD1 A:ASP411 2.4 50.1 1.0
O A:HOH1123 2.4 50.0 1.0
OD2 A:ASP411 2.6 56.1 1.0
CG A:ASP411 2.9 51.8 1.0
O3A A:DTP1001 3.0 50.1 1.0
PB A:DTP1001 3.1 49.5 1.0
PG A:DTP1001 3.4 47.5 1.0
CG A:ASP623 3.4 52.3 1.0
C A:LEU412 3.5 47.7 1.0
O3B A:DTP1001 3.6 50.4 1.0
CA A:CA1003 3.8 60.9 1.0
O2A A:DTP1001 4.0 53.4 1.0
PA A:DTP1001 4.1 48.8 1.0
O2G A:DTP1001 4.2 46.9 1.0
N A:LEU412 4.2 49.2 1.0
CB A:ASP623 4.3 51.8 1.0
N A:SER414 4.3 42.3 1.0
OD2 A:ASP623 4.3 45.9 1.0
CB A:ASP411 4.3 49.4 1.0
N A:THR413 4.4 44.3 1.0
CA A:LEU412 4.4 50.2 1.0
CA A:THR413 4.5 50.8 1.0
O3G A:DTP1001 4.6 48.5 1.0
O1B A:DTP1001 4.6 50.0 1.0
C A:THR413 4.6 48.0 1.0
C A:ASP411 4.7 50.6 1.0
C5' A:DTP1001 4.7 47.5 1.0
CA A:CA1005 4.8 86.0 1.0
N A:LEU415 4.9 38.3 1.0
O A:ASP623 4.9 47.0 1.0
O5' A:DTP1001 4.9 49.1 1.0
CA A:ASP411 5.0 46.9 1.0
CB A:LEU412 5.0 53.2 1.0

Calcium binding site 2 out of 7 in 4du4

Go back to Calcium Binding Sites List in 4du4
Calcium binding site 2 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand


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 with 3- Deaza-Adenine at the N-3 Position of Primer Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:60.9
occ:1.00
 O2A A:DTP1001 2.2 53.4 1.0
O A:HOH1119 2.6 39.7 1.0
OD2 A:ASP623 2.7 45.9 1.0
O A:HOH1123 2.7 50.0 1.0
OD1 A:ASP623 2.9 56.5 1.0
OD2 A:ASP411 3.0 56.1 1.0
CG A:ASP623 3.1 52.3 1.0
PA A:DTP1001 3.7 48.8 1.0
CA A:CA1002 3.8 47.9 1.0
CB A:SER624 3.9 62.4 1.0
C3' P:DOC115 3.9 50.0 1.0
O3A A:DTP1001 4.0 50.1 1.0
CG A:ASP411 4.1 51.8 1.0
OG A:SER624 4.2 85.0 1.0
C5' P:DOC115 4.3 51.2 1.0
O5' A:DTP1001 4.6 49.1 1.0
C4' P:DOC115 4.6 51.5 1.0
CB A:ASP623 4.6 51.8 1.0
C5' A:DTP1001 4.6 47.5 1.0
OD1 A:ASP411 4.7 50.1 1.0
O1A A:DTP1001 4.7 51.0 1.0
N A:SER624 4.7 47.2 1.0
C A:ASP623 4.8 46.4 1.0
O A:ASP621 4.8 43.6 1.0
CA A:SER624 4.9 59.9 1.0

Calcium binding site 3 out of 7 in 4du4

Go back to Calcium Binding Sites List in 4du4
Calcium binding site 3 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand


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 with 3- Deaza-Adenine at the N-3 Position of Primer Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1004

b:93.1
occ:1.00
 O A:LYS531 2.3 78.6 1.0
O A:ASN505 2.4 79.6 1.0
OD1 A:ASN507 2.6 83.2 1.0
O A:HOH1143 2.8 65.1 1.0
O A:HOH1218 2.8 58.4 1.0
C A:LYS531 3.4 78.7 1.0
C A:ASN505 3.6 81.1 1.0
CG A:ASN507 3.7 83.6 1.0
CB A:ASN505 4.0 85.3 1.0
CA A:LYS531 4.1 77.0 1.0
ND2 A:ASN507 4.2 83.5 1.0
CA A:ASN505 4.4 84.0 1.0
N A:LYS532 4.4 78.8 1.0
C A:PRO506 4.6 82.8 1.0
N A:PRO506 4.6 78.8 1.0
O A:ALA502 4.6 79.6 1.0
CA A:PRO506 4.6 81.0 1.0
CB A:LYS531 4.6 78.4 1.0
CA A:LYS532 4.7 82.2 1.0
N A:ASN507 4.7 84.4 1.0
O A:PRO506 4.9 86.8 1.0

Calcium binding site 4 out of 7 in 4du4

Go back to Calcium Binding Sites List in 4du4
Calcium binding site 4 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand


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 with 3- Deaza-Adenine at the N-3 Position of Primer Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1005

b:86.0
occ:1.00
 O A:HOH1142 2.3 71.8 1.0
OE1 A:GLU716 2.9 63.7 1.0
OD1 A:ASP411 3.1 50.1 1.0
CD A:GLU716 3.7 72.1 1.0
NZ A:LYS486 3.8 59.7 1.0
O1G A:DTP1001 3.8 48.0 1.0
OE1 A:GLU686 3.9 83.2 1.0
CG A:ASP411 4.0 51.8 1.0
CB A:ASP411 4.3 49.4 1.0
CG A:GLU716 4.4 67.3 1.0
OE2 A:GLU716 4.5 69.2 1.0
PG A:DTP1001 4.6 47.5 1.0
O2G A:DTP1001 4.7 46.9 1.0
O A:HOH1123 4.8 50.0 1.0
CA A:CA1002 4.8 47.9 1.0
CD A:GLU686 4.8 98.1 1.0
OG1 A:THR413 4.8 58.5 1.0
O A:ASP411 4.9 45.9 1.0
CG A:GLU686 5.0 68.1 1.0

Calcium binding site 5 out of 7 in 4du4

Go back to Calcium Binding Sites List in 4du4
Calcium binding site 5 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand


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 with 3- Deaza-Adenine at the N-3 Position of Primer Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:88.7
occ:1.00
 O A:HOH1185 2.5 62.8 1.0
OE2 A:GLU116 2.8 72.2 1.0
OE1 A:GLU116 2.9 59.0 1.0
CD A:GLU116 3.2 62.6 1.0
OD2 A:ASP114 4.1 82.7 1.0
CG A:GLU116 4.8 58.1 1.0
O A:ILE115 4.8 51.4 1.0

Calcium binding site 6 out of 7 in 4du4

Go back to Calcium Binding Sites List in 4du4
Calcium binding site 6 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand


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 with 3- Deaza-Adenine at the N-3 Position of Primer Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:0.3
occ:1.00
 OD1 A:ASP861 2.7 98.2 1.0
O A:LEU857 2.8 90.2 1.0
CG A:ASP861 3.9 92.1 1.0
C A:LEU857 4.1 87.9 1.0
OD2 A:ASP860 4.2 90.5 1.0
OD1 A:ASP860 4.3 0.3 1.0
OD2 A:ASP861 4.5 90.3 1.0
CA A:ILE858 4.6 74.5 1.0
CG A:ASP860 4.7 0.2 1.0
N A:ILE858 4.8 78.3 1.0
CG2 A:ILE858 4.9 75.1 1.0

Calcium binding site 7 out of 7 in 4du4

Go back to Calcium Binding Sites List in 4du4
Calcium binding site 7 out of 7 in the RB69 Dna Polymerase Ternary Complex with Datp Opposite Dt with 3- Deaza-Adenine at the N-3 Position of Primer Strand


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 with 3- Deaza-Adenine at the N-3 Position of Primer Strand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1008

b:95.8
occ:1.00
 OD1 A:ASP684 2.5 77.5 1.0
O A:HOH1177 2.7 72.2 1.0
OE1 A:GLU660 3.1 63.3 1.0
CG A:ASP684 3.7 69.7 1.0
CD A:GLU660 4.0 58.5 1.0
CB A:GLU660 4.4 55.8 1.0
OD2 A:ASP684 4.4 77.3 1.0
OD1 A:ASP664 4.4 87.1 1.0
CG A:GLU660 4.4 57.8 1.0
CB A:ASP684 4.8 59.9 1.0
OE2 A:GLU660 4.9 58.8 1.0
OD2 A:ASP664 4.9 81.1 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: Sat Jul 13 23:40:59 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy