Atomistry » Calcium » PDB 3so0-3t2i » 3suo
Atomistry »
  Calcium »
    PDB 3so0-3t2i »
      3suo »

Calcium in PDB 3suo: RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence)

Enzymatic activity of RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence)

All present enzymatic activity of RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence):
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence), PDB code: 3suo 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) 88.48 / 2.23
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.401, 120.073, 130.885, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.5

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence) (pdb code 3suo). 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 (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence), PDB code: 3suo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3suo

Go back to Calcium Binding Sites List in 3suo
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence)


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 (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:34.0
occ:1.00
 OD1 A:ASP623 2.2 38.5 1.0
O2B A:TTP901 2.2 52.9 1.0
O1G A:TTP901 2.3 48.1 1.0
O A:LEU412 2.4 39.9 1.0
O2A A:TTP901 2.4 46.6 1.0
OD1 A:ASP411 2.5 47.2 1.0
OD2 A:ASP411 2.6 48.4 1.0
CG A:ASP411 2.8 41.4 1.0
CG A:ASP623 3.4 37.1 1.0
PB A:TTP901 3.4 49.8 1.0
C A:LEU412 3.5 37.6 1.0
PG A:TTP901 3.6 47.5 1.0
PA A:TTP901 3.6 48.4 1.0
O3A A:TTP901 3.8 52.7 1.0
CA A:CA903 3.9 68.9 1.0
OD2 A:ASP623 3.9 35.5 1.0
O3B A:TTP901 3.9 45.8 1.0
N A:LEU412 4.0 37.9 1.0
O A:HOH982 4.1 38.5 1.0
C5' A:TTP901 4.2 46.4 1.0
O2G A:TTP901 4.2 48.5 1.0
CB A:ASP411 4.3 38.8 1.0
CA A:LEU412 4.3 38.2 1.0
N A:SER414 4.4 32.6 1.0
O5' A:TTP901 4.4 46.3 1.0
N A:THR413 4.5 34.9 1.0
C A:ASP411 4.5 38.5 1.0
CB A:ASP623 4.6 35.9 1.0
O1B A:TTP901 4.7 49.2 1.0
O A:HOH979 4.7 49.1 1.0
CA A:THR413 4.7 34.0 1.0
O3G A:TTP901 4.7 50.5 1.0
C A:THR413 4.8 32.9 1.0
O1A A:TTP901 4.8 44.5 1.0
N A:LEU415 4.8 29.0 1.0
CA A:ASP411 4.8 37.9 1.0
CB A:LEU412 4.9 38.7 1.0

Calcium binding site 2 out of 5 in 3suo

Go back to Calcium Binding Sites List in 3suo
Calcium binding site 2 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence)


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 (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:68.9
occ:1.00
 OD2 A:ASP411 2.6 48.4 1.0
O2A A:TTP901 2.8 46.6 1.0
OD2 A:ASP623 2.8 35.5 1.0
O A:HOH979 3.1 49.1 1.0
CG A:ASP623 3.7 37.1 1.0
CB A:SER624 3.7 40.8 1.0
OD1 A:ASP623 3.8 38.5 1.0
CG A:ASP411 3.8 41.4 1.0
CA A:CA902 3.9 34.0 1.0
C3' P:2DA115 3.9 35.8 1.0
PA A:TTP901 3.9 48.4 1.0
OG A:SER624 4.2 46.8 1.0
O1A A:TTP901 4.2 44.5 1.0
O A:HOH1005 4.3 27.1 1.0
C5' P:2DA115 4.3 39.8 1.0
O5' A:TTP901 4.5 46.3 1.0
C4' P:2DA115 4.5 39.4 1.0
N A:SER624 4.6 38.9 1.0
CB A:ASP411 4.6 38.8 1.0
C5' A:TTP901 4.6 46.4 1.0
OD1 A:ASP411 4.7 47.2 1.0
CA A:SER624 4.7 39.2 1.0
O A:ASP621 4.7 32.7 1.0
C A:ASP623 4.9 37.3 1.0

Calcium binding site 3 out of 5 in 3suo

Go back to Calcium Binding Sites List in 3suo
Calcium binding site 3 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence)


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 (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:65.6
occ:1.00
 O A:ASN505 2.4 71.2 1.0
O A:LYS531 2.4 63.1 1.0
OD1 A:ASN507 2.4 64.6 1.0
C A:LYS531 3.3 61.8 1.0
CG A:ASN507 3.5 71.3 1.0
C A:ASN505 3.6 70.5 1.0
CB A:ASN505 3.9 73.1 1.0
ND2 A:ASN507 3.9 69.0 1.0
CA A:LYS531 4.0 61.6 1.0
N A:LYS532 4.3 60.3 1.0
CA A:ASN505 4.4 71.9 1.0
N A:ASN507 4.4 72.4 1.0
N A:PRO506 4.6 70.4 1.0
O A:ALA502 4.6 60.0 1.0
CB A:LYS531 4.6 62.9 1.0
C A:PRO506 4.6 71.3 1.0
CA A:PRO506 4.6 70.1 1.0
CA A:LYS532 4.6 60.2 1.0
CB A:ASN507 4.8 72.5 1.0
O A:LEU533 4.9 57.4 1.0
O A:ILE530 4.9 55.8 1.0

Calcium binding site 4 out of 5 in 3suo

Go back to Calcium Binding Sites List in 3suo
Calcium binding site 4 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence)


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 (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:65.2
occ:1.00
 O A:HOH982 3.0 38.5 1.0
OE2 A:GLU716 3.4 49.7 1.0
NZ A:LYS486 4.0 41.7 1.0
OD1 A:ASP411 4.3 47.2 1.0
OE1 A:GLU686 4.5 59.6 1.0
CD A:GLU716 4.6 48.5 1.0
OG1 A:THR413 4.6 40.9 1.0
CB A:GLU716 4.6 42.4 1.0
CB A:ASP684 4.7 43.5 1.0
O A:ASP411 4.8 40.8 1.0
OD2 A:ASP684 4.8 55.2 1.0
CG A:GLU686 4.9 51.2 1.0

Calcium binding site 5 out of 5 in 3suo

Go back to Calcium Binding Sites List in 3suo
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence)


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 (Y567A) Ternary Complex with Dttp Opposite 2AP (Gc Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:68.9
occ:1.00
 OE1 A:GLU116 2.6 50.1 1.0
O A:HOH1128 2.6 39.7 1.0
O A:HOH986 2.8 34.6 1.0
OE2 A:GLU116 2.9 47.6 1.0
CD A:GLU116 3.1 44.4 1.0
O A:ILE115 4.6 37.5 1.0
CD1 A:ILE309 4.6 60.2 1.0
CG A:GLU116 4.6 39.2 1.0
O A:HOH1129 4.7 39.3 1.0
OD2 A:ASP114 4.7 52.4 1.0

Reference:

L.J.Reha-Krantz, C.Hariharan, U.Subuddhi, S.Xia, C.Zhao, J.Beckman, T.Christian, W.Konigsberg. Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-Dna Polymerase. Biochemistry V. 50 10136 2011.
ISSN: ISSN 0006-2960
PubMed: 22023103
DOI: 10.1021/BI2014618
Page generated: Sat Jul 13 19:25:17 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy