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

Calcium in PDB 3suq: RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 2AP (at Rich Sequence)

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

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

Protein crystallography data

The structure of RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 2AP (at Rich Sequence), PDB code: 3suq 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) 87.23 / 3.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.005, 121.596, 125.196, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 30

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 3suq

Go back to Calcium Binding Sites List in 3suq
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 2AP (at 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 Dctp Opposite 2AP (at Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca899

b:0.8
occ:1.00
 O1G A:DCP898 2.1 0.6 1.0
OD1 A:ASP623 2.2 99.9 1.0
O2B A:DCP898 2.2 94.5 1.0
O2A A:DCP898 2.4 94.4 1.0
O A:LEU412 2.5 98.2 1.0
OD2 A:ASP411 2.5 0.1 1.0
OD1 A:ASP411 2.9 0.9 1.0
CG A:ASP411 3.1 0.7 1.0
PB A:DCP898 3.2 97.1 1.0
PG A:DCP898 3.2 0.7 1.0
CG A:ASP623 3.4 99.6 1.0
PA A:DCP898 3.5 92.7 1.0
O3A A:DCP898 3.6 93.9 1.0
CA A:CA900 3.6 0.1 1.0
O3B A:DCP898 3.6 1.0 1.0
C A:LEU412 3.6 98.6 1.0
O2G A:DCP898 3.7 0.7 1.0
OD2 A:ASP623 3.9 0.1 1.0
C5' A:DCP898 4.2 89.9 1.0
N A:LEU412 4.2 99.2 1.0
O5' A:DCP898 4.4 89.9 1.0
N A:SER414 4.4 97.1 1.0
CA A:LEU412 4.4 99.0 1.0
O3G A:DCP898 4.5 0.0 1.0
CB A:ASP623 4.6 99.4 1.0
O1B A:DCP898 4.6 98.3 1.0
CB A:ASP411 4.6 0.9 1.0
N A:THR413 4.6 99.7 1.0
O1A A:DCP898 4.7 91.8 1.0
CA A:THR413 4.8 99.9 1.0
N A:LEU415 4.9 94.3 1.0
C A:THR413 4.9 99.2 1.0
CA A:CA902 4.9 0.8 1.0
C A:ASP411 4.9 0.8 1.0
CB A:LEU412 5.0 98.2 1.0

Calcium binding site 2 out of 5 in 3suq

Go back to Calcium Binding Sites List in 3suq
Calcium binding site 2 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 2AP (at 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 Dctp Opposite 2AP (at Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca900

b:0.1
occ:1.00
 O2A A:DCP898 2.6 94.4 1.0
OD2 A:ASP411 3.0 0.1 1.0
OD2 A:ASP623 3.0 0.1 1.0
CA A:CA899 3.6 0.8 1.0
OD1 A:ASP623 3.6 99.9 1.0
CG A:ASP411 3.7 0.7 1.0
CG A:ASP623 3.7 99.6 1.0
PA A:DCP898 3.8 92.7 1.0
O1A A:DCP898 4.0 91.8 1.0
OD1 A:ASP411 4.2 0.9 1.0
OG A:SER624 4.2 0.1 1.0
C3' P:2DA115 4.2 93.5 1.0
OE2 A:GLU686 4.2 0.8 1.0
CB A:SER624 4.2 99.2 1.0
O1G A:DCP898 4.5 0.6 1.0
CB A:ASP411 4.6 0.9 1.0
C5' P:2DA115 4.6 95.8 1.0
O5' A:DCP898 4.8 89.9 1.0
C5' A:DCP898 4.8 89.9 1.0
O5' P:2DA115 4.9 94.3 1.0

Calcium binding site 3 out of 5 in 3suq

Go back to Calcium Binding Sites List in 3suq
Calcium binding site 3 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 2AP (at 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 Dctp Opposite 2AP (at Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:0.9
occ:1.00
 O A:ASN505 2.2 1.0 1.0
OD1 A:ASN507 2.5 0.4 1.0
O A:LYS531 2.7 0.6 1.0
C A:ASN505 3.4 0.9 1.0
C A:LYS531 3.5 0.1 1.0
CG A:ASN507 3.7 0.5 1.0
N A:ASN507 3.9 0.0 1.0
CA A:PRO506 4.0 0.5 1.0
C A:PRO506 4.1 0.4 1.0
CA A:LYS531 4.1 0.0 1.0
N A:PRO506 4.2 0.2 1.0
O A:ALA502 4.2 1.0 1.0
CB A:ASN505 4.3 0.2 1.0
N A:LYS532 4.3 0.4 1.0
CA A:ASN505 4.5 0.4 1.0
O A:LEU533 4.5 0.1 1.0
ND2 A:ASN507 4.5 0.5 1.0
CA A:LYS532 4.6 0.7 1.0
CA A:ASN507 4.7 0.5 1.0
CB A:ASN507 4.7 0.6 1.0
N A:LEU533 4.8 0.5 1.0
O A:PRO506 4.8 0.0 1.0
C A:LYS532 4.8 0.9 1.0
O A:ILE530 4.8 0.2 1.0
CB A:LYS531 4.9 0.8 1.0

Calcium binding site 4 out of 5 in 3suq

Go back to Calcium Binding Sites List in 3suq
Calcium binding site 4 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 2AP (at 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 Dctp Opposite 2AP (at Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:0.8
occ:1.00
 OD1 A:ASP411 2.7 0.9 1.0
OE1 A:GLU686 3.2 0.7 1.0
OE2 A:GLU716 3.2 0.1 1.0
CG A:ASP411 3.8 0.7 1.0
NZ A:LYS486 3.9 93.7 1.0
O2G A:DCP898 4.0 0.7 1.0
O1G A:DCP898 4.0 0.6 1.0
CD A:GLU716 4.2 0.9 1.0
CB A:ASP411 4.2 0.9 1.0
CD A:GLU686 4.4 0.7 1.0
OE1 A:GLU716 4.4 0.2 1.0
PG A:DCP898 4.4 0.7 1.0
O3G A:DCP898 4.6 0.0 1.0
O A:ASP411 4.7 0.6 1.0
O A:LEU412 4.7 98.2 1.0
CA A:THR413 4.8 99.9 1.0
OD2 A:ASP411 4.8 0.1 1.0
C A:LEU412 4.9 98.6 1.0
C A:ASP411 4.9 0.8 1.0
OG1 A:THR413 4.9 0.6 1.0
N A:THR413 4.9 99.7 1.0
CA A:CA899 4.9 0.8 1.0

Calcium binding site 5 out of 5 in 3suq

Go back to Calcium Binding Sites List in 3suq
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite 2AP (at 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 Dctp Opposite 2AP (at Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:0.8
occ:1.00
 OE2 A:GLU116 2.3 0.2 1.0
CD A:GLU116 3.0 0.4 1.0
OE1 A:GLU116 3.1 0.7 1.0
OD2 A:ASP114 3.7 0.8 1.0
O A:ILE115 4.3 0.3 1.0
CG A:GLU116 4.5 0.5 1.0
CG A:ASP114 4.6 0.2 1.0
OD1 A:ASP114 4.7 0.0 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: Tue Jul 8 16:46:35 2025

Last articles

Mg in 4JU2
Mg in 4JU4
Mg in 4JU1
Mg in 4JTZ
Mg in 4JU3
Mg in 4JTW
Mg in 4JSV
Mg in 4JTY
Mg in 4JT4
Mg in 4JSP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy