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

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

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

Protein crystallography data

The structure of RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp Opposite 2AP (at Rich Sequence), PDB code: 3sun 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) 87.72 / 2.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.839, 120.987, 127.366, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.5

Calcium Binding Sites:

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

Calcium binding site 1 out of 5 in 3sun

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Calcium binding site 1 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp 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 Dttp Opposite 2AP (at Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca897

b:38.9
occ:1.00
 OD1 A:ASP623 2.2 42.5 1.0
O1G A:TTP896 2.2 52.9 1.0
O2B A:TTP896 2.2 51.1 1.0
OD2 A:ASP411 2.2 49.8 1.0
O A:LEU412 2.3 41.8 1.0
O2A A:TTP896 2.4 58.5 1.0
CG A:ASP411 3.0 44.1 1.0
OD1 A:ASP411 3.1 48.3 1.0
PB A:TTP896 3.3 53.6 1.0
CG A:ASP623 3.4 38.1 1.0
C A:LEU412 3.5 38.7 1.0
PG A:TTP896 3.5 53.3 1.0
PA A:TTP896 3.6 57.5 1.0
O3A A:TTP896 3.8 56.0 1.0
O3B A:TTP896 3.8 49.0 1.0
O A:HOH1027 3.9 38.1 1.0
OD2 A:ASP623 3.9 45.2 1.0
N A:LEU412 4.0 36.5 1.0
CA A:CA898 4.0 72.3 1.0
C5' A:TTP896 4.1 55.1 1.0
O2G A:TTP896 4.2 48.8 1.0
CA A:LEU412 4.2 38.3 1.0
N A:SER414 4.3 36.1 1.0
CB A:ASP411 4.4 39.4 1.0
O5' A:TTP896 4.4 57.4 1.0
N A:THR413 4.5 40.0 1.0
C A:ASP411 4.5 37.9 1.0
CB A:ASP623 4.6 35.2 1.0
O1B A:TTP896 4.6 54.6 1.0
O3G A:TTP896 4.6 50.9 1.0
CA A:THR413 4.7 38.5 1.0
N A:LEU415 4.7 33.0 1.0
C A:THR413 4.8 37.1 1.0
O1A A:TTP896 4.8 54.1 1.0
CB A:LEU412 4.8 38.8 1.0
CA A:SER414 5.0 35.9 1.0
CA A:ASP411 5.0 37.6 1.0
O A:HOH1001 5.0 54.0 1.0

Calcium binding site 2 out of 5 in 3sun

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp 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 Dttp Opposite 2AP (at Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca898

b:72.3
occ:1.00
 OD2 A:ASP411 2.7 49.8 1.0
OD2 A:ASP623 2.8 45.2 1.0
O2A A:TTP896 2.9 58.5 1.0
CG A:ASP623 3.7 38.1 1.0
CG A:ASP411 3.7 44.1 1.0
OD1 A:ASP623 3.8 42.5 1.0
CA A:CA897 4.0 38.9 1.0
CB A:SER624 4.0 37.6 1.0
PA A:TTP896 4.0 57.5 1.0
O A:HOH1027 4.0 38.1 1.0
C3' P:2DA115 4.1 43.1 1.0
CB A:ASP411 4.1 39.4 1.0
O1A A:TTP896 4.2 54.1 1.0
OE2 A:GLU686 4.3 60.7 1.0
OG A:SER624 4.5 40.5 1.0
C5' P:2DA115 4.6 44.4 1.0
O5' A:TTP896 4.7 57.4 1.0
OD1 A:ASP411 4.7 48.3 1.0
C5' A:TTP896 4.9 55.1 1.0
N A:SER624 4.9 37.0 1.0
O5' P:2DA115 4.9 41.9 1.0
C4' P:2DA115 4.9 43.3 1.0
CA A:SER624 5.0 37.8 1.0

Calcium binding site 3 out of 5 in 3sun

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Calcium binding site 3 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp 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 Dttp Opposite 2AP (at Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca899

b:78.9
occ:1.00
 OD1 A:ASN507 2.3 77.0 1.0
O A:LYS531 2.4 63.2 1.0
O A:ASN505 2.4 65.9 1.0
C A:LYS531 3.3 61.5 1.0
CG A:ASN507 3.6 74.5 1.0
C A:ASN505 3.6 65.0 1.0
CA A:LYS531 3.9 61.9 1.0
N A:ASN507 4.1 71.2 1.0
CB A:ASN505 4.2 68.0 1.0
O A:ALA502 4.2 56.2 1.0
N A:LYS532 4.3 60.8 1.0
ND2 A:ASN507 4.4 74.2 1.0
CA A:PRO506 4.4 66.4 1.0
C A:PRO506 4.4 70.0 1.0
N A:PRO506 4.4 65.3 1.0
CA A:ASN505 4.5 65.8 1.0
CB A:LYS531 4.6 65.0 1.0
CB A:ASN507 4.6 72.3 1.0
CA A:LYS532 4.6 60.8 1.0
O A:LEU533 4.7 55.7 1.0
O A:ILE530 4.8 55.6 1.0
CA A:ASN507 4.8 72.9 1.0
N A:LEU533 4.9 56.7 1.0

Calcium binding site 4 out of 5 in 3sun

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dttp 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 Dttp Opposite 2AP (at Rich Sequence) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca900

b:0.5
occ:1.00
 O A:HOH1001 2.9 54.0 1.0
OE2 A:GLU716 3.6 62.9 1.0
OD1 A:ASP411 4.2 48.3 1.0
OG1 A:THR413 4.4 42.4 1.0
CB A:ASP684 4.4 46.1 1.0
OD2 A:ASP684 4.4 55.2 1.0
NZ A:LYS486 4.5 37.6 1.0
CB A:GLU716 4.6 46.7 1.0
CD A:GLU716 4.7 60.0 1.0
O A:ASP411 4.9 41.6 1.0
OE1 A:GLU686 4.9 64.1 1.0
CG A:ASP684 4.9 50.3 1.0
O A:ARG685 5.0 44.4 1.0

Calcium binding site 5 out of 5 in 3sun

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

b:73.0
occ:1.00
 O A:HOH943 2.6 54.5 1.0
OE1 A:GLU116 2.8 49.4 1.0
OE2 A:GLU116 2.9 50.8 1.0
CD A:GLU116 3.2 48.8 1.0
O A:HOH1039 3.4 46.7 1.0
OD2 A:ASP114 4.2 47.1 1.0
O A:ILE115 4.7 38.6 1.0
CG A:GLU116 4.7 43.3 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 16:45:32 2025

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