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Calcium in PDB 3qnn: RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO

Enzymatic activity of RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO

All present enzymatic activity of RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO, PDB code: 3qnn was solved by S.Xia, M.Wang, J.Wang, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.811, 120.042, 130.409, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.4

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO (pdb code 3qnn). 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 (Y567A) Ternary Complex with Dgt Opposite 3TCO, PDB code: 3qnn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3qnn

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Calcium binding site 1 out of 7 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO


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 Dgt Opposite 3TCO within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:20.0
occ:1.00
 OD1 A:ASP623 2.2 24.4 1.0
O1G A:DGT902 2.2 19.4 1.0
O A:LEU412 2.3 17.2 1.0
O2B A:DGT902 2.3 14.9 1.0
OD2 A:ASP411 2.5 35.1 1.0
O2A A:DGT902 2.6 23.5 1.0
OD1 A:ASP411 2.7 35.2 1.0
CG A:ASP411 2.9 27.8 1.0
CG A:ASP623 3.3 20.5 1.0
PB A:DGT902 3.4 18.3 1.0
C A:LEU412 3.5 18.3 1.0
PG A:DGT902 3.5 20.2 1.0
O3A A:DGT902 3.7 21.6 1.0
PA A:DGT902 3.7 22.4 1.0
O A:HOH1380 3.7 33.8 1.0
O3B A:DGT902 3.8 21.1 1.0
CA A:CA904 3.9 38.1 1.0
OD2 A:ASP623 3.9 19.8 1.0
N A:LEU412 4.1 18.7 1.0
O2G A:DGT902 4.2 20.2 1.0
CA A:LEU412 4.3 18.9 1.0
N A:SER414 4.3 16.2 1.0
C5' A:DGT902 4.3 15.5 1.0
CB A:ASP411 4.4 25.6 1.0
N A:THR413 4.4 19.1 1.0
C A:ASP411 4.5 20.6 1.0
CB A:ASP623 4.5 20.6 1.0
O5' A:DGT902 4.5 16.8 1.0
CA A:THR413 4.6 17.3 1.0
O3G A:DGT902 4.6 21.8 1.0
C A:THR413 4.7 17.9 1.0
O1B A:DGT902 4.7 19.8 1.0
N A:LEU415 4.8 14.7 1.0
O A:HOH1358 4.8 46.4 1.0
CB A:LEU412 4.9 17.4 1.0
O1A A:DGT902 4.9 19.0 1.0
CA A:ASP411 4.9 21.1 1.0

Calcium binding site 2 out of 7 in 3qnn

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Calcium binding site 2 out of 7 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO


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 Dgt Opposite 3TCO within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:38.1
occ:1.00
 O A:HOH1459 2.5 35.4 1.0
OD2 A:ASP623 2.5 19.8 1.0
O2A A:DGT902 2.5 23.5 1.0
OD2 A:ASP411 2.7 35.1 1.0
CG A:ASP623 3.4 20.5 1.0
OD1 A:ASP623 3.6 24.4 1.0
CG A:ASP411 3.8 27.8 1.0
C3' P:DOC115 3.8 18.6 1.0
PA A:DGT902 3.8 22.4 1.0
CA A:CA903 3.9 20.0 1.0
CB A:SER624 3.9 23.2 1.0
O A:HOH1380 4.1 33.8 1.0
O1A A:DGT902 4.2 19.0 1.0
O P:HOH101 4.3 22.4 1.0
OG A:SER624 4.4 27.4 1.0
O5' A:DGT902 4.5 16.8 1.0
O P:HOH332 4.5 35.5 1.0
OD1 A:ASP411 4.5 35.2 1.0
C5' P:DOC115 4.5 24.9 1.0
C5' A:DGT902 4.6 15.5 1.0
CB A:ASP411 4.6 25.6 1.0
C4' P:DOC115 4.8 19.3 1.0
C A:ASP623 4.8 20.0 1.0
N A:SER624 4.8 19.3 1.0
O5' P:DOC115 4.8 25.9 1.0
O A:ASP621 4.8 16.9 1.0
CB A:ASP623 4.8 20.6 1.0
CA A:SER624 4.9 20.3 1.0
C2' P:DOC115 5.0 19.8 1.0
O A:ASP623 5.0 19.0 1.0

Calcium binding site 3 out of 7 in 3qnn

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Calcium binding site 3 out of 7 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO


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 Dgt Opposite 3TCO within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:39.9
occ:1.00
 O A:ASN505 2.3 42.2 1.0
OD1 A:ASN507 2.3 51.2 1.0
O A:LYS531 2.3 42.6 1.0
O A:HOH1051 2.4 24.9 1.0
O A:HOH1094 2.5 23.8 1.0
O A:HOH1071 2.5 22.6 1.0
C A:LYS531 3.3 41.8 1.0
CG A:ASN507 3.4 50.3 1.0
C A:ASN505 3.5 44.1 1.0
ND2 A:ASN507 4.1 51.4 1.0
CA A:LYS531 4.1 40.9 1.0
CB A:ASN505 4.2 46.1 1.0
N A:ASN507 4.2 46.8 1.0
N A:LYS532 4.2 41.6 1.0
CA A:PRO506 4.3 44.0 1.0
C A:PRO506 4.3 45.2 1.0
N A:PRO506 4.4 44.0 1.0
CA A:LYS532 4.4 42.3 1.0
CA A:ASN505 4.5 45.1 1.0
O A:LEU533 4.5 37.8 1.0
O A:ALA502 4.6 37.1 1.0
CB A:ASN507 4.6 49.0 1.0
CB A:LYS531 4.8 42.2 1.0
C A:LYS532 4.8 41.7 1.0
CA A:ASN507 4.8 48.4 1.0
N A:LEU533 4.8 39.4 1.0
O A:PRO506 4.9 45.3 1.0
O A:ILE530 4.9 34.5 1.0

Calcium binding site 4 out of 7 in 3qnn

Go back to Calcium Binding Sites List in 3qnn
Calcium binding site 4 out of 7 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO


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 Dgt Opposite 3TCO within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:56.0
occ:1.00
 O A:HOH1391 2.2 31.6 1.0
O A:HOH1483 2.3 32.8 1.0
O A:HOH917 2.6 23.6 1.0
OE1 A:GLU116 2.7 25.7 1.0
O A:HOH1468 2.7 43.4 1.0
OE2 A:GLU116 2.8 27.6 1.0
CD A:GLU116 3.1 25.6 1.0
O A:HOH1365 4.3 30.8 1.0
OD2 A:ASP114 4.3 36.3 1.0
O A:HOH1451 4.3 36.8 1.0
O A:HOH1524 4.5 44.7 1.0
CG A:GLU116 4.6 21.1 1.0
O A:ILE115 4.7 17.8 1.0
CD1 A:ILE309 4.7 41.6 1.0

Calcium binding site 5 out of 7 in 3qnn

Go back to Calcium Binding Sites List in 3qnn
Calcium binding site 5 out of 7 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO


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 Dgt Opposite 3TCO within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:58.2
occ:1.00
 O A:HOH1593 2.3 33.2 1.0
OD1 A:ASP684 2.4 34.9 1.0
O A:HOH1376 2.5 29.5 1.0
OE1 A:GLU660 3.4 37.3 1.0
CG A:ASP684 3.4 32.2 1.0
OD2 A:ASP684 4.0 34.8 1.0
CD A:GLU660 4.0 32.5 1.0
OD1 A:ASP664 4.4 39.1 1.0
O A:MET683 4.5 25.5 1.0
OD2 A:ASP664 4.5 39.0 1.0
CG A:GLU660 4.6 28.7 1.0
CB A:ASP684 4.6 26.9 1.0
CB A:GLU660 4.6 27.0 1.0
OE2 A:GLU660 4.7 34.5 1.0
CA A:ASP684 4.8 25.1 1.0
CG A:ASP664 4.9 33.9 1.0
C A:MET683 5.0 23.5 1.0

Calcium binding site 6 out of 7 in 3qnn

Go back to Calcium Binding Sites List in 3qnn
Calcium binding site 6 out of 7 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO


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 (Y567A) Ternary Complex with Dgt Opposite 3TCO within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:65.2
occ:1.00
 O A:HOH1594 2.4 22.9 1.0
O A:ASP792 2.4 39.5 1.0
O A:ALA789 3.1 43.5 1.0
O A:HOH1498 3.3 37.4 1.0
C A:ASP792 3.6 39.4 1.0
C A:ALA789 4.3 41.1 1.0
CB A:ASP792 4.4 38.0 1.0
CA A:ASP792 4.4 38.1 1.0
N A:VAL793 4.6 39.0 1.0
N A:ASP792 4.6 37.6 1.0
CA A:VAL793 4.8 40.0 1.0
CA A:ALA789 5.0 40.1 1.0

Calcium binding site 7 out of 7 in 3qnn

Go back to Calcium Binding Sites List in 3qnn
Calcium binding site 7 out of 7 in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dgt Opposite 3TCO


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 (Y567A) Ternary Complex with Dgt Opposite 3TCO within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:77.7
occ:1.00
 O A:HOH1330 2.6 40.1 1.0
OE1 A:GLU716 2.6 43.1 1.0
O A:HOH1421 2.6 47.1 1.0
O A:HOH1358 2.7 46.4 1.0
O A:HOH1296 2.8 33.8 1.0
O A:HOH1470 3.0 38.4 1.0
CD A:GLU716 3.8 40.1 1.0
O A:HOH1209 3.8 23.3 1.0
NZ A:LYS486 4.1 34.3 1.0
CG A:GLU716 4.3 37.3 1.0
OG1 A:THR413 4.4 22.1 1.0
OD1 A:ASP411 4.4 35.2 1.0
CB A:ASP684 4.6 26.9 1.0
OD2 A:ASP684 4.7 34.8 1.0
OE2 A:GLU716 4.8 41.7 1.0
CE A:LYS486 4.9 29.3 1.0

Reference:

S.Xia, J.Beckman, J.Wang, W.H.Konigsberg. Using A Fluorescent Cytosine Analogue Tc(O) to Probe the Effect of the Y567 to Ala Substitution on the Preinsertion Steps of Dnmp Incorporation By RB69 Dna Polymerase. Biochemistry V. 51 4609 2012.
ISSN: ISSN 0006-2960
PubMed: 22616982
DOI: 10.1021/BI300241M
Page generated: Sat Jul 13 17:37:04 2024

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