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Calcium in PDB 3s9h: RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+

Enzymatic activity of RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+

All present enzymatic activity of RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+, PDB code: 3s9h was solved by 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) 63.63 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.050, 119.821, 130.791, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.3

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+ (pdb code 3s9h). 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 Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+, PDB code: 3s9h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3s9h

Go back to Calcium Binding Sites List in 3s9h
Calcium binding site 1 out of 7 in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+


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 Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca19

b:78.2
occ:1.00
 O T:HOH539 2.6 26.5 1.0
O T:HOH1405 2.7 36.4 1.0
O T:HOH1046 2.7 32.9 1.0
O T:HOH1366 2.8 37.6 1.0
O P:HOH1194 2.9 41.1 1.0
O T:HOH1202 4.4 44.9 1.0
N7 P:DG105 4.6 54.0 1.0
O T:HOH1094 4.6 54.0 1.0
C8 P:DG105 4.7 55.9 1.0
N7 T:DG12 4.7 35.6 1.0
O P:HOH1018 4.7 42.1 1.0
O4 T:DT13 4.8 36.4 1.0
O6 T:DG12 4.8 37.3 1.0

Calcium binding site 2 out of 7 in 3s9h

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Calcium binding site 2 out of 7 in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+


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 Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:43.7
occ:1.00
 OD1 A:ASP623 2.1 36.6 1.0
O1G A:DUP904 2.2 33.6 1.0
O2B A:DUP904 2.2 36.6 1.0
O A:LEU412 2.3 25.6 1.0
OD1 A:ASP411 2.4 38.0 1.0
O A:HOH917 2.4 24.9 1.0
O2A A:DUP904 2.9 41.4 1.0
OD2 A:ASP411 3.0 39.6 1.0
CG A:ASP411 3.0 34.0 1.0
CG A:ASP623 3.2 30.6 1.0
PB A:DUP904 3.4 36.5 1.0
O A:HOH1782 3.4 32.4 1.0
PG A:DUP904 3.5 35.4 1.0
C A:LEU412 3.5 27.1 1.0
O3B A:DUP904 3.8 36.0 1.0
OD2 A:ASP623 3.9 29.5 1.0
CA A:CA906 3.9 63.5 1.0
N3A A:DUP904 3.9 39.1 1.0
PA A:DUP904 4.0 41.7 1.0
N A:LEU412 4.1 26.1 1.0
O2G A:DUP904 4.1 34.4 1.0
N A:SER414 4.2 26.7 1.0
CA A:LEU412 4.3 25.9 1.0
CB A:ASP623 4.3 27.3 1.0
C5' A:DUP904 4.4 29.7 1.0
CB A:ASP411 4.4 29.8 1.0
N A:THR413 4.5 26.6 1.0
O A:HOH932 4.5 54.9 1.0
C A:ASP411 4.6 27.4 1.0
C A:THR413 4.6 26.4 1.0
CA A:THR413 4.6 27.7 1.0
N A:LEU415 4.6 21.8 1.0
O3G A:DUP904 4.6 40.5 1.0
O5' A:DUP904 4.7 37.6 1.0
O1B A:DUP904 4.8 34.7 1.0
CB A:LEU412 4.8 24.9 1.0
CA A:SER414 4.9 25.5 1.0
O A:ASP623 4.9 25.4 1.0
CA A:ASP411 4.9 27.9 1.0

Calcium binding site 3 out of 7 in 3s9h

Go back to Calcium Binding Sites List in 3s9h
Calcium binding site 3 out of 7 in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+


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 Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:63.5
occ:1.00
 OD2 A:ASP623 2.4 29.5 1.0
O A:HOH917 2.5 24.9 1.0
OD2 A:ASP411 2.5 39.6 1.0
O A:HOH921 2.5 38.5 1.0
O2A A:DUP904 2.7 41.4 1.0
O A:HOH930 3.1 38.9 1.0
CG A:ASP623 3.2 30.6 1.0
OD1 A:ASP623 3.4 36.6 1.0
CG A:ASP411 3.7 34.0 1.0
C3' P:DOC115 3.7 25.7 1.0
CB A:SER624 3.8 27.7 1.0
CA A:CA905 3.9 43.7 1.0
PA A:DUP904 4.0 41.7 1.0
OG A:SER624 4.0 29.4 1.0
O A:HOH932 4.0 54.9 1.0
O A:HOH1536 4.2 24.3 1.0
OD1 A:ASP411 4.3 38.0 1.0
O1A A:DUP904 4.4 44.5 1.0
N A:SER624 4.5 25.4 1.0
C A:ASP623 4.6 26.0 1.0
C5' A:DUP904 4.6 29.7 1.0
CB A:ASP623 4.6 27.3 1.0
O A:ASP621 4.7 22.4 1.0
O5' A:DUP904 4.7 37.6 1.0
CA A:SER624 4.7 26.8 1.0
O5' P:DOC115 4.7 30.8 1.0
CB A:ASP411 4.8 29.8 1.0
O A:ASP623 4.8 25.4 1.0
C4' P:DOC115 4.8 27.5 1.0
C5' P:DOC115 4.8 26.7 1.0
O P:HOH413 4.8 26.6 1.0
C2' P:DOC115 4.9 27.6 1.0
O1G A:DUP904 4.9 33.6 1.0
N A:ASP623 5.0 24.6 1.0
CA A:ASP623 5.0 26.5 1.0

Calcium binding site 4 out of 7 in 3s9h

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Calcium binding site 4 out of 7 in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+


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 Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:74.8
occ:1.00
 O3G A:DUP904 2.2 40.5 1.0
O A:HOH1501 3.0 63.3 1.0
O A:HOH932 3.1 54.9 1.0
PG A:DUP904 3.2 35.4 1.0
O1G A:DUP904 3.4 33.6 1.0
O A:HOH1228 3.5 21.3 1.0
NZ A:LYS486 3.5 36.4 1.0
O A:HOH933 3.5 43.0 1.0
O A:HOH1782 3.5 32.4 1.0
O A:HOH1845 3.8 34.2 1.0
NZ A:LYS560 3.8 40.3 1.0
NH2 A:ARG482 3.8 29.1 1.0
O2G A:DUP904 3.9 34.4 1.0
O A:HOH917 4.3 24.9 1.0
CE A:LYS486 4.5 34.2 1.0
O3B A:DUP904 4.5 36.0 1.0
OE1 A:GLU716 4.6 47.8 1.0
OE1 A:GLU686 4.6 40.9 1.0
OE2 A:GLU716 4.7 45.0 1.0
N3A A:DUP904 4.8 39.1 1.0
O A:HOH1696 4.9 31.2 1.0
CD A:GLU716 5.0 44.3 1.0
OD1 A:ASP411 5.0 38.0 1.0

Calcium binding site 5 out of 7 in 3s9h

Go back to Calcium Binding Sites List in 3s9h
Calcium binding site 5 out of 7 in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+


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 Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:57.7
occ:1.00
 O A:HOH941 2.3 27.6 1.0
O A:HOH945 2.4 23.6 1.0
O A:HOH937 2.5 43.5 1.0
OE1 A:GLU116 2.5 30.0 1.0
OE2 A:GLU116 2.7 32.7 1.0
O A:HOH944 2.9 45.4 1.0
CD A:GLU116 3.0 31.3 1.0
O A:HOH1435 3.1 45.3 1.0
O A:HOH940 4.1 40.0 1.0
O A:HOH1647 4.2 30.8 1.0
OD2 A:ASP114 4.2 41.6 1.0
O A:ILE115 4.5 25.1 1.0
CG A:GLU116 4.5 27.8 1.0
O A:HOH1846 4.6 41.4 1.0
CD1 A:ILE309 4.9 46.4 1.0

Calcium binding site 6 out of 7 in 3s9h

Go back to Calcium Binding Sites List in 3s9h
Calcium binding site 6 out of 7 in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+


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 Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:39.4
occ:1.00
 OD1 A:ASN507 2.2 45.3 1.0
O A:ASN505 2.2 44.1 1.0
O A:LYS531 2.3 40.9 1.0
O A:HOH948 2.4 26.8 1.0
O A:HOH946 2.4 21.8 1.0
O A:HOH952 2.5 25.5 1.0
O A:HOH947 2.7 46.9 1.0
C A:LYS531 3.3 40.7 1.0
CG A:ASN507 3.3 47.0 1.0
C A:ASN505 3.5 45.3 1.0
ND2 A:ASN507 4.0 47.0 1.0
N A:ASN507 4.0 47.0 1.0
CA A:LYS531 4.1 39.9 1.0
N A:LYS532 4.1 40.3 1.0
CB A:ASN505 4.2 47.1 1.0
C A:PRO506 4.3 46.6 1.0
CA A:PRO506 4.3 45.8 1.0
N A:PRO506 4.3 45.1 1.0
CA A:LYS532 4.3 41.6 1.0
CA A:ASN505 4.5 46.0 1.0
CB A:ASN507 4.5 48.0 1.0
O A:HOH1577 4.6 22.5 1.0
O A:LEU533 4.6 39.4 1.0
O A:ALA502 4.7 37.2 1.0
CA A:ASN507 4.7 48.4 1.0
C A:LYS532 4.7 41.5 1.0
CB A:LYS531 4.7 41.0 1.0
N A:LEU533 4.9 40.5 1.0
O A:ILE530 4.9 37.6 1.0
O A:PRO506 5.0 47.5 1.0

Calcium binding site 7 out of 7 in 3s9h

Go back to Calcium Binding Sites List in 3s9h
Calcium binding site 7 out of 7 in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+


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 Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Dideoxy-Terminated Primer in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:92.0
occ:1.00
 O A:HOH962 2.1 31.0 1.0
O A:HOH965 2.3 31.5 1.0
NH2 A:ARG559 3.7 25.4 1.0
O A:HOH1157 3.7 19.6 1.0
OE1 A:GLN481 3.9 44.0 1.0
O A:HOH1826 4.0 39.1 1.0
O A:ASP346 4.1 23.8 1.0
CB A:ASP346 4.2 25.2 1.0
CD A:GLN481 4.3 42.3 1.0
O A:HOH1671 4.3 30.7 1.0
CD1 A:TYR350 4.3 26.6 1.0
CB A:TYR350 4.4 24.2 1.0
NE2 A:GLN481 4.4 44.9 1.0
C A:ASP346 4.5 25.2 1.0
CG A:ASP346 4.5 29.7 1.0
CG A:TYR350 4.6 23.8 1.0
CA A:ASP346 4.6 23.6 1.0
CZ A:ARG559 4.7 25.0 1.0
NE A:ARG559 4.7 24.0 1.0
OD2 A:ASP346 4.8 32.8 1.0
O A:HOH1484 4.8 32.9 1.0
OD1 A:ASP346 4.9 32.2 1.0

Reference:

S.Xia, M.Wang, G.Blaha, W.H.Konigsberg, J.Wang. Structural Insights Into Complete Metal Ion Coordination From Ternary Complexes of B Family RB69 Dna Polymerase. Biochemistry V. 50 9114 2011.
ISSN: ISSN 0006-2960
PubMed: 21923197
DOI: 10.1021/BI201260H
Page generated: Sat Jul 13 19:06:04 2024

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