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

Enzymatic activity of RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-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 Deoxy-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 Deoxy-Terminated Primer in the Presence of CA2+, PDB code: 3scx 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) 88.04 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.022, 119.333, 130.663, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.9

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 Deoxy-Terminated Primer in the Presence of CA2+ (pdb code 3scx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-Terminated Primer in the Presence of CA2+, PDB code: 3scx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3scx

Go back to Calcium Binding Sites List in 3scx
Calcium binding site 1 out of 4 in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-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 Deoxy-Terminated Primer in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:68.1
occ:1.00
 O A:LYS531 2.0 65.2 1.0
O A:ASN505 2.3 67.4 1.0
ND2 A:ASN507 2.3 69.0 1.0
C A:LYS531 3.1 64.5 1.0
CG A:ASN507 3.4 73.1 1.0
C A:ASN505 3.5 67.1 1.0
CA A:LYS531 3.8 63.9 1.0
OD1 A:ASN507 3.9 74.3 1.0
N A:LYS532 4.1 63.9 1.0
N A:ASN507 4.1 70.3 1.0
CB A:ASN505 4.2 69.3 1.0
CB A:LYS531 4.3 66.5 1.0
N A:PRO506 4.4 66.5 1.0
CA A:LYS532 4.4 65.6 1.0
CA A:ASN505 4.5 67.6 1.0
C A:PRO506 4.5 68.8 1.0
CA A:PRO506 4.5 66.2 1.0
CB A:ASN507 4.6 73.4 1.0
O A:LEU533 4.8 61.1 1.0
CA A:ASN507 4.8 73.3 1.0
N A:LEU533 4.9 62.2 1.0
O A:ILE530 4.9 61.8 1.0
C A:LYS532 4.9 64.5 1.0
O A:ALA502 4.9 58.2 1.0

Calcium binding site 2 out of 4 in 3scx

Go back to Calcium Binding Sites List in 3scx
Calcium binding site 2 out of 4 in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-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 Deoxy-Terminated Primer in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:50.4
occ:1.00
 OD1 A:ASP623 2.1 33.5 1.0
O1G A:DUP904 2.2 40.9 1.0
O2B A:DUP904 2.3 40.4 1.0
O A:LEU412 2.3 34.8 1.0
OD1 A:ASP411 2.4 45.1 1.0
OD2 A:ASP411 2.7 42.2 1.0
O2A A:DUP904 2.8 45.9 1.0
CG A:ASP411 2.9 40.7 1.0
O A:HOH1012 3.3 2.0 1.0
CG A:ASP623 3.3 33.6 1.0
PB A:DUP904 3.3 42.1 1.0
PG A:DUP904 3.4 40.4 1.0
C A:LEU412 3.5 35.4 1.0
O3B A:DUP904 3.6 41.4 1.0
N3A A:DUP904 3.8 40.8 1.0
PA A:DUP904 3.9 44.5 1.0
OD2 A:ASP623 4.0 33.7 1.0
N A:SER414 4.0 34.4 1.0
N A:LEU412 4.1 36.0 1.0
O2G A:DUP904 4.1 40.7 1.0
CA A:CA907 4.2 85.9 1.0
CA A:LEU412 4.4 35.7 1.0
CB A:ASP411 4.4 36.7 1.0
CB A:ASP623 4.4 33.5 1.0
C5' A:DUP904 4.4 40.2 1.0
N A:THR413 4.5 35.9 1.0
C A:ASP411 4.5 36.8 1.0
C A:THR413 4.5 34.8 1.0
N A:LEU415 4.6 32.8 1.0
CA A:THR413 4.6 35.8 1.0
O3G A:DUP904 4.6 40.1 1.0
O5' A:DUP904 4.6 42.0 1.0
CA A:SER414 4.7 33.6 1.0
O1B A:DUP904 4.8 39.8 1.0
CB A:LEU412 4.9 35.0 1.0
CA A:CA908 4.9 47.9 1.0
CA A:ASP411 4.9 37.0 1.0
O A:ASP411 5.0 37.4 1.0

Calcium binding site 3 out of 4 in 3scx

Go back to Calcium Binding Sites List in 3scx
Calcium binding site 3 out of 4 in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-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 Deoxy-Terminated Primer in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:85.9
occ:1.00
 O2A A:DUP904 2.6 45.9 1.0
OD2 A:ASP411 2.6 42.2 1.0
OD2 A:ASP623 3.0 33.7 1.0
O3' P:DC115 3.3 40.9 1.0
C3' P:DC115 3.7 40.6 1.0
CG A:ASP623 3.8 33.6 1.0
OD1 A:ASP623 3.8 33.5 1.0
CG A:ASP411 3.8 40.7 1.0
PA A:DUP904 3.8 44.5 1.0
O1A A:DUP904 4.1 46.4 1.0
CA A:CA906 4.2 50.4 1.0
CB A:SER624 4.2 35.9 1.0
OG A:SER624 4.2 39.5 1.0
O5' P:DC115 4.4 41.2 1.0
OD1 A:ASP411 4.6 45.1 1.0
O P:HOH99 4.6 2.0 1.0
C5' P:DC115 4.6 41.2 1.0
CB A:ASP411 4.7 36.7 1.0
C4' P:DC115 4.7 40.8 1.0
O5' A:DUP904 4.7 42.0 1.0
C5' A:DUP904 4.8 40.2 1.0
C2' P:DC115 4.8 40.1 1.0
O A:HOH1013 4.9 20.6 1.0
O1G A:DUP904 4.9 40.9 1.0
OE2 A:GLU686 5.0 48.9 1.0

Calcium binding site 4 out of 4 in 3scx

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Calcium binding site 4 out of 4 in the RB69 Dna Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with Dupnpp and A Deoxy-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 Deoxy-Terminated Primer in the Presence of CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:47.9
occ:1.00
 O3G A:DUP904 2.3 40.1 1.0
O A:HOH1013 2.7 20.6 1.0
PG A:DUP904 2.7 40.4 1.0
O1G A:DUP904 2.8 40.9 1.0
O A:HOH1012 3.0 2.0 1.0
NZ A:LYS486 3.0 43.5 1.0
O2G A:DUP904 3.2 40.7 1.0
O A:HOH1072 3.5 2.0 1.0
NH2 A:ARG482 3.7 33.3 1.0
O3B A:DUP904 4.2 41.4 1.0
CE A:LYS486 4.3 37.5 1.0
NZ A:LYS560 4.3 33.0 1.0
N3A A:DUP904 4.5 40.8 1.0
O A:HOH970 4.6 2.2 1.0
O A:HOH929 4.6 2.0 1.0
OE2 A:GLU686 4.8 48.9 1.0
OE1 A:GLU716 4.8 46.5 1.0
OE2 A:GLU716 4.8 45.2 1.0
CZ A:ARG482 4.8 33.2 1.0
OD1 A:ASP411 4.9 45.1 1.0
CA A:CA906 4.9 50.4 1.0
CD A:LYS486 4.9 35.3 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 Dec 12 04:29:51 2020

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