Atomistry » Calcium » PDB 3s9w-3snz » 3scx
Atomistry »
  Calcium »
    PDB 3s9w-3snz »
      3scx »

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

Go back to Calcium Binding Sites List in 3scx
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: Tue Jul 8 16:35:01 2025

Last articles

Mg in 3CC2
Mg in 3CCE
Mg in 3CC7
Mg in 3CC4
Mg in 3CB3
Mg in 3CC6
Mg in 3C9U
Mg in 3CBT
Mg in 3CBQ
Mg in 3CBG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy