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Calcium in PDB 3nhg: RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg

Enzymatic activity of RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg

All present enzymatic activity of RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg:
2.7.7.7;

Protein crystallography data

The structure of RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg, PDB code: 3nhg 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) 50.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.052, 119.999, 130.382, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 24.4

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg (pdb code 3nhg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg, PDB code: 3nhg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3nhg

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Calcium binding site 1 out of 6 in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg


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 (S565G/Y567A) Ternary Complex with Dttp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:73.1
occ:1.00
 O A:HOH933 2.2 56.3 1.0
O A:HOH1020 2.3 53.8 1.0
O A:LYS531 2.4 79.1 1.0
O A:ASN505 2.5 88.7 1.0
OD1 A:ASN507 2.6 93.0 1.0
C A:LYS531 3.4 79.6 1.0
C A:ASN505 3.7 88.4 1.0
CG A:ASN507 3.8 93.6 1.0
CB A:ASN505 4.0 91.5 1.0
CA A:LYS531 4.1 79.7 1.0
N A:ASN507 4.2 90.5 1.0
N A:LYS532 4.4 78.6 1.0
CA A:ASN505 4.5 89.2 1.0
ND2 A:ASN507 4.6 93.8 1.0
CB A:LYS531 4.6 81.0 1.0
N A:PRO506 4.7 87.9 1.0
C A:PRO506 4.7 89.2 1.0
CA A:LYS532 4.7 79.5 1.0
CA A:PRO506 4.7 87.5 1.0
CB A:ASN507 4.8 93.1 1.0
O A:ALA502 4.9 75.6 1.0
CA A:ASN507 4.9 93.5 1.0

Calcium binding site 2 out of 6 in 3nhg

Go back to Calcium Binding Sites List in 3nhg
Calcium binding site 2 out of 6 in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg


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 (S565G/Y567A) Ternary Complex with Dttp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:79.8
occ:1.00
 OD2 A:ASP623 2.5 53.4 1.0
O2A A:TTP904 2.5 51.3 1.0
OD2 A:ASP411 2.8 60.2 1.0
O A:HOH1021 3.2 57.0 1.0
CG A:ASP623 3.4 51.6 1.0
OD1 A:ASP623 3.6 53.1 1.0
PA A:TTP904 3.8 49.1 1.0
CB A:SER624 3.8 54.7 1.0
CG A:ASP411 3.8 57.7 1.0
C3' P:DOC115 3.8 49.5 1.0
O A:HOH1048 3.9 75.0 1.0
CA A:CA908 3.9 50.8 1.0
O1A A:TTP904 4.0 52.1 1.0
OG A:SER624 4.2 57.2 1.0
C5' P:DOC115 4.5 48.3 1.0
CB A:ASP411 4.5 55.2 1.0
O5' A:TTP904 4.6 46.9 1.0
OD1 A:ASP411 4.6 59.6 1.0
N A:SER624 4.7 52.0 1.0
C4' P:DOC115 4.7 47.9 1.0
CA A:SER624 4.8 52.7 1.0
C A:ASP623 4.8 53.0 1.0
C5' A:TTP904 4.8 41.9 1.0
CB A:ASP623 4.9 50.9 1.0
OE1 A:GLU686 4.9 66.2 1.0
O A:ASP621 4.9 47.1 1.0

Calcium binding site 3 out of 6 in 3nhg

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Calcium binding site 3 out of 6 in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg


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 (S565G/Y567A) Ternary Complex with Dttp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:94.1
occ:1.00
 O A:HOH927 2.3 60.9 1.0
O A:HOH925 2.4 50.9 1.0
O A:HOH926 2.5 54.4 1.0
OE2 A:GLU116 2.8 51.2 1.0
OE1 A:GLU116 2.9 49.8 1.0
CD A:GLU116 3.2 49.5 1.0
O A:HOH1022 3.7 59.6 1.0
O A:HOH1172 3.8 57.8 1.0
OD2 A:ASP114 4.2 63.5 1.0
O A:ILE115 4.6 47.1 1.0
CG A:GLU116 4.7 46.6 1.0

Calcium binding site 4 out of 6 in 3nhg

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Calcium binding site 4 out of 6 in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg


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 (S565G/Y567A) Ternary Complex with Dttp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:50.8
occ:1.00
 OD1 A:ASP623 2.2 53.1 1.0
O1G A:TTP904 2.3 46.3 1.0
O A:LEU412 2.3 50.3 1.0
O2B A:TTP904 2.3 46.9 1.0
OD2 A:ASP411 2.4 60.2 1.0
O2A A:TTP904 2.6 51.3 1.0
OD1 A:ASP411 2.7 59.6 1.0
CG A:ASP411 2.9 57.7 1.0
CG A:ASP623 3.3 51.6 1.0
PB A:TTP904 3.3 46.9 1.0
C A:LEU412 3.4 47.9 1.0
O A:HOH1048 3.5 75.0 1.0
PG A:TTP904 3.5 45.3 1.0
O3A A:TTP904 3.5 50.0 1.0
PA A:TTP904 3.6 49.1 1.0
CA A:CA909 3.7 0.7 1.0
O3B A:TTP904 3.8 45.6 1.0
OD2 A:ASP623 3.9 53.4 1.0
CA A:CA906 3.9 79.8 1.0
N A:LEU412 4.0 48.9 1.0
CA A:LEU412 4.2 47.3 1.0
O2G A:TTP904 4.2 46.7 1.0
C5' A:TTP904 4.2 41.9 1.0
N A:SER414 4.3 48.0 1.0
N A:THR413 4.3 46.8 1.0
CB A:ASP411 4.4 55.2 1.0
O5' A:TTP904 4.4 46.9 1.0
CB A:ASP623 4.5 50.9 1.0
CA A:THR413 4.6 46.3 1.0
C A:ASP411 4.6 52.1 1.0
C A:THR413 4.6 47.0 1.0
O1B A:TTP904 4.7 47.1 1.0
N A:LEU415 4.7 44.5 1.0
O3G A:TTP904 4.7 45.8 1.0
CB A:LEU412 4.8 47.2 1.0
O1A A:TTP904 4.8 52.1 1.0
CA A:ASP411 4.9 52.2 1.0

Calcium binding site 5 out of 6 in 3nhg

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Calcium binding site 5 out of 6 in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg


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 (S565G/Y567A) Ternary Complex with Dttp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:0.7
occ:1.00
 O1G A:TTP904 2.2 46.3 1.0
O A:HOH1176 2.5 73.1 1.0
OD1 A:ASP411 2.5 59.6 1.0
O A:HOH1048 2.7 75.0 1.0
PG A:TTP904 2.9 45.3 1.0
O2G A:TTP904 3.1 46.7 1.0
O A:HOH1023 3.1 51.1 1.0
O3G A:TTP904 3.3 45.8 1.0
O A:HOH1049 3.4 56.8 1.0
CG A:ASP411 3.6 57.7 1.0
CA A:CA908 3.7 50.8 1.0
NZ A:LYS486 3.7 56.9 1.0
OE1 A:GLU686 3.9 66.2 1.0
O A:HOH958 4.0 59.3 1.0
OE1 A:GLU716 4.2 66.7 1.0
OD2 A:ASP411 4.2 60.2 1.0
O3B A:TTP904 4.5 45.6 1.0
O A:LEU412 4.6 50.3 1.0
CB A:ASP411 4.6 55.2 1.0
CD A:GLU716 4.8 65.8 1.0
CA A:THR413 4.9 46.3 1.0
O2A A:TTP904 4.9 51.3 1.0
OE2 A:GLU716 5.0 65.4 1.0

Calcium binding site 6 out of 6 in 3nhg

Go back to Calcium Binding Sites List in 3nhg
Calcium binding site 6 out of 6 in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dttp Opposite Dg


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 (S565G/Y567A) Ternary Complex with Dttp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:74.0
occ:1.00
 OD1 A:ASP684 2.1 62.2 1.0
O A:HOH921 2.3 59.5 1.0
O A:HOH1040 2.4 55.6 1.0
O A:HOH1186 2.9 62.9 1.0
OE1 A:GLU660 3.1 67.9 1.0
CG A:ASP684 3.4 60.5 1.0
CD A:GLU660 3.7 66.8 1.0
OD2 A:ASP684 4.1 60.3 1.0
CG A:GLU660 4.2 65.6 1.0
CB A:GLU660 4.2 66.0 1.0
CB A:ASP684 4.4 56.6 1.0
CA A:ASP684 4.5 52.4 1.0
O A:MET683 4.5 56.3 1.0
OE2 A:GLU660 4.5 65.9 1.0
OD1 A:ASP664 4.6 54.2 0.5
OD2 A:ASP664 4.7 52.7 0.5
C A:MET683 4.8 53.1 1.0
N A:ASP684 4.8 51.5 1.0

Reference:

S.Xia, M.Wang, H.R.Lee, A.Sinha, G.Blaha, T.Christian, J.Wang, W.Konigsberg. Variation in Mutation Rates Caused By RB69POL Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures. J.Mol.Biol. V. 406 558 2011.
ISSN: ISSN 0022-2836
PubMed: 21216248
DOI: 10.1016/J.JMB.2010.12.033
Page generated: Sat Jul 13 15:00:00 2024

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