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Calcium in PDB 3ne6: RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dctp Opposite Dg

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

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

Protein crystallography data

The structure of RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dctp Opposite Dg, PDB code: 3ne6 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) 49.30 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.135, 119.783, 130.652, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.6

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dctp Opposite Dg (pdb code 3ne6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dctp Opposite Dg, PDB code: 3ne6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 3ne6

Go back to Calcium Binding Sites List in 3ne6
Calcium binding site 1 out of 5 in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dctp 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 Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:30.4
occ:1.00
 OD1 A:ASP623 2.2 40.8 1.0
O1G A:DCP909 2.3 26.4 1.0
O2B A:DCP909 2.3 26.2 1.0
O A:LEU412 2.3 29.1 1.0
OD2 A:ASP411 2.5 44.4 1.0
O2A A:DCP909 2.6 30.4 1.0
OD1 A:ASP411 2.7 42.7 1.0
CG A:ASP411 2.9 37.3 1.0
CG A:ASP623 3.3 34.1 1.0
PB A:DCP909 3.3 26.8 1.0
C A:LEU412 3.5 30.1 1.0
PG A:DCP909 3.5 27.4 1.0
CA A:CA905 3.7 53.2 1.0
PA A:DCP909 3.7 29.9 1.0
O3A A:DCP909 3.7 29.0 1.0
O3B A:DCP909 3.8 27.0 1.0
OD2 A:ASP623 3.8 35.2 1.0
O A:HOH1105 4.0 33.5 1.0
N A:LEU412 4.1 29.7 1.0
O2G A:DCP909 4.3 23.2 1.0
CA A:LEU412 4.3 29.6 1.0
C5' A:DCP909 4.3 26.9 1.0
N A:SER414 4.4 26.8 1.0
CB A:ASP411 4.4 34.4 1.0
N A:THR413 4.4 29.8 1.0
CB A:ASP623 4.5 31.8 1.0
O5' A:DCP909 4.5 29.5 1.0
C A:ASP411 4.6 30.3 1.0
CA A:THR413 4.6 28.7 1.0
O3G A:DCP909 4.7 30.5 1.0
C A:THR413 4.7 28.9 1.0
O1B A:DCP909 4.7 27.6 1.0
N A:LEU415 4.7 27.0 1.0
CB A:LEU412 4.8 29.3 1.0
O1A A:DCP909 4.9 33.0 1.0
CA A:ASP411 4.9 31.1 1.0

Calcium binding site 2 out of 5 in 3ne6

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Calcium binding site 2 out of 5 in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dctp 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 Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:53.2
occ:1.00
 O A:HOH1217 2.3 36.5 1.0
O2A A:DCP909 2.5 30.4 1.0
O A:HOH1218 2.5 37.4 1.0
OD2 A:ASP411 2.5 44.4 1.0
O A:HOH1219 2.6 41.9 1.0
OD2 A:ASP623 2.8 35.2 1.0
CG A:ASP623 3.6 34.1 1.0
OD1 A:ASP623 3.6 40.8 1.0
CG A:ASP411 3.7 37.3 1.0
CA A:CA904 3.7 30.4 1.0
PA A:DCP909 3.8 29.9 1.0
C3' P:DOC115 4.0 10.8 1.0
CB A:SER624 4.1 34.0 1.0
O1A A:DCP909 4.1 33.0 1.0
O A:HOH943 4.3 23.4 1.0
OG A:SER624 4.4 37.9 1.0
OD1 A:ASP411 4.5 42.7 1.0
CB A:ASP411 4.5 34.4 1.0
O5' A:DCP909 4.5 29.5 1.0
OE2 A:GLU686 4.6 48.9 1.0
O P:HOH53 4.7 31.7 1.0
C5' A:DCP909 4.7 26.9 1.0
N A:SER624 4.8 30.3 1.0
O1G A:DCP909 4.9 26.4 1.0
O5' P:DOC115 4.9 9.2 1.0
C5' P:DOC115 4.9 13.2 1.0
C A:ASP623 4.9 30.5 1.0
O A:ASP621 5.0 29.5 1.0
CA A:SER624 5.0 31.8 1.0
CB A:ASP623 5.0 31.8 1.0
C4' P:DOC115 5.0 12.0 1.0

Calcium binding site 3 out of 5 in 3ne6

Go back to Calcium Binding Sites List in 3ne6
Calcium binding site 3 out of 5 in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dctp 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 Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:43.8
occ:1.00
 O A:LYS531 2.2 46.7 1.0
O A:HOH1094 2.3 26.1 1.0
O A:ASN505 2.3 50.4 1.0
OD1 A:ASN507 2.4 51.5 1.0
O A:HOH1092 2.6 14.0 1.0
O A:HOH1093 2.6 12.8 1.0
O A:HOH1095 2.6 21.8 1.0
C A:LYS531 3.2 47.1 1.0
CG A:ASN507 3.5 50.8 1.0
C A:ASN505 3.5 51.0 1.0
CA A:LYS531 4.0 45.9 1.0
N A:ASN507 4.1 49.7 1.0
N A:LYS532 4.1 46.4 1.0
CB A:ASN505 4.2 52.7 0.5
ND2 A:ASN507 4.2 49.4 1.0
CB A:ASN505 4.2 50.7 0.5
C A:PRO506 4.3 49.7 1.0
CA A:PRO506 4.3 49.6 1.0
CA A:LYS532 4.4 46.8 1.0
N A:PRO506 4.4 50.4 1.0
O A:LEU533 4.5 41.1 1.0
CA A:ASN505 4.5 52.0 0.5
CA A:ASN505 4.5 51.2 0.5
CB A:ASN507 4.6 51.6 1.0
CB A:LYS531 4.7 46.9 1.0
C A:LYS532 4.7 45.5 1.0
O A:HOH1096 4.7 19.8 1.0
CA A:ASN507 4.7 51.0 1.0
O A:ALA502 4.8 43.0 1.0
N A:LEU533 4.8 42.7 1.0
O A:ILE530 4.9 43.0 1.0
O A:PRO506 5.0 48.5 1.0

Calcium binding site 4 out of 5 in 3ne6

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Calcium binding site 4 out of 5 in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dctp 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 Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:76.6
occ:1.00
 O A:HOH1104 2.2 50.2 1.0
O A:HOH1103 2.3 46.2 1.0
O A:HOH1550 2.7 34.4 1.0
O A:HOH1311 2.9 30.0 1.0
OE1 A:GLU716 2.9 54.8 1.0
O A:HOH1355 3.0 44.1 1.0
CD A:GLU716 3.7 50.0 1.0
O A:HOH1105 3.7 33.5 1.0
O A:HOH1549 3.7 49.5 1.0
O A:HOH1102 3.9 21.6 1.0
OD1 A:ASP411 3.9 42.7 1.0
NZ A:LYS486 4.3 42.2 1.0
CG A:GLU716 4.3 47.8 1.0
OE2 A:GLU716 4.4 52.7 1.0
OG1 A:THR413 4.4 29.8 1.0
O A:ASP411 4.6 33.0 1.0
CB A:ASP684 4.7 42.0 1.0
OE1 A:GLU686 4.7 53.0 1.0
CG A:ASP411 4.9 37.3 1.0
CB A:ASP411 5.0 34.4 1.0
OD2 A:ASP684 5.0 49.5 1.0

Calcium binding site 5 out of 5 in 3ne6

Go back to Calcium Binding Sites List in 3ne6
Calcium binding site 5 out of 5 in the RB69 Dna Polymerase (S565G/Y567A) Ternary Complex with Dctp 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 Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:59.5
occ:1.00
 O A:HOH1238 2.3 39.1 1.0
O A:HOH1568 2.3 38.1 1.0
O A:HOH1039 2.6 19.3 1.0
OE1 A:GLU116 2.7 40.1 1.0
OE2 A:GLU116 2.7 39.7 1.0
CD A:GLU116 3.1 37.2 1.0
O A:HOH1469 4.1 31.4 1.0
OD2 A:ASP114 4.2 42.6 1.0
O A:HOH1291 4.2 45.6 1.0
O A:HOH1381 4.4 37.6 1.0
O A:HOH1316 4.4 49.7 1.0
CG A:GLU116 4.6 32.2 1.0
O A:ILE115 4.7 27.3 1.0
O A:HOH1023 4.7 44.9 1.0
CD1 A:ILE309 4.9 50.2 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 14:56:26 2024

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