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

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

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

Protein crystallography data

The structure of RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite Dg, PDB code: 3ndk 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.006, 120.015, 130.781, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.9

Calcium Binding Sites:

The binding sites of Calcium atom in the RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite Dg (pdb code 3ndk). 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 (Y567A) Ternary Complex with Dctp Opposite Dg, PDB code: 3ndk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3ndk

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Calcium binding site 1 out of 7 in the RB69 Dna Polymerase (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 (Y567A) Ternary Complex with Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:21.8
occ:1.00
 OD1 A:ASP623 2.2 24.0 1.0
O2B A:DCP904 2.2 20.3 1.0
O1G A:DCP904 2.3 21.5 1.0
O A:LEU412 2.3 16.2 1.0
O2A A:DCP904 2.5 17.7 1.0
OD2 A:ASP411 2.5 30.5 1.0
OD1 A:ASP411 2.7 31.5 1.0
CG A:ASP411 2.9 27.5 1.0
PB A:DCP904 3.3 18.4 1.0
CG A:ASP623 3.4 20.8 1.0
C A:LEU412 3.5 18.8 1.0
PG A:DCP904 3.5 21.0 1.0
PA A:DCP904 3.6 21.8 1.0
CA A:CA906 3.7 52.3 1.0
O3A A:DCP904 3.7 22.1 1.0
O3B A:DCP904 3.8 22.3 1.0
OD2 A:ASP623 3.9 23.1 1.0
O A:HOH1283 4.0 40.0 1.0
N A:LEU412 4.1 18.5 1.0
O2G A:DCP904 4.2 21.8 1.0
C5' A:DCP904 4.2 18.8 1.0
CA A:LEU412 4.3 18.7 1.0
CB A:ASP411 4.4 24.2 1.0
N A:SER414 4.4 19.1 1.0
N A:THR413 4.4 18.3 1.0
O5' A:DCP904 4.4 21.4 1.0
CB A:ASP623 4.5 20.9 1.0
CA A:CA908 4.5 71.9 1.0
C A:ASP411 4.6 20.8 1.0
CA A:THR413 4.6 19.2 1.0
O1B A:DCP904 4.6 22.4 1.0
O A:HOH1282 4.6 42.0 1.0
O3G A:DCP904 4.7 25.0 1.0
C A:THR413 4.7 19.2 1.0
N A:LEU415 4.7 17.0 1.0
O1A A:DCP904 4.8 22.4 1.0
CB A:LEU412 4.8 18.0 1.0
CA A:ASP411 5.0 21.5 1.0

Calcium binding site 2 out of 7 in 3ndk

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Calcium binding site 2 out of 7 in the RB69 Dna Polymerase (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 (Y567A) Ternary Complex with Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:52.3
occ:1.00
 O A:HOH1281 2.3 34.9 1.0
O A:HOH1282 2.4 42.0 1.0
OD2 A:ASP411 2.5 30.5 1.0
O2A A:DCP904 2.6 17.7 1.0
OD2 A:ASP623 2.7 23.1 1.0
CG A:ASP623 3.5 20.8 1.0
OD1 A:ASP623 3.5 24.0 1.0
CG A:ASP411 3.6 27.5 1.0
CA A:CA905 3.7 21.8 1.0
C3' P:DOC115 3.8 23.1 1.0
PA A:DCP904 3.9 21.8 1.0
CB A:SER624 4.0 22.6 1.0
O A:HOH1283 4.1 40.0 1.0
O1A A:DCP904 4.2 22.4 1.0
OD1 A:ASP411 4.3 31.5 1.0
O A:HOH1080 4.4 21.6 1.0
CB A:ASP411 4.4 24.2 1.0
OG A:SER624 4.5 23.4 1.0
O5' A:DCP904 4.6 21.4 1.0
N A:SER624 4.7 22.5 1.0
O5' P:DOC115 4.7 26.9 1.0
C5' A:DCP904 4.7 18.8 1.0
C5' P:DOC115 4.7 25.8 1.0
O A:ASP621 4.8 17.7 1.0
C A:ASP623 4.8 21.3 1.0
CA A:SER624 4.8 21.4 1.0
C4' P:DOC115 4.9 23.6 1.0
CB A:ASP623 4.9 20.9 1.0
OE1 A:GLU686 4.9 39.9 1.0
O1G A:DCP904 4.9 21.5 1.0
O P:HOH199 4.9 26.6 1.0
C2' P:DOC115 5.0 22.9 1.0
O A:ASP623 5.0 20.9 1.0

Calcium binding site 3 out of 7 in 3ndk

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Calcium binding site 3 out of 7 in the RB69 Dna Polymerase (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 (Y567A) Ternary Complex with Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:33.3
occ:1.00
 O A:LYS531 2.2 35.1 1.0
OD1 A:ASN507 2.3 38.6 1.0
O A:HOH1015 2.3 32.0 1.0
O A:ASN505 2.3 41.3 1.0
O A:HOH1014 2.4 21.0 1.0
O A:HOH1258 2.4 39.3 1.0
O A:HOH1476 2.7 46.0 1.0
C A:LYS531 3.2 36.5 1.0
CG A:ASN507 3.4 40.6 1.0
C A:ASN505 3.6 41.4 1.0
CA A:LYS531 3.9 36.3 1.0
ND2 A:ASN507 4.0 40.0 1.0
CB A:ASN505 4.1 41.7 0.5
CB A:ASN505 4.1 42.0 0.5
N A:LYS532 4.2 36.4 1.0
N A:ASN507 4.2 42.3 1.0
O A:HOH1257 4.4 41.0 1.0
C A:PRO506 4.4 41.8 1.0
CA A:LYS532 4.4 36.4 1.0
CA A:PRO506 4.4 41.7 1.0
CA A:ASN505 4.5 41.5 0.5
CA A:ASN505 4.5 41.7 0.5
N A:PRO506 4.5 41.3 1.0
O A:LEU533 4.6 32.9 1.0
CB A:LYS531 4.6 36.9 1.0
CB A:ASN507 4.6 41.6 1.0
O A:ALA502 4.7 33.8 1.0
C A:LYS532 4.8 36.2 1.0
CA A:ASN507 4.8 42.3 1.0
O A:ILE530 4.9 34.5 1.0
N A:LEU533 4.9 35.7 1.0

Calcium binding site 4 out of 7 in 3ndk

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Calcium binding site 4 out of 7 in the RB69 Dna Polymerase (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 (Y567A) Ternary Complex with Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:71.9
occ:1.00
 O A:HOH1283 2.7 40.0 1.0
OD1 A:ASP411 2.7 31.5 1.0
O A:HOH1164 2.7 42.7 1.0
O A:HOH1284 2.7 47.5 1.0
OE1 A:GLU686 2.8 39.9 1.0
OE1 A:GLU716 3.2 41.4 1.0
O1G A:DCP904 3.3 21.5 1.0
O A:HOH1287 3.5 55.9 1.0
CG A:ASP411 3.6 27.5 1.0
NZ A:LYS486 3.9 28.1 1.0
CD A:GLU686 4.0 36.2 1.0
CD A:GLU716 4.0 37.2 1.0
PG A:DCP904 4.1 21.0 1.0
O3G A:DCP904 4.1 25.0 1.0
CB A:ASP411 4.2 24.2 1.0
O2G A:DCP904 4.2 21.8 1.0
O A:HOH1285 4.3 40.9 1.0
OD2 A:ASP411 4.4 30.5 1.0
CG A:GLU686 4.5 33.6 1.0
O A:HOH1194 4.5 25.2 1.0
O A:HOH1282 4.5 42.0 1.0
CA A:CA905 4.5 21.8 1.0
O A:HOH1286 4.6 40.9 1.0
OE2 A:GLU716 4.7 38.7 1.0
CG A:GLU716 4.7 34.6 1.0
O A:HOH1362 4.8 41.0 1.0
O A:HOH1291 4.9 45.5 1.0

Calcium binding site 5 out of 7 in 3ndk

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Calcium binding site 5 out of 7 in the RB69 Dna Polymerase (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 (Y567A) Ternary Complex with Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:54.8
occ:1.00
 O A:HOH1083 2.3 24.6 1.0
O A:HOH1232 2.4 38.6 1.0
O A:HOH947 2.6 25.3 1.0
OE1 A:GLU116 2.7 23.7 1.0
OE2 A:GLU116 2.8 28.0 1.0
O A:HOH1276 3.0 55.9 1.0
CD A:GLU116 3.1 24.0 1.0
O A:HOH1275 3.3 49.0 1.0
O A:HOH1274 4.3 36.1 1.0
OD2 A:ASP114 4.4 34.0 1.0
CG A:GLU116 4.6 19.6 1.0
O A:HOH1231 4.6 39.6 1.0
O A:ILE115 4.7 18.9 1.0
CD1 A:ILE309 4.8 40.4 1.0

Calcium binding site 6 out of 7 in 3ndk

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Calcium binding site 6 out of 7 in the RB69 Dna Polymerase (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 6 of RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:70.7
occ:1.00
 O A:HOH1370 2.3 44.1 1.0
O A:HOH1371 2.4 44.4 1.0
O A:ASP792 2.4 41.8 1.0
O A:HOH1373 2.4 50.0 1.0
O A:HOH1372 2.7 53.2 1.0
C A:ASP792 3.6 41.1 1.0
O A:ALA789 4.0 42.8 1.0
CB A:ASP792 4.4 40.9 1.0
N A:VAL793 4.4 41.7 1.0
CA A:VAL793 4.5 42.7 1.0
CA A:ASP792 4.5 40.1 1.0
OD1 A:ASP792 4.5 41.6 1.0
CG A:ASP792 4.8 40.2 1.0
N A:GLY794 4.9 43.3 1.0
N A:ASP792 4.9 38.2 1.0

Calcium binding site 7 out of 7 in 3ndk

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Calcium binding site 7 out of 7 in the RB69 Dna Polymerase (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 7 of RB69 Dna Polymerase (Y567A) Ternary Complex with Dctp Opposite Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca911

b:58.9
occ:1.00
 O A:HOH1102 2.2 36.2 1.0
O A:HOH1007 2.5 55.3 1.0
NZ A:LYS185 3.5 19.4 1.0
OD1 A:ASP144 3.6 26.2 1.0
CD A:LYS185 3.9 17.3 1.0
CG2 A:ILE182 4.1 20.3 1.0
CE1 A:PHE146 4.2 20.2 1.0
CE A:LYS185 4.2 17.8 1.0
OH A:TYR139 4.3 21.7 1.0
CE2 A:TYR139 4.4 19.9 1.0
CE1 A:TYR329 4.4 20.9 1.0
CZ A:PHE146 4.4 19.9 1.0
CG A:ASP144 4.5 25.5 1.0
CZ A:TYR139 4.7 22.0 1.0
OD2 A:ASP144 4.7 23.8 1.0
CD1 A:TYR329 4.9 18.8 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: Tue Jul 8 14:51:01 2025

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