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Sodium in PDB 3rrg: Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and A Ddgtp

Enzymatic activity of Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and A Ddgtp

All present enzymatic activity of Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and A Ddgtp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and A Ddgtp, PDB code: 3rrg was solved by A.Marx, K.Diederichs, S.Obeid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.75 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.279, 110.279, 90.966, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 25

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and A Ddgtp (pdb code 3rrg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and A Ddgtp, PDB code: 3rrg:

Sodium binding site 1 out of 1 in 3rrg

Go back to Sodium Binding Sites List in 3rrg
Sodium binding site 1 out of 1 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and A Ddgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and A Ddgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na833

b:58.4
occ:1.00
 O A:HOH4 3.0 40.8 1.0
OD2 A:ASP372 3.1 53.5 1.0
O A:HOH5 3.1 33.3 1.0
N A:LYS354 3.2 36.4 1.0
O A:HOH36 3.3 29.4 1.0
N A:ALA353 3.5 34.7 1.0
CB A:ASP372 3.6 40.6 1.0
CG A:ASP372 3.7 50.7 1.0
CB A:ALA353 3.7 30.7 1.0
CB A:LYS354 3.8 30.5 1.0
CA A:ALA353 3.9 34.1 1.0
C A:ALA353 4.0 39.5 1.0
CA A:LYS354 4.1 34.5 1.0
C A:LEU352 4.2 35.8 1.0
CB A:SER438 4.4 26.2 1.0
CA A:LEU352 4.5 36.4 1.0
CD1 A:LEU375 4.6 43.4 1.0
CG A:LEU375 4.7 38.0 1.0
N A:LEU352 4.8 37.7 1.0
OG A:SER438 4.8 30.7 1.0
OD1 A:ASP372 4.9 56.4 1.0
OE1 A:GLN566 4.9 32.8 1.0
CB A:PRO369 5.0 46.1 1.0
O A:GLY350 5.0 32.8 1.0

Reference:

S.Obeid, W.Welte, K.Diederichs, A.Marx. Amino Acid Templating Mechanisms in Selection of Nucleotides Opposite Abasic Sites By A Family A Dna Polymerase. J.Biol.Chem. V. 287 14099 2012.
ISSN: ISSN 0021-9258
PubMed: 22318723
DOI: 10.1074/JBC.M111.334904
Page generated: Tue Dec 15 06:24:07 2020

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