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Magnesium in PDB 4dqq: Ternary Complex of Bacillus Dna Polymerase I Large Fragment E658A, Dna Duplex, and Rctp (Paired with Dg of Template) in Presence of MG2+

Enzymatic activity of Ternary Complex of Bacillus Dna Polymerase I Large Fragment E658A, Dna Duplex, and Rctp (Paired with Dg of Template) in Presence of MG2+

All present enzymatic activity of Ternary Complex of Bacillus Dna Polymerase I Large Fragment E658A, Dna Duplex, and Rctp (Paired with Dg of Template) in Presence of MG2+:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Bacillus Dna Polymerase I Large Fragment E658A, Dna Duplex, and Rctp (Paired with Dg of Template) in Presence of MG2+, PDB code: 4dqq was solved by W.Wang, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.35 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.540, 107.970, 149.880, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 17.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Bacillus Dna Polymerase I Large Fragment E658A, Dna Duplex, and Rctp (Paired with Dg of Template) in Presence of MG2+ (pdb code 4dqq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Ternary Complex of Bacillus Dna Polymerase I Large Fragment E658A, Dna Duplex, and Rctp (Paired with Dg of Template) in Presence of MG2+, PDB code: 4dqq:

Magnesium binding site 1 out of 1 in 4dqq

Go back to Magnesium Binding Sites List in 4dqq
Magnesium binding site 1 out of 1 in the Ternary Complex of Bacillus Dna Polymerase I Large Fragment E658A, Dna Duplex, and Rctp (Paired with Dg of Template) in Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Bacillus Dna Polymerase I Large Fragment E658A, Dna Duplex, and Rctp (Paired with Dg of Template) in Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg902

b:22.8
occ:0.51
 O2A D:CTP901 2.0 21.8 1.0
O D:HOH1595 2.0 35.4 1.0
OD2 D:ASP830 2.1 20.3 1.0
O2B D:CTP901 2.3 23.8 1.0
O2G D:CTP901 2.5 33.6 1.0
O D:HOH1035 3.1 18.5 1.0
PA D:CTP901 3.2 21.3 1.0
PB D:CTP901 3.2 20.7 1.0
CG D:ASP830 3.3 19.4 1.0
O3A D:CTP901 3.5 20.4 1.0
H5'1 D:CTP901 3.6 24.7 1.0
O3B D:CTP901 3.6 20.8 1.0
O D:HOH1527 3.6 45.2 1.0
PG D:CTP901 3.6 27.8 1.0
O D:TYR654 3.6 24.3 1.0
OD1 D:ASP830 3.7 16.6 1.0
H D:GLN656 3.9 17.2 1.0
O5' D:CTP901 4.1 19.6 1.0
C5' D:CTP901 4.2 20.6 1.0
H5'2 D:CTP901 4.2 24.7 1.0
O1A D:CTP901 4.3 24.3 1.0
O D:HOH1330 4.3 48.7 1.0
OD2 D:ASP653 4.4 30.7 1.0
HB2 D:ASP653 4.4 25.9 1.0
HA D:SER655 4.4 18.9 1.0
O3G D:CTP901 4.5 29.8 1.0
HB2 D:ASP830 4.5 16.3 1.0
CB D:ASP830 4.5 13.6 1.0
O1B D:CTP901 4.6 21.8 1.0
N D:GLN656 4.7 14.3 1.0
O1G D:CTP901 4.7 37.0 1.0
HB3 D:ASP830 4.8 16.3 1.0
C D:TYR654 4.9 22.1 1.0

Reference:

W.Wang, E.Y.Wu, H.W.Hellinga, L.S.Beese. Structural Factors That Determine Selectivity of A High Fidelity Dna Polymerase For Deoxy-, Dideoxy-, and Ribonucleotides. J.Biol.Chem. V. 287 28215 2012.
ISSN: ISSN 0021-9258
PubMed: 22648417
DOI: 10.1074/JBC.M112.366609
Page generated: Thu Aug 15 17:19:41 2024

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