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Magnesium in PDB 3t3f: Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp

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

All present enzymatic activity of Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp:
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 Dnitp, PDB code: 3t3f 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) 42.16 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.778, 109.778, 91.219, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 20.6

Other elements in 3t3f:

The structure of Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp (pdb code 3t3f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp, PDB code: 3t3f:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3t3f

Go back to Magnesium Binding Sites List in 3t3f
Magnesium binding site 1 out of 4 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg833

b:57.2
occ:0.79
 O2A A:N5P836 2.1 40.2 0.8
O A:HOH258 2.1 72.2 0.9
OD1 A:ASP610 2.1 35.9 0.6
OD1 A:ASP785 2.3 34.2 1.0
OE2 A:GLU786 2.6 30.9 0.3
OD2 A:ASP610 2.6 28.7 0.6
CG A:ASP610 2.7 32.1 0.6
OD2 A:ASP785 3.0 56.3 1.0
CG A:ASP785 3.0 41.8 1.0
O A:HOH220 3.1 43.7 0.9
OD2 A:ASP610 3.1 40.4 0.4
CD A:GLU786 3.3 30.7 0.3
PA A:N5P836 3.3 45.9 0.8
MG A:MG834 3.3 34.2 0.6
O1A A:N5P836 3.7 44.8 0.8
O5' A:N5P836 3.8 52.7 0.8
OE1 A:GLU786 3.8 35.1 0.3
C3' B:DOC112 3.9 30.8 1.0
CG A:ASP610 3.9 34.5 0.4
O3G A:N5P836 4.0 48.4 0.8
CG A:GLU786 4.1 25.5 0.3
CB A:GLU786 4.1 25.4 0.3
CB A:ASP610 4.2 32.3 0.6
CB A:GLU786 4.2 24.7 0.7
CB A:ASP610 4.2 31.3 0.4
CB A:ASP785 4.4 29.0 1.0
C A:ASP785 4.5 20.7 1.0
OE1 A:GLU786 4.5 31.6 0.7
O A:ASP785 4.6 23.6 1.0
O3A A:N5P836 4.6 0.5 0.8
C4' B:DOC112 4.6 31.1 1.0
C5' B:DOC112 4.6 31.5 1.0
N A:GLU786 4.7 21.0 1.0
O2B A:N5P836 4.7 39.1 0.8
NZ A:LYS831 4.8 59.8 1.0
C5' A:N5P836 4.8 50.8 0.8
O A:TYR611 4.9 30.1 1.0
OD1 A:ASP610 4.9 36.7 0.4
CA A:GLU786 4.9 22.7 0.7
CA A:ASP785 4.9 19.8 1.0
CA A:ASP610 4.9 26.9 0.6
CA A:GLU786 5.0 22.3 0.3
CA A:ASP610 5.0 26.2 0.4
O A:VAL783 5.0 21.2 1.0

Magnesium binding site 2 out of 4 in 3t3f

Go back to Magnesium Binding Sites List in 3t3f
Magnesium binding site 2 out of 4 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg834

b:34.2
occ:0.58
 O3G A:N5P836 1.8 48.4 0.8
OD2 A:ASP610 2.1 28.7 0.6
O2A A:N5P836 2.1 40.2 0.8
O2B A:N5P836 2.1 39.1 0.8
O A:TYR611 2.2 30.1 1.0
OD2 A:ASP785 2.2 56.3 1.0
PB A:N5P836 2.9 42.5 0.8
PG A:N5P836 3.0 53.2 0.8
PA A:N5P836 3.1 45.9 0.8
O3B A:N5P836 3.2 52.0 0.8
CG A:ASP610 3.2 32.1 0.6
MG A:MG833 3.3 57.2 0.8
O3A A:N5P836 3.3 0.5 0.8
C A:TYR611 3.4 29.2 1.0
CG A:ASP785 3.4 41.8 1.0
O A:HOH220 3.5 43.7 0.9
O5' A:N5P836 3.7 52.7 0.8
O A:HOH174 3.7 46.8 1.0
OD1 A:ASP610 3.8 35.9 0.6
O1G A:N5P836 3.9 55.0 0.8
OD1 A:ASP785 3.9 34.2 1.0
O2G A:N5P836 4.1 52.2 0.8
N A:GLN613 4.1 31.8 1.0
CA A:SER612 4.1 32.0 1.0
N A:SER612 4.2 27.4 1.0
N A:TYR611 4.2 24.1 1.0
CB A:ASP610 4.3 31.3 0.4
O1B A:N5P836 4.4 36.7 0.8
CB A:ASP610 4.4 32.3 0.6
CA A:TYR611 4.4 27.6 1.0
O A:HOH258 4.4 72.2 0.9
C A:ASP610 4.5 25.7 0.6
O1A A:N5P836 4.5 44.8 0.8
C A:SER612 4.5 30.9 1.0
C A:ASP610 4.5 25.9 0.4
CB A:ASP785 4.6 29.0 1.0
OD2 A:ASP610 4.8 40.4 0.4
O A:ASP610 4.9 28.7 0.6
CA A:ASP610 4.9 26.9 0.6
CA A:ASP610 4.9 26.2 0.4
CB A:TYR611 4.9 26.2 1.0
NZ A:LYS663 5.0 63.1 1.0
O A:ASP785 5.0 23.6 1.0

Magnesium binding site 3 out of 4 in 3t3f

Go back to Magnesium Binding Sites List in 3t3f
Magnesium binding site 3 out of 4 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1401

b:47.6
occ:1.00
 O B:HOH1403 2.2 39.1 1.0
O B:HOH1402 2.2 46.3 1.0
O B:HOH1405 2.2 42.8 1.0
O B:HOH1404 2.2 21.4 1.0
H1 B:HOH1403 2.8 46.9 1.0
H1 B:HOH1402 2.8 55.5 1.0
H1 B:HOH1405 2.8 51.4 1.0
H1 B:HOH1404 2.8 25.7 1.0
O6 B:DG108 4.1 27.5 1.0
O B:HOH136 4.3 36.6 1.0
O C:HOH91 4.4 31.2 1.0
O C:HOH50 4.4 28.9 1.0
N7 B:DG107 4.5 16.3 1.0
O6 B:DG107 4.5 17.4 1.0
O B:HOH202 4.5 41.3 1.0
N4 C:DC209 4.6 18.9 1.0
O B:HOH86 4.6 42.3 1.0
O2 C:GOL6 4.8 63.5 1.0
C3 B:GOL12 4.9 73.2 1.0
C5 B:DC106 5.0 22.5 1.0

Magnesium binding site 4 out of 4 in 3t3f

Go back to Magnesium Binding Sites List in 3t3f
Magnesium binding site 4 out of 4 in the Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ternary Structure of the Large Fragment of Taq Dna Polymerase Bound to An Abasic Site and Dnitp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1501

b:60.9
occ:1.00
 O C:HOH1504 2.2 40.5 1.0
O C:HOH1505 2.2 51.0 1.0
O C:HOH1503 2.2 53.3 1.0
O C:HOH1502 2.2 57.3 1.0
O C:HOH1506 2.2 40.1 1.0
H1 C:HOH1504 2.8 48.6 1.0
H1 C:HOH1503 2.8 63.9 1.0
H1 C:HOH1505 2.8 61.2 1.0
H1 C:HOH1502 2.8 68.8 1.0
H1 C:HOH1506 2.8 48.1 1.0
O6 C:DG214 4.0 38.1 1.0
N7 C:DG213 4.0 36.6 1.0
O B:HOH318 4.2 48.0 1.0
N7 C:DG214 4.3 39.7 1.0
O6 C:DG213 4.3 32.3 1.0
O C:HOH241 4.5 47.0 1.0
C6 C:DG214 4.8 36.7 1.0
C5 C:DG213 4.8 34.3 1.0
C7 C:DT212 4.9 27.4 1.0
C6 C:DG213 4.9 32.9 1.0
C5 C:DG214 4.9 36.9 1.0
C8 C:DG213 5.0 36.5 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: Thu Aug 15 11:51:11 2024

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