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Magnesium in PDB 3py8: Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp

Enzymatic activity of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp

All present enzymatic activity of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp, PDB code: 3py8 was solved by A.Schnur, A.Marx, W.Welte, K.Diederichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.74 / 1.74
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.610, 108.610, 90.570, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 19.9

Other elements in 3py8:

The structure of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp also contains other interesting chemical elements:

Manganese (Mn) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp (pdb code 3py8). 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 Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp, PDB code: 3py8:

Magnesium binding site 1 out of 1 in 3py8

Go back to Magnesium Binding Sites List in 3py8
Magnesium binding site 1 out of 1 in the Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:29.3
occ:1.00
 OD1 A:ASP785 2.4 24.6 1.0
O A:HOH870 2.4 30.6 1.0
OD2 A:ASP610 2.4 35.1 1.0
O2A A:DCT113 2.5 26.6 1.0
O A:HOH205 2.6 29.9 1.0
CG A:ASP610 3.1 33.7 1.0
OD1 A:ASP610 3.2 30.6 1.0
CG A:ASP785 3.4 30.2 1.0
MN A:MN833 3.5 29.0 1.0
O A:HOH212 3.6 37.5 1.0
C3' B:DOC112 3.6 21.2 1.0
PA A:DCT113 3.7 30.6 1.0
OD2 A:ASP785 3.7 27.2 1.0
O1A A:DCT113 3.9 29.9 1.0
O5' A:DCT113 4.0 24.1 1.0
C5' B:DOC112 4.2 21.3 1.0
CB A:GLU786 4.2 22.2 1.0
C4' B:DOC112 4.2 23.8 1.0
OE1 A:GLU786 4.2 31.3 1.0
NZ A:LYS831 4.3 34.9 1.0
C5' A:DCT113 4.4 27.0 1.0
O A:VAL783 4.5 21.7 1.0
O1G A:DCT113 4.5 30.4 1.0
CB A:ASP610 4.5 22.0 1.0
C A:ASP785 4.6 22.9 1.0
O A:ASP785 4.7 20.7 1.0
O5' B:DOC112 4.7 21.5 1.0
N A:GLU786 4.7 17.4 1.0
CB A:ASP785 4.7 24.3 1.0
C2' B:DOC112 4.8 18.8 1.0
OP1 B:DOC112 4.9 25.8 1.0
N A:ASP785 5.0 19.1 1.0
CA A:GLU786 5.0 17.7 1.0

Reference:

S.Obeid, A.Schnur, C.Gloeckner, N.Blatter, W.Welte, K.Diederichs, A.Marx. Learning From Directed Evolution: Thermus Aquaticus Dna Polymerase Mutants with Translesion Synthesis Activity. Chembiochem V. 12 1574 2011.
ISSN: ISSN 1439-4227
PubMed: 21480455
DOI: 10.1002/CBIC.201000783
Page generated: Thu Aug 15 09:51:34 2024

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