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Magnesium in PDB 3m8r: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Trapped 4'- Ethylated Dttp

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Trapped 4'- Ethylated Dttp

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Trapped 4'- Ethylated Dttp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Trapped 4'- Ethylated Dttp, PDB code: 3m8r was solved by K.Diederichs, A.Marx, K.Betz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.11 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.789, 108.789, 90.520, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Trapped 4'- Ethylated Dttp (pdb code 3m8r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Trapped 4'- Ethylated Dttp, PDB code: 3m8r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3m8r

Go back to Magnesium Binding Sites List in 3m8r
Magnesium binding site 1 out of 2 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Trapped 4'- Ethylated Dttp


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 the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Trapped 4'- Ethylated Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:36.0
occ:1.00
 OD1 A:ASP785 2.2 30.3 1.0
OD2 A:ASP610 2.3 36.3 1.0
O10 A:HXZ113 2.3 40.7 1.0
O A:HOH231 2.4 38.3 1.0
O A:HOH27 2.7 33.8 1.0
CG A:ASP610 3.1 42.0 1.0
CG A:ASP785 3.1 32.8 1.0
OD1 A:ASP610 3.2 33.1 1.0
MG A:MG2 3.3 36.1 1.0
OD2 A:ASP785 3.4 33.0 1.0
P1 A:HXZ113 3.4 38.7 1.0
C3' B:DOC112 3.6 27.9 1.0
O11 A:HXZ113 3.7 35.1 1.0
O5' A:HXZ113 3.8 40.8 1.0
O A:HOH84 3.9 34.6 1.0
C5' A:HXZ113 4.0 35.8 1.0
CB A:GLU786 4.2 27.2 1.0
C4' B:DOC112 4.3 28.4 1.0
C5' B:DOC112 4.4 35.2 1.0
CB A:ASP610 4.4 35.1 1.0
O A:VAL783 4.5 24.1 1.0
C A:ASP785 4.5 30.6 1.0
CB A:ASP785 4.5 34.1 1.0
OE1 A:GLU786 4.5 45.8 1.0
O7 A:HXZ113 4.6 41.6 1.0
NZ A:LYS831 4.6 41.9 1.0
N A:GLU786 4.6 30.8 1.0
O A:ASP785 4.6 32.7 1.0
C2' B:DOC112 4.8 22.2 1.0
N A:ASP785 4.8 23.7 1.0
O9 A:HXZ113 4.8 44.5 1.0
CA A:ASP785 4.8 26.3 1.0
O1 A:HXZ113 4.8 43.2 1.0
O5' B:DOC112 4.9 31.7 1.0
CA A:GLU786 4.9 24.9 1.0

Magnesium binding site 2 out of 2 in 3m8r

Go back to Magnesium Binding Sites List in 3m8r
Magnesium binding site 2 out of 2 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Trapped 4'- Ethylated Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Trapped 4'- Ethylated Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:36.1
occ:1.00
 O7 A:HXZ113 1.8 41.6 1.0
O10 A:HXZ113 2.0 40.7 1.0
OD1 A:ASP610 2.0 33.1 1.0
O9 A:HXZ113 2.1 44.5 1.0
O A:TYR611 2.2 33.4 1.0
OD2 A:ASP785 2.2 33.0 1.0
CG A:ASP610 3.1 42.0 1.0
P2 A:HXZ113 3.2 40.6 1.0
P3 A:HXZ113 3.2 49.1 1.0
CG A:ASP785 3.2 32.8 1.0
P1 A:HXZ113 3.2 38.7 1.0
MG A:MG1 3.3 36.0 1.0
C A:TYR611 3.4 45.8 1.0
OD1 A:ASP785 3.5 30.3 1.0
OD2 A:ASP610 3.5 36.3 1.0
O1 A:HXZ113 3.6 43.2 1.0
O3 A:HXZ113 3.6 45.0 1.0
O A:HOH160 3.8 37.1 1.0
O A:HOH84 3.8 34.6 1.0
C5' A:HXZ113 4.0 35.8 1.0
N A:TYR611 4.1 30.9 1.0
O5' A:HXZ113 4.1 40.8 1.0
O5 A:HXZ113 4.2 62.3 1.0
O6 A:HXZ113 4.2 51.9 1.0
CA A:TYR611 4.3 33.5 1.0
O11 A:HXZ113 4.3 35.1 1.0
C A:ASP610 4.3 36.0 1.0
CB A:ASP610 4.4 35.1 1.0
N A:SER612 4.4 36.0 1.0
N A:GLN613 4.4 38.3 1.0
O8 A:HXZ113 4.5 37.5 1.0
CA A:SER612 4.5 49.9 1.0
CB A:ASP785 4.6 34.1 1.0
CB A:TYR611 4.7 40.6 1.0
O A:ASP610 4.7 33.6 1.0
C A:SER612 4.7 42.8 1.0
O A:HOH27 4.8 33.8 1.0
CA A:ASP610 4.8 30.7 1.0
O A:ASP785 4.9 32.7 1.0

Reference:

K.Betz, F.Streckenbach, A.Schnur, T.Exner, W.Welte, K.Diederichs, A.Marx. Structures of Dna Polymerases Caught Processing Size-Augmented Nucleotide Probes. Angew.Chem.Int.Ed.Engl. V. 49 5181 2010.
ISSN: ISSN 1433-7851
PubMed: 20572212
DOI: 10.1002/ANIE.200905724
Page generated: Wed Aug 14 19:11:51 2024

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