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Magnesium in PDB 4df8: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp:
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 Aminopentinyl-7- Deaza-2-Datp, PDB code: 4df8 was solved by K.Bergen, A.Steck, S.Struett, A.Baccaro, W.Welte, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.03 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.609, 108.609, 90.516, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 23.4

Other elements in 4df8:

The structure of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

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 Aminopentinyl-7- Deaza-2-Datp (pdb code 4df8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 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 Aminopentinyl-7- Deaza-2-Datp, PDB code: 4df8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4df8

Go back to Magnesium Binding Sites List in 4df8
Magnesium binding site 1 out of 3 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp


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 Aminopentinyl-7- Deaza-2-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:26.6
occ:1.00
 OD1 A:ASP785 2.3 23.2 1.0
OD2 A:ASP610 2.3 24.0 1.0
O2A A:0L4901 2.5 24.5 1.0
O A:HOH1002 2.5 17.5 1.0
O A:HOH1019 2.7 24.0 1.0
CG A:ASP610 2.9 29.0 1.0
OD1 A:ASP610 2.9 19.7 1.0
MG A:MG903 3.3 25.6 1.0
CG A:ASP785 3.3 18.8 1.0
PA A:0L4901 3.5 28.8 1.0
OD2 A:ASP785 3.8 29.4 1.0
O A:HOH1049 3.8 27.8 1.0
C3' B:DOC112 3.9 19.2 1.0
O5' A:0L4901 3.9 21.7 1.0
O1A A:0L4901 4.0 22.6 1.0
CB A:GLU786 4.1 16.7 1.0
OE1 A:GLU786 4.2 24.5 1.0
C5' A:0L4901 4.3 23.5 1.0
CB A:ASP610 4.3 28.9 1.0
NZ A:LYS831 4.4 39.5 1.0
C4' B:DOC112 4.4 28.1 1.0
O2G A:0L4901 4.5 24.1 1.0
C A:ASP785 4.5 21.1 1.0
O A:VAL783 4.5 15.8 1.0
C5' B:DOC112 4.5 27.1 1.0
O A:ASP785 4.6 23.2 1.0
N A:GLU786 4.6 19.7 1.0
CB A:ASP785 4.7 19.9 1.0
N A:ASP785 4.8 16.5 1.0
O2B A:0L4901 4.8 24.3 1.0
CA A:GLU786 4.9 16.5 1.0
CA A:ASP785 4.9 14.3 1.0
O3A A:0L4901 4.9 22.0 1.0
C2' B:DOC112 5.0 17.8 1.0

Magnesium binding site 2 out of 3 in 4df8

Go back to Magnesium Binding Sites List in 4df8
Magnesium binding site 2 out of 3 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp


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 Aminopentinyl-7- Deaza-2-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:25.6
occ:1.00
 OD2 A:ASP785 1.9 29.4 1.0
O2A A:0L4901 2.1 24.5 1.0
OD1 A:ASP610 2.1 19.7 1.0
O2B A:0L4901 2.1 24.3 1.0
O A:TYR611 2.2 32.3 1.0
O2G A:0L4901 2.2 24.1 1.0
CG A:ASP785 2.8 18.8 1.0
OD1 A:ASP785 3.0 23.2 1.0
CG A:ASP610 3.3 29.0 1.0
MG A:MG902 3.3 26.6 1.0
PB A:0L4901 3.3 24.9 1.0
C A:TYR611 3.3 26.9 1.0
PA A:0L4901 3.4 28.8 1.0
PG A:0L4901 3.6 31.8 1.0
C5' A:0L4901 3.8 23.5 1.0
O3A A:0L4901 3.8 22.0 1.0
OD2 A:ASP610 3.8 24.0 1.0
N A:TYR611 3.9 26.9 1.0
O3B A:0L4901 3.9 22.3 1.0
O5' A:0L4901 4.0 21.7 1.0
CA A:TYR611 4.1 27.8 1.0
O A:HOH1001 4.1 23.1 1.0
CB A:ASP785 4.2 19.9 1.0
O A:HOH1049 4.2 27.8 1.0
C A:ASP610 4.2 26.1 1.0
CB A:TYR611 4.4 23.1 1.0
N A:SER612 4.4 20.9 1.0
CB A:ASP610 4.5 28.9 1.0
O1G A:0L4901 4.5 27.7 1.0
CG2 A:ILE614 4.5 22.3 1.0
O A:ASP785 4.6 23.2 1.0
O3T A:0L4901 4.6 30.3 1.0
O1A A:0L4901 4.6 22.6 1.0
N A:GLN613 4.6 22.0 1.0
CA A:SER612 4.7 27.2 1.0
O1B A:0L4901 4.7 21.8 1.0
CA A:ASP610 4.7 20.8 1.0
O A:ASP610 4.7 24.2 1.0
N A:ILE614 4.9 22.3 1.0
O A:HOH1019 4.9 24.0 1.0
C A:SER612 4.9 30.4 1.0
CB A:ILE614 4.9 21.5 1.0

Magnesium binding site 3 out of 3 in 4df8

Go back to Magnesium Binding Sites List in 4df8
Magnesium binding site 3 out of 3 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Aminopentinyl-7- Deaza-2-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:47.9
occ:1.00
 O B:HOH305 2.2 39.0 1.0
O B:HOH303 2.2 35.4 1.0
O B:HOH304 2.2 23.7 1.0
O B:HOH302 2.2 42.5 1.0
O B:HOH301 2.2 49.3 1.0
O C:HOH401 2.2 56.0 1.0
O6 B:DG108 4.0 32.8 1.0
O C:HOH409 4.1 30.8 1.0
O B:HOH312 4.2 42.0 1.0
O B:HOH310 4.3 34.2 1.0
O C:HOH405 4.3 29.2 1.0
N7 B:DG107 4.4 22.7 1.0
O6 B:DG107 4.5 17.9 1.0
N4 C:DC209 4.6 23.1 1.0
O B:HOH311 4.8 36.3 1.0
C5 B:DC106 4.9 24.2 1.0

Reference:

K.Bergen, A.L.Steck, S.Strutt, A.Baccaro, W.Welte, K.Diederichs, A.Marx. Structures of Klentaq Dna Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates. J.Am.Chem.Soc. V. 134 11840 2012.
ISSN: ISSN 0002-7863
PubMed: 22475415
DOI: 10.1021/JA3017889
Page generated: Thu Aug 15 17:04:56 2024

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