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Magnesium in PDB 4df4: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 7-(N-(10- Hydroxydecanoyl)-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 7-(N-(10- Hydroxydecanoyl)-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 7-(N-(10- Hydroxydecanoyl)-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 7-(N-(10- Hydroxydecanoyl)-Aminopentinyl)-7-Deaza-2 -Datp, PDB code: 4df4 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) 46.20 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.815, 107.815, 89.678, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 22.7

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 7-(N-(10- Hydroxydecanoyl)-Aminopentinyl)-7-Deaza-2 -Datp (pdb code 4df4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 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 7-(N-(10- Hydroxydecanoyl)-Aminopentinyl)-7-Deaza-2 -Datp, PDB code: 4df4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4df4

Go back to Magnesium Binding Sites List in 4df4
Magnesium binding site 1 out of 5 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 7-(N-(10- Hydroxydecanoyl)-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 7-(N-(10- Hydroxydecanoyl)-Aminopentinyl)-7-Deaza-2 -Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:24.9
occ:1.00
 O A:TYR611 2.0 13.4 1.0
OD1 A:ASP610 2.0 15.3 0.6
O3G A:0L3903 2.0 21.7 1.0
OD2 A:ASP785 2.0 25.1 1.0
O2B A:0L3903 2.1 25.8 1.0
O2A A:0L3903 2.1 26.5 1.0
CG A:ASP785 3.0 17.7 1.0
CG A:ASP610 3.1 17.6 0.6
C A:TYR611 3.2 14.0 1.0
MG A:MG902 3.2 27.6 1.0
PB A:0L3903 3.3 27.1 1.0
OD1 A:ASP785 3.4 18.4 1.0
PG A:0L3903 3.4 26.5 1.0
PA A:0L3903 3.5 24.3 1.0
OD2 A:ASP610 3.5 20.9 0.6
O A:HOH1123 3.6 32.0 1.0
O3A A:0L3903 3.8 42.6 1.0
N A:TYR611 3.8 12.1 1.0
O A:HOH1279 3.8 36.9 1.0
O3B A:0L3903 3.8 34.1 1.0
CA A:TYR611 3.9 13.7 1.0
N A:SER612 4.2 14.6 1.0
C A:ASP610 4.2 12.6 1.0
C5' A:0L3903 4.3 23.5 1.0
CB A:ASP610 4.3 13.4 0.6
CB A:ASP785 4.3 9.2 1.0
CB A:ASP610 4.3 12.5 0.4
CB A:TYR611 4.3 11.2 1.0
O1G A:0L3903 4.4 27.4 1.0
O5' A:0L3903 4.4 24.0 1.0
CA A:SER612 4.4 14.8 1.0
N A:GLN613 4.4 8.6 1.0
O2G A:0L3903 4.4 28.0 1.0
O1A A:0L3903 4.6 25.8 1.0
O1B A:0L3903 4.6 24.2 1.0
O A:ASP785 4.6 12.6 1.0
C A:SER612 4.7 11.3 1.0
CA A:ASP610 4.7 11.8 0.6
CA A:ASP610 4.7 11.8 0.4
CG2 A:ILE614 4.8 9.4 1.0
O A:ASP610 4.8 12.1 0.9
N A:ILE614 4.9 10.8 1.0

Magnesium binding site 2 out of 5 in 4df4

Go back to Magnesium Binding Sites List in 4df4
Magnesium binding site 2 out of 5 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 7-(N-(10- Hydroxydecanoyl)-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 7-(N-(10- Hydroxydecanoyl)-Aminopentinyl)-7-Deaza-2 -Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:27.6
occ:1.00
 OD1 A:ASP785 2.1 18.4 1.0
OD2 A:ASP610 2.2 20.9 0.6
O2A A:0L3903 2.2 26.5 1.0
O A:HOH1287 2.8 35.8 1.0
CG A:ASP610 2.9 17.6 0.6
OD1 A:ASP610 2.9 15.3 0.6
O A:HOH1279 3.0 36.9 1.0
OE2 A:GLU786 3.0 17.7 0.5
CG A:ASP785 3.1 17.7 1.0
MG A:MG901 3.2 24.9 1.0
CG A:GLU786 3.2 13.5 0.5
PA A:0L3903 3.2 24.3 1.0
OD2 A:ASP785 3.3 25.1 1.0
O1A A:0L3903 3.5 25.8 1.0
CD A:GLU786 3.6 16.5 0.5
C3' B:DOC112 3.6 11.6 1.0
O5' A:0L3903 4.1 24.0 1.0
C5' A:0L3903 4.2 23.5 1.0
C5' B:DOC112 4.3 12.4 1.0
C4' B:DOC112 4.3 14.2 1.0
O3G A:0L3903 4.3 21.7 1.0
CB A:ASP610 4.3 13.4 0.6
CB A:ASP610 4.4 12.5 0.4
O2B A:0L3903 4.5 25.8 1.0
CB A:ASP785 4.5 9.2 1.0
CB A:GLU786 4.5 11.7 0.5
C A:ASP785 4.5 10.8 1.0
O A:ASP785 4.6 12.6 1.0
CB A:GLU786 4.6 11.7 0.5
OE1 A:GLU786 4.6 17.2 0.5
O3A A:0L3903 4.6 42.6 1.0
O A:HOH1277 4.6 44.6 1.0
N A:GLU786 4.8 11.0 1.0
OE1 A:GLU786 4.8 17.0 0.5
O A:VAL783 4.8 9.7 1.0
OD1 A:ASP610 4.8 14.0 0.4
C2' B:DOC112 4.9 12.4 1.0
CA A:ASP785 4.9 10.1 1.0
O5' B:DOC112 4.9 14.1 1.0
O A:TYR611 4.9 13.4 1.0

Magnesium binding site 3 out of 5 in 4df4

Go back to Magnesium Binding Sites List in 4df4
Magnesium binding site 3 out of 5 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 7-(N-(10- Hydroxydecanoyl)-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 7-(N-(10- Hydroxydecanoyl)-Aminopentinyl)-7-Deaza-2 -Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:0.3
occ:0.71
 O A:HOH1295 2.2 80.9 0.7
O A:HOH1297 2.2 60.4 0.7
O A:HOH1296 2.2 45.6 0.7
O A:HOH1299 2.2 73.7 0.7
O A:HOH1298 2.2 73.8 0.7
O A:HOH1300 2.2 60.4 0.7
O A:HOH1075 4.2 25.3 1.0
OE1 A:GLU808 4.4 22.5 1.0
O A:HOH1224 4.4 46.1 1.0
OE2 A:GLU805 4.6 39.7 1.0

Magnesium binding site 4 out of 5 in 4df4

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Magnesium binding site 4 out of 5 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 7-(N-(10- Hydroxydecanoyl)-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 4 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 7-(N-(10- Hydroxydecanoyl)-Aminopentinyl)-7-Deaza-2 -Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg906

b:53.4
occ:1.00
 O A:HOH1172 2.1 25.6 1.0
O A:HOH1174 2.1 24.6 1.0
CH2 A:TRP318 3.5 18.0 1.0
CZ3 A:TRP318 3.5 19.7 1.0
CZ2 A:TRP318 3.8 19.1 1.0
CE3 A:TRP318 3.8 16.1 1.0
CE2 A:TRP318 4.1 21.7 1.0
CD2 A:TRP318 4.1 17.1 1.0
O A:ASP551 4.2 24.6 1.0
CD2 A:LEU552 4.3 14.7 1.0
NH1 A:ARG313 4.6 24.5 1.0
CA A:LEU552 4.9 18.9 1.0
NE1 A:TRP318 4.9 22.1 1.0

Magnesium binding site 5 out of 5 in 4df4

Go back to Magnesium Binding Sites List in 4df4
Magnesium binding site 5 out of 5 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 7-(N-(10- Hydroxydecanoyl)-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 5 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 7-(N-(10- Hydroxydecanoyl)-Aminopentinyl)-7-Deaza-2 -Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:52.4
occ:1.00
 O B:HOH323 2.2 18.9 1.0
O B:HOH322 2.2 37.0 1.0
O B:HOH320 2.2 31.3 1.0
O B:HOH324 2.2 28.1 1.0
O B:HOH321 2.2 28.8 1.0
O C:HOH332 2.2 74.1 1.0
O6 B:DG108 4.1 19.6 1.0
O B:HOH308 4.1 28.9 1.0
O C:HOH325 4.1 22.5 1.0
O C:HOH313 4.5 28.2 1.0
N7 B:DG107 4.5 18.9 1.0
O B:HOH312 4.5 21.6 1.0
O6 B:DG107 4.6 16.4 1.0
O B:HOH302 4.6 23.5 1.0
N4 C:DC209 4.6 8.3 1.0
C5 B:DC106 4.7 16.5 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 17:04:44 2024

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