Atomistry » Magnesium » PDB 4d4i-4dh8 » 4df4
Atomistry »
  Magnesium »
    PDB 4d4i-4dh8 »
      4df4 »

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

Go back to Magnesium Binding Sites List in 4df4
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy