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Magnesium in PDB 4dfp: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp, PDB code: 4dfp 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) 46.96 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.448, 108.448, 90.435, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 22.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp (pdb code 4dfp). 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 Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp, PDB code: 4dfp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4dfp

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Magnesium binding site 1 out of 5 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp


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 Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:34.2
occ:1.00
 OD1 A:ASP785 2.0 31.3 1.0
OD1 A:ASP610 2.1 28.5 1.0
O A:TYR611 2.1 28.2 1.0
O2A A:0L7908 2.2 30.9 1.0
O1B A:0L7908 2.2 29.5 1.0
O1G A:0L7908 2.3 35.1 1.0
CG A:ASP785 2.9 30.5 1.0
OD2 A:ASP785 3.2 33.5 1.0
C A:TYR611 3.3 28.7 1.0
CG A:ASP610 3.3 33.9 1.0
MG A:MG902 3.4 34.2 1.0
PB A:0L7908 3.5 31.2 1.0
PA A:0L7908 3.6 31.9 1.0
PG A:0L7908 3.7 39.6 1.0
N A:TYR611 3.7 26.1 1.0
OD2 A:ASP610 3.9 37.4 1.0
CA A:TYR611 3.9 28.5 1.0
C5' A:0L7908 3.9 29.4 1.0
O A:HOH1031 4.0 31.8 1.0
O3A A:0L7908 4.1 33.7 1.0
O3B A:0L7908 4.1 30.9 1.0
C A:ASP610 4.2 25.0 1.0
CB A:TYR611 4.2 25.6 1.0
CB A:ASP785 4.3 25.0 1.0
O5' A:0L7908 4.3 29.0 1.0
O A:HOH1047 4.4 31.1 1.0
O3G A:0L7908 4.4 41.3 1.0
N A:SER612 4.4 28.1 1.0
CB A:ASP610 4.4 28.1 1.0
O A:ASP785 4.5 24.8 1.0
N A:GLN613 4.5 25.5 1.0
CA A:ASP610 4.6 24.5 1.0
O A:ASP610 4.7 25.5 1.0
CA A:SER612 4.7 31.7 1.0
CG2 A:ILE614 4.7 24.9 1.0
O1A A:0L7908 4.8 27.8 1.0
O2B A:0L7908 4.8 26.1 1.0
N A:ILE614 4.8 29.8 1.0
O2G A:0L7908 4.8 39.5 1.0
C A:SER612 4.9 28.8 1.0
CB A:ILE614 5.0 26.4 1.0

Magnesium binding site 2 out of 5 in 4dfp

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Magnesium binding site 2 out of 5 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp


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 Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:34.2
occ:1.00
 O A:HOH1001 2.0 31.9 1.0
OD2 A:ASP785 2.2 33.5 1.0
O2A A:0L7908 2.6 30.9 1.0
OD2 A:ASP610 2.9 37.4 1.0
OD1 A:ASP610 3.1 28.5 1.0
O A:HOH1057 3.1 37.8 1.0
CG A:ASP785 3.3 30.5 1.0
CG A:ASP610 3.3 33.9 1.0
MG A:MG901 3.4 34.2 1.0
PA A:0L7908 3.5 31.9 1.0
C3' B:DOC112 3.5 26.9 1.0
OD1 A:ASP785 3.7 31.3 1.0
O5' A:0L7908 3.9 29.0 1.0
O1A A:0L7908 3.9 27.8 1.0
C5' A:0L7908 4.0 29.4 1.0
CB A:GLU786 4.1 25.9 1.0
O A:HOH1047 4.1 31.1 1.0
C4' B:DOC112 4.2 30.9 1.0
O A:VAL783 4.3 22.0 1.0
C5' B:DOC112 4.4 31.1 1.0
C A:ASP785 4.4 21.5 1.0
OE1 A:GLU786 4.4 32.1 1.0
N A:GLU786 4.4 22.6 1.0
NZ A:LYS831 4.5 49.2 1.0
CB A:ASP785 4.5 25.0 1.0
O A:ASP785 4.6 24.8 1.0
O1G A:0L7908 4.6 35.1 1.0
C2' B:DOC112 4.6 27.2 1.0
N A:ASP785 4.7 23.0 1.0
CB A:ASP610 4.7 28.1 1.0
CA A:ASP785 4.8 21.8 1.0
CA A:GLU786 4.8 21.9 1.0
O1B A:0L7908 4.8 29.5 1.0
O3A A:0L7908 5.0 33.7 1.0
O5' B:DOC112 5.0 29.1 1.0

Magnesium binding site 3 out of 5 in 4dfp

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Magnesium binding site 3 out of 5 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp


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 Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg910

b:48.1
occ:1.00
 O B:HOH327 2.2 36.4 1.0
O A:HOH1207 2.2 41.3 1.0
O C:HOH432 2.2 57.8 1.0
O A:HOH1204 2.2 43.3 1.0
O A:HOH1205 2.2 51.9 1.0
O A:HOH1206 2.2 35.2 1.0
O A:HOH1100 3.8 40.4 1.0
OD2 A:ASP488 4.1 40.2 1.0
O2 B:DC106 4.2 27.3 1.0
O2 C:DT212 4.3 35.6 1.0
OD1 A:ASP488 4.3 37.6 1.0
O A:HOH1110 4.4 38.4 1.0
CD A:ARG487 4.4 36.5 1.0
CG A:ASP488 4.5 37.3 1.0
O B:HOH316 4.6 43.8 1.0
O4' B:DG107 4.8 27.2 1.0
O C:HOH406 4.8 40.4 1.0
O4' C:DG213 4.8 43.3 1.0
C1' B:DC106 4.9 25.6 1.0
N2 C:DG211 4.9 25.0 1.0

Magnesium binding site 4 out of 5 in 4dfp

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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 Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp


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 Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg913

b:73.7
occ:1.00
 O A:HOH1212 2.2 79.0 1.0
O A:HOH1211 2.2 86.6 1.0
O A:HOH1214 2.2 64.1 1.0
O A:HOH1210 2.2 65.1 1.0
O A:HOH1215 2.2 52.9 1.0
O A:HOH1213 2.2 78.5 1.0
OE1 A:GLU825 3.5 47.9 1.0
O A:ALA600 4.0 25.6 1.0
O A:HOH1040 4.1 46.8 1.0
CD A:GLU825 4.3 47.9 1.0
NH1 A:ARG450 4.4 65.5 1.0
CD1 A:ILE599 4.8 37.9 1.0
CB A:ILE599 4.9 28.0 1.0
CB A:GLU825 4.9 39.4 1.0
O A:GLU825 4.9 32.3 1.0
OE2 A:GLU825 5.0 48.9 1.0

Magnesium binding site 5 out of 5 in 4dfp

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Magnesium binding site 5 out of 5 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp


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 Aqauticus in A Ternary Complex with 7-(Aminopentinyl)-7- Deaza-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:45.7
occ:1.00
 O B:HOH325 2.2 35.7 1.0
O B:HOH326 2.2 40.0 1.0
O C:HOH431 2.2 59.6 1.0
O B:HOH324 2.2 31.4 1.0
O B:HOH323 2.2 36.0 1.0
O B:HOH322 2.2 51.8 1.0
O6 B:DG108 4.0 32.0 1.0
O B:HOH313 4.2 38.5 1.0
O B:HOH319 4.2 39.7 1.0
O C:HOH417 4.3 35.9 1.0
O C:HOH418 4.4 43.5 1.0
O6 B:DG107 4.4 22.1 1.0
N7 B:DG107 4.4 26.1 1.0
N4 C:DC209 4.5 24.4 1.0
O C:HOH401 4.6 38.0 1.0
C5 B:DC106 4.7 27.5 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 17:06:17 2024

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