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Magnesium in PDB 4dfm: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Ternary Complex with 5-(Aminopentinyl)-2-Dctp

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Ternary Complex with 5-(Aminopentinyl)-2-Dctp

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Ternary Complex with 5-(Aminopentinyl)-2-Dctp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Ternary Complex with 5-(Aminopentinyl)-2-Dctp, PDB code: 4dfm 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) 46.88 / 1.89
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.260, 108.260, 90.070, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 21.6

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 Ternary Complex with 5-(Aminopentinyl)-2-Dctp (pdb code 4dfm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Ternary Complex with 5-(Aminopentinyl)-2-Dctp, PDB code: 4dfm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4dfm

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Ternary Complex with 5-(Aminopentinyl)-2-Dctp


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 Ternary Complex with 5-(Aminopentinyl)-2-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:18.4
occ:1.00
 O1B A:0L6901 2.0 23.1 1.0
O2G A:0L6901 2.0 25.6 1.0
O2A A:0L6901 2.0 21.1 1.0
OD2 A:ASP785 2.0 20.4 1.0
OD1 A:ASP610 2.1 22.4 1.0
O A:TYR611 2.1 17.3 1.0
CG A:ASP785 3.1 18.4 1.0
PB A:0L6901 3.1 24.4 1.0
CG A:ASP610 3.2 22.5 1.0
PA A:0L6901 3.3 24.0 1.0
C A:TYR611 3.3 18.2 1.0
PG A:0L6901 3.4 28.6 1.0
OD1 A:ASP785 3.5 19.7 1.0
MG A:MG903 3.5 21.9 1.0
O3A A:0L6901 3.6 27.2 1.0
O3B A:0L6901 3.6 25.2 1.0
OD2 A:ASP610 3.8 24.9 1.0
O A:HOH1004 3.8 21.0 1.0
O A:HOH1061 4.0 24.3 1.0
C5' A:0L6901 4.0 22.5 1.0
N A:TYR611 4.0 16.4 1.0
O5' A:0L6901 4.2 22.1 1.0
CA A:TYR611 4.2 18.1 1.0
N A:SER612 4.2 18.2 1.0
O3G A:0L6901 4.3 28.0 1.0
C A:ASP610 4.3 15.7 1.0
O1G A:0L6901 4.4 28.3 1.0
CA A:SER612 4.4 21.3 1.0
N A:GLN613 4.4 23.1 1.0
CB A:ASP785 4.4 16.2 1.0
CB A:ASP610 4.5 19.0 1.0
O1A A:0L6901 4.5 23.0 1.0
O2B A:0L6901 4.5 23.5 1.0
O A:HOH1001 4.6 34.2 1.0
CB A:TYR611 4.6 17.7 1.0
C A:SER612 4.7 21.7 1.0
CG2 A:ILE614 4.7 21.5 1.0
O A:ASP610 4.7 15.8 1.0
O A:ASP785 4.8 16.6 1.0
N A:ILE614 4.8 18.8 1.0
CA A:ASP610 4.8 15.3 1.0

Magnesium binding site 2 out of 4 in 4dfm

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Ternary Complex with 5-(Aminopentinyl)-2-Dctp


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 Ternary Complex with 5-(Aminopentinyl)-2-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:21.9
occ:1.00
 O A:HOH1002 2.1 19.6 1.0
O A:HOH1001 2.1 34.2 1.0
OD2 A:ASP610 2.2 24.9 1.0
OD1 A:ASP785 2.3 19.7 1.0
O2A A:0L6901 2.4 21.1 1.0
CG A:ASP610 2.9 22.5 1.0
OD1 A:ASP610 3.0 22.4 1.0
CG A:ASP785 3.3 18.4 1.0
PA A:0L6901 3.4 24.0 1.0
MG A:MG902 3.5 18.4 1.0
OD2 A:ASP785 3.6 20.4 1.0
O A:HOH1061 3.6 24.3 1.0
O1A A:0L6901 3.7 23.0 1.0
C3' B:DDG112 3.9 16.2 1.0
O5' A:0L6901 4.0 22.1 1.0
CB A:GLU786 4.1 17.1 1.0
OE1 A:GLU786 4.2 23.0 1.0
C5' A:0L6901 4.3 22.5 1.0
CB A:ASP610 4.3 19.0 1.0
C4' B:DDG112 4.4 18.2 1.0
C5' B:DDG112 4.4 19.2 1.0
NZ A:LYS831 4.5 42.9 1.0
C A:ASP785 4.5 15.2 1.0
O A:VAL783 4.6 12.5 1.0
O2G A:0L6901 4.6 25.6 1.0
CB A:ASP785 4.6 16.2 1.0
O A:ASP785 4.6 16.6 1.0
N A:GLU786 4.7 13.4 1.0
N A:ASP785 4.9 12.6 1.0
O3A A:0L6901 4.9 27.2 1.0
CA A:ASP785 4.9 15.0 1.0
O1B A:0L6901 4.9 23.1 1.0
CA A:GLU786 4.9 14.1 1.0

Magnesium binding site 3 out of 4 in 4dfm

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Ternary Complex with 5-(Aminopentinyl)-2-Dctp


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 Ternary Complex with 5-(Aminopentinyl)-2-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:45.4
occ:1.00
 O A:HOH1194 2.2 41.6 1.0
O A:HOH1192 2.2 52.5 1.0
O C:HOH328 2.2 53.0 1.0
O B:HOH321 2.2 32.3 1.0
O A:HOH1193 2.2 37.2 1.0
O A:HOH1191 2.2 40.3 1.0
O A:HOH1127 3.9 40.9 1.0
O2 B:DC106 4.2 17.1 1.0
OD2 A:ASP488 4.2 31.7 1.0
O2 C:DT212 4.2 25.6 1.0
O A:HOH1104 4.2 30.0 1.0
OD1 A:ASP488 4.3 29.9 1.0
NZ A:LYS511 4.4 42.2 1.0
O B:HOH313 4.4 37.2 1.0
CD A:ARG487 4.5 24.7 1.0
CG A:ASP488 4.5 30.6 1.0
O4' B:DG107 4.8 17.4 1.0
O4' C:DG213 4.8 37.4 1.0
C1' B:DC106 4.9 19.7 1.0
N2 C:DG211 4.9 14.7 1.0
O C:HOH305 4.9 30.8 1.0
C5' B:DG107 4.9 17.3 1.0

Magnesium binding site 4 out of 4 in 4dfm

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Ternary Complex with 5-(Aminopentinyl)-2-Dctp


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 Ternary Complex with 5-(Aminopentinyl)-2-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:29.5
occ:1.00
 O B:HOH302 2.1 17.5 1.0
O B:HOH319 2.1 27.2 1.0
O C:HOH318 2.1 42.8 1.0
O B:HOH308 2.1 27.5 1.0
O B:HOH304 2.1 32.7 1.0
O C:HOH312 4.1 32.7 1.0
O6 B:DG108 4.1 19.5 1.0
O B:HOH310 4.3 32.1 1.0
O B:HOH314 4.3 32.3 1.0
N7 B:DG107 4.4 16.9 1.0
O6 B:DG107 4.4 15.2 1.0
O B:HOH307 4.5 30.8 1.0
N4 C:DC209 4.5 20.0 1.0
O B:HOH316 4.6 38.7 1.0
C5 B:DC106 4.8 18.8 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: Mon Aug 11 07:28:28 2025

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