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Magnesium in PDB 4dfk: Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp

Enzymatic activity of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp

All present enzymatic activity of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp:
2.7.7.7;

Protein crystallography data

The structure of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp, PDB code: 4dfk 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) 46.86 / 1.65
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.211, 108.211, 90.115, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 19.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp (pdb code 4dfk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp, PDB code: 4dfk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4dfk

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Magnesium binding site 1 out of 6 in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:27.0
occ:1.00
 O1B A:0L5901 2.0 28.2 1.0
OD2 A:ASP785 2.0 27.7 1.0
O2G A:0L5901 2.0 27.4 1.0
OD1 A:ASP610 2.1 28.5 1.0
O2A A:0L5901 2.1 25.6 1.0
O A:TYR611 2.1 24.4 1.0
CG A:ASP785 3.1 27.5 1.0
PB A:0L5901 3.1 27.7 1.0
CG A:ASP610 3.2 30.0 1.0
C A:TYR611 3.3 23.1 1.0
PA A:0L5901 3.3 26.5 1.0
PG A:0L5901 3.4 28.9 1.0
OD1 A:ASP785 3.5 26.9 1.0
MG A:MG903 3.6 27.7 1.0
O3A A:0L5901 3.6 27.4 1.0
O3B A:0L5901 3.6 26.2 1.0
OD2 A:ASP610 3.7 30.8 1.0
O A:HOH1010 3.8 27.9 1.0
N A:TYR611 4.0 23.3 1.0
O A:HOH1002 4.1 33.0 1.0
CA A:TYR611 4.1 23.5 1.0
C5' A:0L5901 4.1 25.0 1.0
O1G A:0L5901 4.2 29.0 1.0
N A:SER612 4.3 25.2 1.0
O5' A:0L5901 4.3 24.5 1.0
C A:ASP610 4.3 24.6 1.0
CB A:ASP785 4.4 25.5 1.0
CB A:ASP610 4.4 27.4 1.0
N A:GLN613 4.4 28.0 1.0
O3G A:0L5901 4.4 29.4 1.0
CA A:SER612 4.4 27.5 1.0
O1A A:0L5901 4.5 25.7 1.0
O2B A:0L5901 4.5 28.4 1.0
CB A:TYR611 4.6 23.1 1.0
C A:SER612 4.7 27.6 1.0
O A:ASP610 4.7 25.2 1.0
O A:HOH1161 4.7 36.2 1.0
CG2 A:ILE614 4.7 25.7 1.0
O A:ASP785 4.8 23.2 1.0
N A:ILE614 4.8 24.5 1.0
CA A:ASP610 4.8 24.4 1.0

Magnesium binding site 2 out of 6 in 4dfk

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Magnesium binding site 2 out of 6 in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:27.7
occ:1.00
 O A:HOH1160 2.2 28.0 1.0
O A:HOH1161 2.2 36.2 1.0
OD2 A:ASP610 2.2 30.8 1.0
OD1 A:ASP785 2.3 26.9 1.0
O2A A:0L5901 2.5 25.6 1.0
CG A:ASP610 3.1 30.0 1.0
OD1 A:ASP610 3.2 28.5 1.0
CG A:ASP785 3.3 27.5 1.0
PA A:0L5901 3.4 26.5 1.0
MG A:MG902 3.6 27.0 1.0
OD2 A:ASP785 3.6 27.7 1.0
C3' B:DOC112 3.7 25.4 1.0
O1A A:0L5901 3.8 25.7 1.0
O A:HOH1002 3.8 33.0 1.0
O5' A:0L5901 4.0 24.5 1.0
CB A:GLU786 4.2 21.9 1.0
C4' B:DOC112 4.2 25.7 1.0
NZ A:LYS831 4.3 49.1 1.0
C5' B:DOC112 4.3 25.9 1.0
C5' A:0L5901 4.3 25.0 1.0
OE1 A:GLU786 4.4 31.6 1.0
CB A:ASP610 4.4 27.4 1.0
O A:VAL783 4.5 22.4 1.0
C A:ASP785 4.5 22.6 1.0
O2G A:0L5901 4.6 27.4 1.0
CB A:ASP785 4.6 25.5 1.0
N A:GLU786 4.7 20.8 1.0
O A:ASP785 4.7 23.2 1.0
N A:ASP785 4.8 22.3 1.0
C2' B:DOC112 4.9 26.0 1.0
O3A A:0L5901 4.9 27.4 1.0
CA A:ASP785 4.9 23.2 1.0
CA A:GLU786 5.0 21.2 1.0
O5' B:DOC112 5.0 26.3 1.0

Magnesium binding site 3 out of 6 in 4dfk

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Magnesium binding site 3 out of 6 in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:57.6
occ:1.00
 O A:HOH1201 2.1 41.5 1.0
O A:HOH1260 4.0 52.0 1.0
CD2 A:LEU802 4.1 38.1 1.0
CE A:MET775 4.3 38.4 1.0
NH2 A:ARG771 4.5 28.9 1.0
O A:HOH1025 4.5 32.9 1.0
SD A:MET775 4.7 36.9 1.0
O A:HOH1128 4.8 39.7 1.0
CD1 A:LEU802 4.9 37.1 1.0
CG A:LEU802 5.0 35.5 1.0

Magnesium binding site 4 out of 6 in 4dfk

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Magnesium binding site 4 out of 6 in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg909

b:54.0
occ:1.00
 O C:HOH441 2.1 49.7 1.0
O A:HOH1058 2.1 43.9 1.0
O B:HOH308 2.1 33.0 1.0
O A:HOH1246 2.1 49.6 1.0
O2 C:FMT302 3.3 50.6 1.0
O A:HOH1261 3.8 48.8 1.0
OD2 A:ASP488 4.1 38.4 1.0
O A:HOH1157 4.1 39.4 1.0
OD1 A:ASP488 4.2 36.2 1.0
O2 B:DC106 4.2 24.3 1.0
CD A:ARG487 4.3 32.8 1.0
O2 C:DT212 4.3 31.8 1.0
C C:FMT302 4.3 49.9 1.0
CG A:ASP488 4.4 36.5 1.0
O B:HOH323 4.5 42.8 1.0
O4' B:DG107 4.8 27.0 1.0
CG A:ARG487 4.9 31.8 1.0
C1' B:DC106 4.9 26.4 1.0
O4' C:DG213 5.0 43.5 1.0
N2 C:DG211 5.0 24.8 1.0
C4' B:DG107 5.0 25.1 1.0

Magnesium binding site 5 out of 6 in 4dfk

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Magnesium binding site 5 out of 6 in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:34.5
occ:1.00
 O B:HOH303 2.2 33.4 1.0
O B:HOH304 2.2 26.7 1.0
O B:HOH302 2.2 36.1 1.0
O C:HOH404 2.2 43.4 1.0
O B:HOH301 2.2 47.5 1.0
O B:HOH305 2.2 34.2 1.0
O B:HOH326 4.1 47.3 1.0
O6 B:DG108 4.2 26.1 1.0
O C:HOH438 4.2 36.7 1.0
O B:HOH310 4.3 36.4 1.0
N7 B:DG107 4.3 22.7 1.0
O B:HOH313 4.4 35.1 1.0
O C:HOH435 4.4 38.3 1.0
O6 B:DG107 4.4 22.4 1.0
C5 B:DC106 4.6 23.4 1.0
N4 C:DC209 4.6 26.1 1.0
O B:HOH325 4.7 51.6 1.0

Magnesium binding site 6 out of 6 in 4dfk

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Magnesium binding site 6 out of 6 in the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(N-(10-Hydroxydecanoyl)-Aminopentinyl)-2-Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:64.0
occ:1.00
 O C:HOH401 2.2 33.7 1.0
O C:HOH403 2.2 29.9 1.0
O C:HOH402 2.2 47.8 1.0
O A:HOH1001 2.2 56.9 1.0
O6 C:DG205 3.3 23.7 1.0
O C:HOH431 3.4 56.1 1.0
N7 C:DG205 3.9 24.8 1.0
N7 C:DA204 4.0 30.2 1.0
N6 C:DA204 4.0 27.6 1.0
NH2 A:ARG677 4.1 38.4 1.0
O A:HOH1224 4.2 39.3 1.0
O C:HOH408 4.2 30.5 1.0
C6 C:DG205 4.2 24.1 1.0
C5 C:DA204 4.2 29.2 1.0
O B:HOH328 4.3 29.7 1.0
C6 C:DA204 4.3 27.2 1.0
C5 C:DG205 4.4 24.0 1.0
O6 C:DG206 4.7 24.4 1.0
C8 C:DA204 4.8 28.7 1.0
N4 B:DOC112 4.9 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: Mon Aug 11 07:28:15 2025

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