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Magnesium in PDB 4dfj: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp

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

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp:
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 5-(Aminopentinyl)- Dttp, PDB code: 4dfj 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) 41.81 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.880, 108.880, 90.440, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 20.4

Other elements in 4dfj:

The structure of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

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 5-(Aminopentinyl)- Dttp (pdb code 4dfj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 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 5-(Aminopentinyl)- Dttp, PDB code: 4dfj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4dfj

Go back to Magnesium Binding Sites List in 4dfj
Magnesium binding site 1 out of 8 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp


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 5-(Aminopentinyl)- Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:30.1
occ:1.00
 OD1 A:ASP785 2.2 30.2 1.0
OD2 A:ASP610 2.3 31.5 1.0
O A:HOH1011 2.3 30.8 1.0
O1A A:0KL903 2.5 25.7 1.0
O A:HOH1026 2.5 35.0 1.0
CG A:ASP610 2.9 31.3 1.0
OD1 A:ASP610 3.0 29.4 1.0
CG A:ASP785 3.2 27.9 1.0
MG A:MG902 3.4 29.8 1.0
PA A:0KL903 3.4 26.7 1.0
OD2 A:ASP785 3.6 28.5 1.0
O A:HOH1050 3.7 32.0 1.0
O2A A:0KL903 3.7 25.9 1.0
C3' B:DOC112 3.8 26.8 1.0
O5' A:0KL903 4.1 27.7 1.0
CB A:GLU786 4.1 28.3 1.0
OE1 A:GLU786 4.3 36.1 1.0
C5' A:0KL903 4.3 24.1 1.0
C4' B:DOC112 4.4 28.8 1.0
CB A:ASP610 4.4 28.9 1.0
C A:ASP785 4.4 26.8 1.0
C5' B:DOC112 4.4 28.9 1.0
O A:VAL783 4.4 25.5 1.0
O3G A:0KL903 4.5 28.4 1.0
CB A:ASP785 4.5 24.6 1.0
O A:ASP785 4.5 25.9 1.0
N A:GLU786 4.6 26.4 1.0
NZ A:LYS831 4.7 67.0 1.0
N A:ASP785 4.7 23.6 1.0
O2B A:0KL903 4.8 28.4 1.0
CA A:ASP785 4.8 25.6 1.0
CA A:GLU786 4.9 25.9 1.0
O3A A:0KL903 4.9 27.3 1.0
C2' B:DOC112 4.9 25.7 1.0

Magnesium binding site 2 out of 8 in 4dfj

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Magnesium binding site 2 out of 8 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp


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 5-(Aminopentinyl)- Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:29.8
occ:1.00
 O3G A:0KL903 2.0 28.4 1.0
O2B A:0KL903 2.0 28.4 1.0
OD1 A:ASP610 2.0 29.4 1.0
OD2 A:ASP785 2.0 28.5 1.0
O1A A:0KL903 2.0 25.7 1.0
O A:TYR611 2.1 26.2 1.0
CG A:ASP785 3.0 27.9 1.0
CG A:ASP610 3.1 31.3 1.0
PB A:0KL903 3.2 28.8 1.0
C A:TYR611 3.3 25.3 1.0
OD1 A:ASP785 3.3 30.2 1.0
PA A:0KL903 3.4 26.7 1.0
PG A:0KL903 3.4 33.3 1.0
MG A:MG901 3.4 30.1 1.0
OD2 A:ASP610 3.7 31.5 1.0
O3A A:0KL903 3.7 27.3 1.0
O3B A:0KL903 3.8 27.4 1.0
O A:HOH1020 3.8 28.9 1.0
O A:HOH1050 3.9 32.0 1.0
N A:TYR611 3.9 27.1 1.0
CA A:TYR611 4.1 26.8 1.0
C5' A:0KL903 4.2 24.1 1.0
C A:ASP610 4.2 26.1 1.0
O1G A:0KL903 4.3 31.5 1.0
O5' A:0KL903 4.3 27.7 1.0
N A:SER612 4.3 26.2 1.0
CB A:ASP610 4.3 28.9 1.0
CB A:ASP785 4.3 24.6 1.0
O2G A:0KL903 4.4 32.3 1.0
CA A:SER612 4.5 30.0 1.0
N A:GLN613 4.5 28.9 1.0
O2A A:0KL903 4.5 25.9 1.0
CB A:TYR611 4.6 27.5 1.0
O1B A:0KL903 4.6 25.8 1.0
O A:ASP610 4.6 26.6 1.0
O A:ASP785 4.6 25.9 1.0
CA A:ASP610 4.7 27.4 1.0
CG2 A:ILE614 4.7 25.7 1.0
C A:SER612 4.8 30.2 1.0
O A:HOH1026 4.8 35.0 1.0
N A:ILE614 4.9 24.5 1.0

Magnesium binding site 3 out of 8 in 4dfj

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Magnesium binding site 3 out of 8 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp


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 5-(Aminopentinyl)- Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:41.9
occ:1.00
 OG1 A:THR386 3.0 32.0 1.0
O A:HOH1038 3.1 33.7 1.0
N A:THR386 3.1 26.2 1.0
N A:THR385 3.2 28.3 1.0
O A:SER383 3.5 29.3 1.0
OG1 A:THR385 3.7 28.6 1.0
O A:THR386 3.8 29.2 1.0
CA A:GLY389 3.8 31.8 1.0
CB A:THR386 3.8 33.1 1.0
CA A:THR386 3.9 30.1 1.0
C A:THR385 4.0 29.8 1.0
CA A:THR385 4.0 29.0 1.0
C A:ASN384 4.0 26.5 1.0
CA A:ASN384 4.0 25.2 1.0
CG2 A:THR386 4.1 37.1 1.0
N A:GLY389 4.2 30.2 1.0
C A:THR386 4.3 30.7 1.0
C A:GLY389 4.4 31.9 1.0
CB A:THR385 4.5 30.8 1.0
N A:VAL390 4.5 27.2 1.0
C A:SER383 4.5 30.3 1.0
N A:ASN384 4.8 25.6 1.0

Magnesium binding site 4 out of 8 in 4dfj

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Magnesium binding site 4 out of 8 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp


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 5-(Aminopentinyl)- Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg906

b:51.3
occ:1.00
 O A:HOH1150 2.1 51.6 1.0
O A:HOH1089 3.0 37.8 1.0
NH2 A:ARG771 3.2 33.0 1.0
CG A:ARG771 4.0 33.9 1.0
CD A:ARG771 4.0 34.5 1.0
CG2 A:VAL806 4.1 32.1 1.0
O A:LYS767 4.3 28.5 1.0
CZ A:ARG771 4.3 36.8 1.0
CG1 A:VAL806 4.6 31.5 1.0
CB A:LYS767 4.6 29.9 1.0
NE A:ARG771 4.6 36.7 1.0
C A:LYS767 4.8 27.6 1.0
CB A:VAL806 4.9 31.4 1.0
O A:HOH1077 4.9 46.5 1.0

Magnesium binding site 5 out of 8 in 4dfj

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Magnesium binding site 5 out of 8 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp


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 5-(Aminopentinyl)- Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg912

b:52.7
occ:1.00
 NE2 A:HIS621 3.1 39.1 1.0
CD1 A:LEU723 3.6 34.7 1.0
CE1 A:HIS621 3.7 39.0 1.0
CD2 A:LEU723 4.0 33.7 1.0
OH A:TYR811 4.1 49.1 1.0
CE1 A:TYR811 4.1 37.0 1.0
CG A:LEU723 4.1 33.1 1.0
CD2 A:HIS621 4.2 39.3 1.0
CZ A:TYR811 4.6 42.9 1.0
ND1 A:HIS621 5.0 39.8 1.0

Magnesium binding site 6 out of 8 in 4dfj

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Magnesium binding site 6 out of 8 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:47.0
occ:1.00
 O B:HOH303 2.2 35.0 1.0
O B:HOH304 2.2 27.4 1.0
O B:HOH305 2.2 37.4 1.0
O C:HOH401 2.2 51.6 1.0
O B:HOH302 2.2 45.2 1.0
O6 B:DG108 4.1 28.9 1.0
O1 B:FMT201 4.1 61.7 1.0
O B:HOH324 4.2 42.0 1.0
O C:HOH420 4.3 37.2 1.0
O C:HOH428 4.4 39.0 1.0
O B:HOH315 4.4 39.8 1.0
N7 B:DG107 4.4 23.2 1.0
O6 B:DG107 4.4 25.1 1.0
C B:FMT201 4.5 63.9 1.0
N4 C:DC209 4.6 25.4 1.0
C5 B:DC106 4.7 25.4 1.0
O2 B:FMT201 4.7 64.5 1.0

Magnesium binding site 7 out of 8 in 4dfj

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Magnesium binding site 7 out of 8 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:66.1
occ:1.00
 O A:HOH1144 2.1 38.8 1.0
O A:HOH1143 2.1 47.7 1.0
O A:HOH1090 3.1 51.0 1.0
O1 A:EDO911 3.2 74.2 1.0
N2 C:DG211 3.4 22.5 1.0
O2 C:DT212 3.4 31.2 1.0
C1' C:DT212 3.7 32.6 1.0
C2 A:EDO911 3.7 71.3 1.0
CG A:ARG487 3.8 34.1 1.0
O4' C:DT212 3.8 32.0 1.0
C1 A:EDO911 3.9 73.2 1.0
O2 A:EDO911 4.1 68.9 1.0
C2 C:DT212 4.2 29.0 1.0
CD A:ARG487 4.2 35.5 1.0
O C:HOH413 4.2 50.2 1.0
O B:HOH316 4.3 40.4 1.0
C4' C:DT212 4.3 33.9 1.0
N1 C:DT212 4.4 30.6 1.0
C2 C:DG211 4.5 25.4 1.0
O2 B:DC106 4.5 26.5 1.0
O3' C:DT212 4.6 34.1 1.0
N3 C:DG211 4.7 27.7 1.0
N A:ARG487 4.7 30.4 1.0
C2' C:DT212 4.8 32.8 1.0
C3' C:DT212 4.9 32.0 1.0
C5' C:DG213 5.0 41.2 1.0

Magnesium binding site 8 out of 8 in 4dfj

Go back to Magnesium Binding Sites List in 4dfj
Magnesium binding site 8 out of 8 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with 5-(Aminopentinyl)- Dttp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:54.0
occ:1.00
 O C:HOH402 2.2 33.5 1.0
O B:HOH306 2.2 50.0 1.0
O C:HOH404 2.2 38.4 1.0
O C:HOH403 2.2 46.9 1.0
O6 C:DG205 3.4 27.1 1.0
O C:HOH424 3.7 47.1 1.0
N7 C:DG205 4.0 24.8 1.0
N7 C:DA204 4.0 28.2 1.0
NH2 A:ARG677 4.0 52.7 1.0
O C:HOH409 4.1 36.9 1.0
N6 C:DA204 4.2 27.4 1.0
O A:HOH1064 4.2 42.0 1.0
C6 C:DG205 4.3 28.0 1.0
O B:HOH309 4.3 34.0 1.0
C5 C:DA204 4.3 27.5 1.0
C6 C:DA204 4.4 29.4 1.0
C5 C:DG205 4.5 25.8 1.0
O6 C:DG206 4.6 25.4 1.0
C8 C:DA204 4.7 28.8 1.0
N4 B:DOC112 5.0 25.5 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 17:05:50 2024

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