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

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

Go back to Magnesium Binding Sites List in 4dfj
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

Go back to Magnesium Binding Sites List in 4dfj
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

Go back to Magnesium Binding Sites List in 4dfj
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

Go back to Magnesium Binding Sites List in 4dfj
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

Go back to Magnesium Binding Sites List in 4dfj
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

Go back to Magnesium Binding Sites List in 4dfj
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy