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Magnesium in PDB 3sv3: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dnam-D5SICSTP

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dnam-D5SICSTP

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dnam-D5SICSTP:
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 the Artificial Base Pair Dnam-D5SICSTP, PDB code: 3sv3 was solved by K.Betz, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.00 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.545, 108.545, 90.978, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 21.5

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 the Artificial Base Pair Dnam-D5SICSTP (pdb code 3sv3). 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 Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dnam-D5SICSTP, PDB code: 3sv3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3sv3

Go back to Magnesium Binding Sites List in 3sv3
Magnesium binding site 1 out of 5 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dnam-D5SICSTP


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 the Artificial Base Pair Dnam-D5SICSTP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg834

b:61.1
occ:1.00
 O A:HOH153 2.1 65.9 1.0
O A:HOH154 2.1 52.0 1.0
O A:HOH170 2.1 53.2 1.0
O2G A:5SI1 2.1 81.4 1.0
O1A A:5SI1 2.3 86.6 1.0
O1B A:5SI1 2.4 66.1 1.0
PG A:5SI1 3.6 83.1 1.0
PA A:5SI1 3.6 88.8 1.0
HZ2 A:LYS804 3.7 53.9 1.0
PB A:5SI1 3.7 66.1 1.0
O A:HOH171 3.7 60.3 1.0
HH22 A:ARG801 3.7 60.3 1.0
HH21 A:ARG801 3.9 60.3 1.0
O A:HOH33 4.0 49.1 1.0
O3B A:5SI1 4.1 45.5 1.0
O5' A:5SI1 4.1 62.9 1.0
NH2 A:ARG801 4.1 50.3 1.0
O3A A:5SI1 4.1 75.4 1.0
OE1 A:GLU808 4.2 40.8 1.0
O1G A:5SI1 4.3 90.1 1.0
OE2 A:GLU805 4.4 54.8 1.0
NZ A:LYS804 4.5 45.0 1.0
HZ1 A:LYS804 4.6 53.9 1.0
O3G A:5SI1 4.7 79.1 1.0
O2A A:5SI1 4.9 91.8 1.0
O A:HOH906 4.9 71.3 1.0
HZ3 A:LYS804 5.0 53.9 1.0
O2B A:5SI1 5.0 55.9 1.0
HD3 A:LYS804 5.0 51.5 1.0

Magnesium binding site 2 out of 5 in 3sv3

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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 Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dnam-D5SICSTP


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 the Artificial Base Pair Dnam-D5SICSTP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg836

b:49.5
occ:1.00
 O2G A:5SI833 2.1 53.4 1.0
O A:TYR611 2.2 37.1 1.0
OD2 A:ASP610 2.2 52.0 1.0
O1A A:5SI833 2.3 39.6 1.0
OD2 A:ASP785 2.3 52.5 1.0
O1B A:5SI833 2.4 52.3 1.0
CG A:ASP610 3.3 63.8 1.0
MG A:MG837 3.3 51.3 1.0
CG A:ASP785 3.4 43.0 1.0
PG A:5SI833 3.4 63.9 1.0
PB A:5SI833 3.4 48.6 1.0
C A:TYR611 3.4 39.5 1.0
O A:HOH191 3.4 44.1 1.0
PA A:5SI833 3.6 48.4 1.0
O A:HOH169 3.6 62.2 1.0
O3B A:5SI833 3.8 67.5 1.0
OD1 A:ASP610 3.8 72.3 1.0
HA A:SER612 3.8 51.1 1.0
OD1 A:ASP785 3.8 40.1 1.0
H A:GLN613 3.9 44.0 0.7
H A:GLN613 3.9 44.0 0.3
O3A A:5SI833 3.9 49.8 1.0
N A:TYR611 4.1 32.2 1.0
O1G A:5SI833 4.2 53.9 1.0
H A:ILE614 4.2 47.1 1.0
C A:ASP610 4.3 34.0 1.0
CA A:TYR611 4.3 36.9 1.0
HB2 A:TYR611 4.3 44.7 1.0
H A:TYR611 4.3 38.6 1.0
N A:SER612 4.4 36.0 1.0
CB A:ASP610 4.4 39.0 1.0
N A:GLN613 4.4 36.7 1.0
C5' A:5SI833 4.4 43.5 1.0
CA A:SER612 4.5 42.6 1.0
HB3 A:ASP610 4.5 46.8 1.0
O5' A:5SI833 4.5 48.1 1.0
O3G A:5SI833 4.5 57.0 1.0
HG22 A:ILE614 4.5 53.6 1.0
HB2 A:ASP785 4.5 36.8 1.0
HZ2 A:LYS663 4.6 83.3 1.0
O A:ASP610 4.6 37.4 1.0
CB A:ASP785 4.6 30.7 1.0
HZ3 A:LYS663 4.7 83.3 1.0
O2A A:5SI833 4.7 48.2 1.0
O A:HOH163 4.7 53.0 1.0
HA A:ASP610 4.7 40.8 1.0
CB A:TYR611 4.8 37.2 1.0
CA A:ASP610 4.8 34.0 1.0
C A:SER612 4.8 39.8 1.0
O2B A:5SI833 4.8 46.8 1.0
HB3 A:TYR611 4.9 44.7 1.0
O A:ASP785 4.9 36.5 1.0

Magnesium binding site 3 out of 5 in 3sv3

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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 Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dnam-D5SICSTP


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 the Artificial Base Pair Dnam-D5SICSTP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg837

b:51.3
occ:1.00
 O A:HOH855 2.1 69.4 1.0
O A:HOH163 2.1 53.0 1.0
OD1 A:ASP785 2.5 40.1 1.0
O1A A:5SI833 2.5 39.6 1.0
OD1 A:ASP610 2.7 72.3 1.0
OD2 A:ASP610 2.8 52.0 1.0
CG A:ASP610 3.1 63.8 1.0
CG A:ASP785 3.2 43.0 1.0
OD2 A:ASP785 3.3 52.5 1.0
MG A:MG836 3.3 49.5 1.0
O A:HOH191 3.4 44.1 1.0
HB2 A:GLU786 3.5 42.4 1.0
HZ1 A:LYS831 3.6 80.5 1.0
PA A:5SI833 3.6 48.4 1.0
C3' B:DOC112 3.7 30.0 1.0
HB3 A:GLU786 4.0 42.4 1.0
O2A A:5SI833 4.1 48.2 1.0
OE1 A:GLU786 4.2 41.4 1.0
CB A:GLU786 4.2 35.4 1.0
O5' A:5SI833 4.2 48.1 1.0
C4' B:DOC112 4.3 36.7 1.0
NZ A:LYS831 4.4 67.1 1.0
HZ2 A:LYS831 4.4 80.5 1.0
H A:ASP785 4.4 41.1 1.0
C5' B:DOC112 4.4 36.0 1.0
O2G A:5SI833 4.5 53.4 1.0
C5' A:5SI833 4.5 43.5 1.0
CB A:ASP610 4.5 39.0 1.0
HZ3 A:LYS831 4.6 80.5 1.0
CB A:ASP785 4.7 30.7 1.0
C A:ASP785 4.7 37.9 1.0
HA A:ASP610 4.7 40.8 1.0
HB2 A:ASP610 4.8 46.8 1.0
O A:ASP785 4.8 36.5 1.0
HZ2 A:LYS663 4.8 83.3 1.0
N A:GLU786 4.8 34.0 1.0
O A:VAL783 4.8 36.6 1.0
O5' B:DOC112 4.9 36.2 1.0
C2' B:DOC112 5.0 37.0 1.0
O1B A:5SI833 5.0 52.3 1.0

Magnesium binding site 4 out of 5 in 3sv3

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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 Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dnam-D5SICSTP


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 the Artificial Base Pair Dnam-D5SICSTP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg842

b:61.3
occ:1.00
 O A:HOH903 2.2 63.9 1.0
O A:HOH905 2.2 64.9 1.0
O A:HOH902 2.2 61.1 1.0
O A:HOH901 2.2 67.1 1.0
O A:HOH904 2.2 87.7 1.0
O1G A:5SI1 2.7 90.1 1.0
O3G A:5SI1 3.3 79.1 1.0
PG A:5SI1 3.4 83.1 1.0
HZ1 A:LYS804 3.5 53.9 1.0
OE2 A:GLU820 3.7 84.5 1.0
O3B A:5SI1 3.7 45.5 1.0
OE1 A:GLU820 4.0 88.4 1.0
CD A:GLU820 4.2 82.2 1.0
NZ A:LYS804 4.3 45.0 1.0
HE2 A:LYS804 4.4 48.3 1.0
HA A:GLU820 4.5 42.8 1.0
HE3 A:LYS804 4.5 48.3 1.0
O A:VAL819 4.6 40.5 1.0
CE A:LYS804 4.7 40.2 1.0
HZ3 A:LYS804 4.8 53.9 1.0
HZ2 A:LYS804 4.8 53.9 1.0
O2G A:5SI1 4.9 81.4 1.0

Magnesium binding site 5 out of 5 in 3sv3

Go back to Magnesium Binding Sites List in 3sv3
Magnesium binding site 5 out of 5 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dnam-D5SICSTP


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 the Artificial Base Pair Dnam-D5SICSTP within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:52.0
occ:1.00
 O B:HOH2 2.2 40.2 1.0
O B:HOH6 2.2 61.2 1.0
O B:HOH5 2.2 42.5 1.0
O C:HOH222 2.2 73.3 1.0
O B:HOH4 2.2 39.7 1.0
O B:HOH3 2.2 28.6 1.0
O6 B:DG108 4.0 30.1 1.0
O B:HOH184 4.1 45.3 1.0
N7 B:DG107 4.3 30.4 1.0
O6 B:DG107 4.4 24.2 1.0
O C:HOH63 4.5 44.0 1.0
O B:HOH159 4.5 40.2 1.0
O C:HOH113 4.5 40.6 1.0
N4 C:DC209 4.5 29.1 1.0
C5 B:DC106 4.7 30.0 1.0

Reference:

K.Betz, D.A.Malyshev, T.Lavergne, W.Welte, K.Diederichs, T.J.Dwyer, P.Ordoukhanian, F.E.Romesberg, A.Marx. Klentaq Polymerase Replicates Unnatural Base Pairs By Inducing A Watson-Crick Geometry. Nat.Chem.Biol. V. 8 612 2012.
ISSN: ISSN 1552-4450
PubMed: 22660438
DOI: 10.1038/NCHEMBIO.966
Page generated: Mon Aug 11 03:15:32 2025

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