Atomistry » Magnesium » PDB 3srf-3t2b » 3sv3
Atomistry »
  Magnesium »
    PDB 3srf-3t2b »
      3sv3 »

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

Go back to Magnesium Binding Sites List in 3sv3
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

Go back to Magnesium Binding Sites List in 3sv3
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

Go back to Magnesium Binding Sites List in 3sv3
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 Dec 14 08:52:03 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy