Magnesium in PDB 5nkl: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with the Artificial Base Pair Dds-Dpxtp
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 Dds-Dpxtp
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 Dds-Dpxtp:
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 Dds-Dpxtp, PDB code: 5nkl
was solved by
K.Betz,
A.Marx,
K.Diederichs,
I.Hirao,
M.Kimoto,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.10 /
1.70
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
108.777,
108.777,
90.571,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.1 /
23.7
|
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 Dds-Dpxtp
(pdb code 5nkl). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 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 Dds-Dpxtp, PDB code: 5nkl:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 5nkl
Go back to
Magnesium Binding Sites List in 5nkl
Magnesium binding site 1 out
of 2 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 Dds-Dpxtp
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 Dds-Dpxtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg901
b:46.1
occ:1.00
|
H22
|
A:91T904
|
1.9
|
43.5
|
0.4
|
OD1
|
A:ASP785
|
2.2
|
40.0
|
1.0
|
O6
|
A:91R905
|
2.3
|
35.3
|
0.5
|
OD2
|
A:ASP610
|
2.3
|
57.6
|
1.0
|
O6
|
A:91T904
|
2.3
|
36.2
|
0.4
|
O
|
A:HOH1006
|
2.4
|
41.6
|
1.0
|
O
|
A:HOH1168
|
2.6
|
42.4
|
1.0
|
H3'2
|
B:DOC112
|
2.8
|
43.2
|
1.0
|
CG
|
A:ASP610
|
3.1
|
54.7
|
1.0
|
CG
|
A:ASP785
|
3.1
|
45.8
|
1.0
|
OD1
|
A:ASP610
|
3.2
|
51.6
|
1.0
|
HB2
|
A:GLU786
|
3.3
|
52.1
|
1.0
|
OD2
|
A:ASP785
|
3.3
|
42.3
|
1.0
|
P
|
A:91R905
|
3.4
|
38.2
|
0.5
|
MG
|
A:MG902
|
3.4
|
45.2
|
1.0
|
P
|
A:91T904
|
3.5
|
38.8
|
0.4
|
H5'
|
B:DOC112
|
3.5
|
39.8
|
1.0
|
H20
|
A:91R905
|
3.6
|
51.5
|
0.5
|
O7
|
A:91R905
|
3.8
|
42.6
|
0.5
|
O7
|
A:91T904
|
3.8
|
42.6
|
0.4
|
O
|
A:HOH1054
|
3.8
|
46.0
|
1.0
|
C3'
|
B:DOC112
|
3.8
|
36.0
|
1.0
|
O5
|
A:91T904
|
3.8
|
33.8
|
0.4
|
H16
|
A:91T904
|
3.8
|
42.8
|
0.4
|
HZ1
|
A:LYS831
|
3.8
|
86.8
|
1.0
|
O5
|
A:91R905
|
3.8
|
34.5
|
0.5
|
H15
|
A:91R905
|
3.9
|
42.5
|
0.5
|
H3'1
|
B:DOC112
|
4.1
|
43.2
|
1.0
|
HZ2
|
A:LYS831
|
4.1
|
86.8
|
1.0
|
HB3
|
A:GLU786
|
4.1
|
52.1
|
1.0
|
CB
|
A:GLU786
|
4.1
|
43.4
|
1.0
|
HZ3
|
A:LYS831
|
4.2
|
86.8
|
1.0
|
H4'
|
B:DOC112
|
4.2
|
41.7
|
1.0
|
H16
|
A:91R905
|
4.2
|
42.5
|
0.5
|
H
|
A:ASP785
|
4.2
|
35.9
|
1.0
|
H15
|
A:91T904
|
4.2
|
42.8
|
0.4
|
OE1
|
A:GLU786
|
4.2
|
42.8
|
1.0
|
C13
|
A:91T904
|
4.2
|
35.7
|
0.4
|
C13
|
A:91R905
|
4.2
|
35.4
|
0.5
|
NZ
|
A:LYS831
|
4.2
|
72.3
|
1.0
|
C4'
|
B:DOC112
|
4.3
|
34.8
|
1.0
|
C5'
|
B:DOC112
|
4.3
|
33.1
|
1.0
|
O
|
A:VAL783
|
4.5
|
35.4
|
1.0
|
CB
|
A:ASP785
|
4.5
|
33.3
|
1.0
|
O13
|
A:91T904
|
4.5
|
42.4
|
0.4
|
O14
|
A:91R905
|
4.5
|
42.9
|
0.5
|
CB
|
A:ASP610
|
4.5
|
34.3
|
1.0
|
C
|
A:ASP785
|
4.6
|
33.2
|
1.0
|
H17
|
A:91R905
|
4.7
|
51.1
|
0.5
|
HB2
|
A:ASP610
|
4.7
|
41.2
|
1.0
|
O
|
A:ASP785
|
4.7
|
32.7
|
1.0
|
N
|
A:GLU786
|
4.7
|
32.4
|
1.0
|
O8
|
A:91R905
|
4.8
|
42.6
|
0.5
|
HA
|
A:ASP610
|
4.8
|
40.2
|
1.0
|
O8
|
A:91T904
|
4.8
|
42.5
|
0.4
|
HB3
|
A:ASP785
|
4.8
|
40.0
|
1.0
|
O5'
|
B:DOC112
|
4.8
|
35.5
|
1.0
|
N
|
A:ASP785
|
4.9
|
29.9
|
1.0
|
CA
|
A:ASP785
|
4.9
|
37.0
|
1.0
|
O9
|
A:91T904
|
4.9
|
41.1
|
0.4
|
O9
|
A:91R905
|
4.9
|
41.8
|
0.5
|
H2''
|
B:DOC112
|
4.9
|
40.9
|
1.0
|
CA
|
A:GLU786
|
5.0
|
34.4
|
1.0
|
C2'
|
B:DOC112
|
5.0
|
34.1
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 5nkl
Go back to
Magnesium Binding Sites List in 5nkl
Magnesium binding site 2 out
of 2 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 Dds-Dpxtp
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 Dds-Dpxtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg902
b:45.2
occ:1.00
|
H20
|
A:91R905
|
1.6
|
51.5
|
0.5
|
O14
|
A:91R905
|
2.0
|
42.9
|
0.5
|
OD1
|
A:ASP610
|
2.0
|
51.6
|
1.0
|
H22
|
A:91T904
|
2.0
|
43.5
|
0.4
|
OD2
|
A:ASP785
|
2.1
|
42.3
|
1.0
|
O13
|
A:91T904
|
2.1
|
42.4
|
0.4
|
O
|
A:TYR611
|
2.1
|
42.3
|
1.0
|
O6
|
A:91T904
|
2.2
|
36.2
|
0.4
|
O6
|
A:91R905
|
2.2
|
35.3
|
0.5
|
O9
|
A:91R905
|
2.2
|
41.8
|
0.5
|
O9
|
A:91T904
|
2.2
|
41.1
|
0.4
|
CG
|
A:ASP610
|
3.1
|
54.7
|
1.0
|
CG
|
A:ASP785
|
3.2
|
45.8
|
1.0
|
P1
|
A:91R905
|
3.2
|
42.5
|
0.5
|
P1
|
A:91T904
|
3.2
|
43.4
|
0.4
|
P2
|
A:91R905
|
3.2
|
48.5
|
0.5
|
P2
|
A:91T904
|
3.3
|
48.1
|
0.4
|
H16
|
A:91R905
|
3.3
|
42.5
|
0.5
|
C
|
A:TYR611
|
3.3
|
49.1
|
1.0
|
H15
|
A:91T904
|
3.3
|
42.8
|
0.4
|
P
|
A:91R905
|
3.4
|
38.2
|
0.5
|
MG
|
A:MG901
|
3.4
|
46.1
|
1.0
|
O11
|
A:91R905
|
3.5
|
41.6
|
0.5
|
O
|
A:HOH1025
|
3.5
|
46.2
|
1.0
|
O11
|
A:91T904
|
3.5
|
42.1
|
0.4
|
P
|
A:91T904
|
3.5
|
38.8
|
0.4
|
O8
|
A:91R905
|
3.6
|
42.6
|
0.5
|
OD1
|
A:ASP785
|
3.6
|
40.0
|
1.0
|
O8
|
A:91T904
|
3.7
|
42.5
|
0.4
|
OD2
|
A:ASP610
|
3.7
|
57.6
|
1.0
|
O
|
A:HOH1054
|
3.8
|
46.0
|
1.0
|
HA
|
A:SER612
|
3.9
|
63.6
|
1.0
|
H
|
A:GLN613
|
3.9
|
56.4
|
1.0
|
N
|
A:TYR611
|
4.0
|
35.9
|
1.0
|
HG22
|
A:ILE614
|
4.0
|
94.8
|
1.0
|
H
|
A:TYR611
|
4.1
|
43.0
|
1.0
|
O12
|
A:91R905
|
4.1
|
51.9
|
0.5
|
C13
|
A:91T904
|
4.2
|
35.7
|
0.4
|
C13
|
A:91R905
|
4.2
|
35.4
|
0.5
|
O14
|
A:91T904
|
4.2
|
51.4
|
0.4
|
CA
|
A:TYR611
|
4.2
|
44.4
|
1.0
|
O5
|
A:91T904
|
4.2
|
33.8
|
0.4
|
H
|
A:ILE614
|
4.2
|
54.3
|
1.0
|
HB2
|
A:TYR611
|
4.2
|
47.4
|
1.0
|
O13
|
A:91R905
|
4.3
|
43.1
|
0.5
|
HZ3
|
A:LYS663
|
4.3
|
75.6
|
1.0
|
C
|
A:ASP610
|
4.3
|
37.6
|
1.0
|
O5
|
A:91R905
|
4.3
|
34.5
|
0.5
|
N
|
A:SER612
|
4.3
|
45.6
|
1.0
|
CB
|
A:ASP610
|
4.3
|
34.3
|
1.0
|
N
|
A:GLN613
|
4.4
|
47.0
|
1.0
|
HB2
|
A:ASP785
|
4.4
|
40.0
|
1.0
|
CB
|
A:ASP785
|
4.4
|
33.3
|
1.0
|
O12
|
A:91T904
|
4.4
|
43.0
|
0.4
|
CA
|
A:SER612
|
4.4
|
53.0
|
1.0
|
H16
|
A:91T904
|
4.4
|
42.8
|
0.4
|
HB3
|
A:ASP610
|
4.4
|
41.2
|
1.0
|
H15
|
A:91R905
|
4.5
|
42.5
|
0.5
|
H21
|
A:91T904
|
4.5
|
51.6
|
0.4
|
O7
|
A:91R905
|
4.5
|
42.6
|
0.5
|
O10
|
A:91R905
|
4.6
|
41.2
|
0.5
|
O7
|
A:91T904
|
4.6
|
42.6
|
0.4
|
O10
|
A:91T904
|
4.6
|
41.3
|
0.4
|
H20
|
A:91T904
|
4.6
|
61.7
|
0.4
|
H19
|
A:91R905
|
4.6
|
51.7
|
0.5
|
C
|
A:SER612
|
4.7
|
44.1
|
1.0
|
CB
|
A:TYR611
|
4.7
|
39.5
|
1.0
|
HA
|
A:ASP610
|
4.7
|
40.2
|
1.0
|
CA
|
A:ASP610
|
4.7
|
33.5
|
1.0
|
O
|
A:ASP785
|
4.7
|
32.7
|
1.0
|
O
|
A:ASP610
|
4.7
|
45.9
|
1.0
|
HB
|
A:ILE614
|
4.7
|
60.2
|
1.0
|
HG21
|
A:ILE614
|
4.8
|
94.8
|
1.0
|
CG2
|
A:ILE614
|
4.8
|
79.0
|
1.0
|
HB3
|
A:ASP785
|
4.8
|
40.0
|
1.0
|
HB3
|
A:TYR611
|
4.9
|
47.4
|
1.0
|
O
|
A:HOH1168
|
4.9
|
42.4
|
1.0
|
|
Reference:
K.Betz,
M.Kimoto,
K.Diederichs,
I.Hirao,
A.Marx.
Structural Basis For Expansion of the Genetic Alphabet with An Artificial Nucleobase Pair. Angew. Chem. Int. Ed. Engl. V. 56 12000 2017.
ISSN: ESSN 1521-3773
PubMed: 28594080
DOI: 10.1002/ANIE.201704190
Page generated: Sun Sep 29 23:20:27 2024
|