Magnesium in PDB 5eao: Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+
Protein crystallography data
The structure of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+, PDB code: 5eao
was solved by
A.Mir,
B.L.Golden,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.36 /
2.99
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.974,
87.016,
105.370,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.8 /
27
|
Other elements in 5eao:
The structure of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+
(pdb code 5eao). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+, PDB code: 5eao:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 5eao
Go back to
Magnesium Binding Sites List in 5eao
Magnesium binding site 1 out
of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg101
b:33.1
occ:1.00
|
OP2
|
A:A22
|
2.2
|
40.8
|
1.0
|
N7
|
A:G23
|
2.7
|
36.0
|
1.0
|
O6
|
A:G23
|
3.3
|
29.5
|
1.0
|
C5
|
A:G23
|
3.5
|
34.2
|
1.0
|
P
|
A:A22
|
3.6
|
49.3
|
1.0
|
C6
|
A:G23
|
3.7
|
32.8
|
1.0
|
C8
|
A:G23
|
3.8
|
40.0
|
1.0
|
O2V
|
B:CVC7
|
4.1
|
36.4
|
1.0
|
O3'
|
A:G21
|
4.1
|
38.0
|
1.0
|
O5'
|
A:A22
|
4.2
|
42.9
|
1.0
|
O5'
|
B:U8
|
4.5
|
25.6
|
1.0
|
O2'
|
A:G21
|
4.7
|
38.2
|
1.0
|
C4
|
A:G23
|
4.8
|
38.0
|
1.0
|
OP1
|
A:A22
|
4.8
|
42.9
|
1.0
|
C8
|
A:A22
|
4.8
|
35.8
|
1.0
|
N9
|
A:G23
|
4.9
|
46.5
|
1.0
|
O1V
|
B:CVC7
|
5.0
|
39.6
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 5eao
Go back to
Magnesium Binding Sites List in 5eao
Magnesium binding site 2 out
of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg102
b:34.4
occ:1.00
|
OP2
|
A:A41
|
2.4
|
47.0
|
1.0
|
P
|
A:A41
|
3.5
|
46.6
|
1.0
|
O5'
|
A:A41
|
3.6
|
37.5
|
1.0
|
N7
|
A:A42
|
4.2
|
31.1
|
1.0
|
OP1
|
A:A41
|
4.3
|
45.0
|
1.0
|
OP2
|
A:A42
|
4.4
|
31.9
|
1.0
|
C8
|
A:A41
|
4.6
|
35.0
|
1.0
|
OP2
|
A:A40
|
4.7
|
34.5
|
1.0
|
O3'
|
A:A40
|
4.7
|
49.5
|
1.0
|
N7
|
A:A41
|
4.7
|
34.4
|
1.0
|
N6
|
A:A42
|
4.8
|
24.6
|
1.0
|
O5'
|
A:A40
|
4.9
|
38.8
|
1.0
|
C5'
|
A:A41
|
5.0
|
33.3
|
1.0
|
C3'
|
A:A40
|
5.0
|
41.1
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 5eao
Go back to
Magnesium Binding Sites List in 5eao
Magnesium binding site 3 out
of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg103
b:53.7
occ:1.00
|
OP2
|
A:G30
|
3.3
|
36.5
|
1.0
|
C8
|
A:G29
|
3.4
|
36.6
|
1.0
|
N7
|
A:G29
|
3.5
|
36.1
|
1.0
|
OP2
|
A:G29
|
3.7
|
47.8
|
1.0
|
O5'
|
A:G29
|
3.8
|
41.6
|
1.0
|
OP2
|
A:G31
|
3.9
|
34.4
|
1.0
|
C3'
|
A:G29
|
4.3
|
38.0
|
1.0
|
N9
|
A:G29
|
4.4
|
34.2
|
1.0
|
P
|
A:G30
|
4.4
|
45.7
|
1.0
|
P
|
A:G29
|
4.4
|
50.5
|
1.0
|
O5'
|
A:G30
|
4.5
|
39.2
|
1.0
|
C5
|
A:G29
|
4.5
|
30.7
|
1.0
|
C5'
|
A:G30
|
4.7
|
34.7
|
1.0
|
O3'
|
A:G29
|
4.9
|
45.2
|
1.0
|
P
|
A:G31
|
4.9
|
31.3
|
1.0
|
C2'
|
A:G29
|
5.0
|
34.8
|
1.0
|
C5'
|
A:G29
|
5.0
|
37.8
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 5eao
Go back to
Magnesium Binding Sites List in 5eao
Magnesium binding site 4 out
of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg104
b:33.7
occ:1.00
|
O4
|
A:U17
|
3.0
|
41.0
|
1.0
|
OP2
|
A:U20
|
3.6
|
37.7
|
1.0
|
OP1
|
A:U20
|
4.0
|
42.4
|
1.0
|
C4
|
A:U17
|
4.0
|
42.0
|
1.0
|
OP1
|
A:A19
|
4.1
|
41.3
|
1.0
|
P
|
A:U20
|
4.2
|
45.3
|
1.0
|
N3
|
A:U17
|
4.3
|
42.1
|
1.0
|
P
|
A:A19
|
5.0
|
36.3
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 5eao
Go back to
Magnesium Binding Sites List in 5eao
Magnesium binding site 5 out
of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg105
b:52.7
occ:1.00
|
O6
|
A:G39
|
2.7
|
32.2
|
1.0
|
O02
|
B:CVC7
|
3.5
|
42.2
|
1.0
|
C6
|
A:G39
|
3.8
|
30.1
|
1.0
|
C8
|
B:CVC7
|
4.1
|
32.1
|
1.0
|
C01
|
B:CVC7
|
4.2
|
27.8
|
1.0
|
N7
|
A:G39
|
4.5
|
32.6
|
1.0
|
C5
|
A:G39
|
4.5
|
29.6
|
1.0
|
OP2
|
A:C38
|
4.8
|
36.9
|
1.0
|
P
|
B:CVC7
|
4.9
|
34.2
|
1.0
|
C2'
|
B:CVC7
|
4.9
|
34.4
|
1.0
|
N1
|
A:G39
|
4.9
|
25.4
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 5eao
Go back to
Magnesium Binding Sites List in 5eao
Magnesium binding site 6 out
of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg101
b:30.7
occ:0.50
|
OP2
|
B:G14
|
2.6
|
32.5
|
1.0
|
O2'
|
B:A13
|
2.9
|
31.6
|
1.0
|
O3'
|
B:A13
|
3.4
|
29.7
|
1.0
|
P
|
B:G14
|
3.6
|
32.8
|
1.0
|
C2'
|
B:A13
|
4.0
|
27.4
|
1.0
|
C3'
|
B:A13
|
4.3
|
29.4
|
1.0
|
C1'
|
B:A13
|
4.6
|
25.6
|
1.0
|
OP1
|
B:G14
|
4.6
|
31.6
|
1.0
|
O5'
|
B:G14
|
4.7
|
29.2
|
1.0
|
N7
|
B:G14
|
4.9
|
27.9
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 5eao
Go back to
Magnesium Binding Sites List in 5eao
Magnesium binding site 7 out
of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg102
b:55.0
occ:1.00
|
OP1
|
B:C19
|
3.8
|
51.8
|
1.0
|
OP2
|
B:C19
|
4.7
|
43.2
|
1.0
|
P
|
B:C19
|
4.8
|
49.5
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 5eao
Go back to
Magnesium Binding Sites List in 5eao
Magnesium binding site 8 out
of 8 in the Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Two Active Site Divalent Ion in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analog-MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg103
b:42.9
occ:1.00
|
OP2
|
B:A16
|
3.1
|
33.5
|
1.0
|
OP2
|
B:U15
|
3.9
|
31.8
|
1.0
|
OP1
|
A:G1
|
4.3
|
65.8
|
1.0
|
P
|
B:A16
|
4.5
|
33.2
|
1.0
|
O5'
|
B:U15
|
4.6
|
31.5
|
1.0
|
N7
|
B:A16
|
4.7
|
30.7
|
1.0
|
C5'
|
A:G1
|
4.7
|
59.3
|
1.0
|
P
|
B:U15
|
4.7
|
33.3
|
1.0
|
C5
|
B:U15
|
4.9
|
28.8
|
1.0
|
C8
|
B:A16
|
4.9
|
31.4
|
1.0
|
P
|
A:G1
|
5.0
|
80.9
|
1.0
|
C6
|
B:U15
|
5.0
|
28.7
|
1.0
|
O5'
|
A:G1
|
5.0
|
66.3
|
1.0
|
O5'
|
B:A16
|
5.0
|
33.2
|
1.0
|
|
Reference:
A.Mir,
B.L.Golden.
Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to A Transition State Analogue. Biochemistry V. 55 633 2016.
ISSN: ISSN 0006-2960
PubMed: 26551631
DOI: 10.1021/ACS.BIOCHEM.5B01139
Page generated: Sun Sep 29 03:33:41 2024
|