Magnesium in PDB 4r4v: Crystal Structure of the Vs Ribozyme - G638A Mutant
Protein crystallography data
The structure of Crystal Structure of the Vs Ribozyme - G638A Mutant, PDB code: 4r4v
was solved by
J.A.Piccirilli,
N.B.Suslov,
S.Dasgupta,
H.Huang,
D.M.J.Lilley,
P.A.Rice,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.07 /
3.07
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.229,
102.229,
215.020,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.9 /
20.4
|
Other elements in 4r4v:
The structure of Crystal Structure of the Vs Ribozyme - G638A Mutant also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Vs Ribozyme - G638A Mutant
(pdb code 4r4v). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Crystal Structure of the Vs Ribozyme - G638A Mutant, PDB code: 4r4v:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 4r4v
Go back to
Magnesium Binding Sites List in 4r4v
Magnesium binding site 1 out
of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant
 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 Vs Ribozyme - G638A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg801
b:68.5
occ:1.00
|
O
|
A:HOH907
|
2.2
|
58.6
|
1.0
|
O
|
A:HOH906
|
2.8
|
29.8
|
1.0
|
H41
|
A:C764
|
3.2
|
50.4
|
1.0
|
N4
|
A:C764
|
4.0
|
42.0
|
1.0
|
H42
|
A:C764
|
4.2
|
50.4
|
1.0
|
H41
|
A:C765
|
4.5
|
46.4
|
1.0
|
H42
|
A:C765
|
4.6
|
46.4
|
1.0
|
O6
|
A:G654
|
4.7
|
39.4
|
1.0
|
H5
|
A:C764
|
4.7
|
51.4
|
1.0
|
N4
|
A:C765
|
4.9
|
38.7
|
1.0
|
|
Magnesium binding site 2 out
of 9 in 4r4v
Go back to
Magnesium Binding Sites List in 4r4v
Magnesium binding site 2 out
of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant
 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 Vs Ribozyme - G638A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg803
b:60.1
occ:1.00
|
O
|
A:HOH912
|
2.2
|
39.5
|
1.0
|
O
|
A:HOH916
|
2.2
|
47.7
|
1.0
|
O
|
A:HOH915
|
2.2
|
28.6
|
1.0
|
O
|
A:HOH913
|
2.2
|
61.1
|
1.0
|
O
|
A:HOH911
|
2.2
|
74.0
|
1.0
|
O
|
A:HOH914
|
2.2
|
36.4
|
1.0
|
H41
|
A:C741
|
3.0
|
45.4
|
1.0
|
H41
|
A:C742
|
3.5
|
39.2
|
1.0
|
N4
|
A:C741
|
3.8
|
37.8
|
1.0
|
H5
|
A:C741
|
4.0
|
37.2
|
1.0
|
H42
|
A:C741
|
4.1
|
45.4
|
1.0
|
N4
|
A:C742
|
4.2
|
32.7
|
1.0
|
H42
|
A:C742
|
4.3
|
39.2
|
1.0
|
C5
|
A:C741
|
4.6
|
31.0
|
1.0
|
C4
|
A:C741
|
4.6
|
35.2
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 4r4v
Go back to
Magnesium Binding Sites List in 4r4v
Magnesium binding site 3 out
of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant
 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 Vs Ribozyme - G638A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg805
b:27.2
occ:1.00
|
O
|
A:HOH920
|
2.2
|
47.9
|
1.0
|
O
|
A:HOH917
|
2.2
|
41.0
|
1.0
|
O
|
A:HOH922
|
2.2
|
58.3
|
1.0
|
O
|
A:HOH921
|
2.2
|
52.0
|
1.0
|
O
|
A:HOH918
|
2.2
|
57.4
|
1.0
|
O
|
A:HOH919
|
2.2
|
52.0
|
1.0
|
H41
|
A:C758
|
2.9
|
37.9
|
1.0
|
H62
|
A:A759
|
3.5
|
55.2
|
1.0
|
N4
|
A:C758
|
3.7
|
31.6
|
1.0
|
H5
|
A:C758
|
3.8
|
35.9
|
1.0
|
H42
|
A:C758
|
4.1
|
37.9
|
1.0
|
N6
|
A:A759
|
4.2
|
46.0
|
1.0
|
H61
|
A:A759
|
4.3
|
55.2
|
1.0
|
C5
|
A:C758
|
4.4
|
29.9
|
1.0
|
C4
|
A:C758
|
4.5
|
29.3
|
1.0
|
H41
|
A:C760
|
4.8
|
74.3
|
1.0
|
H42
|
A:C760
|
4.9
|
74.3
|
1.0
|
O
|
A:HOH926
|
4.9
|
33.2
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 4r4v
Go back to
Magnesium Binding Sites List in 4r4v
Magnesium binding site 4 out
of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant
 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 Vs Ribozyme - G638A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg806
b:42.2
occ:1.00
|
O
|
A:HOH928
|
2.2
|
42.4
|
1.0
|
O
|
A:HOH926
|
2.2
|
33.2
|
1.0
|
O
|
A:HOH924
|
2.2
|
40.5
|
1.0
|
O
|
A:HOH923
|
2.2
|
40.7
|
1.0
|
O
|
A:HOH927
|
2.2
|
42.9
|
1.0
|
O
|
A:HOH925
|
2.2
|
40.7
|
1.0
|
H8
|
A:A756
|
3.2
|
27.8
|
1.0
|
H2'
|
A:A756
|
3.9
|
32.2
|
1.0
|
C8
|
A:A756
|
4.1
|
23.2
|
1.0
|
O2'
|
A:A756
|
4.1
|
32.3
|
1.0
|
HO2'
|
A:A756
|
4.5
|
38.8
|
1.0
|
C2'
|
A:A756
|
4.5
|
26.9
|
1.0
|
N7
|
A:A756
|
4.7
|
18.9
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 4r4v
Go back to
Magnesium Binding Sites List in 4r4v
Magnesium binding site 5 out
of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant
 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 Vs Ribozyme - G638A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg807
b:59.0
occ:1.00
|
O
|
A:HOH929
|
2.2
|
53.7
|
1.0
|
O
|
A:HOH931
|
2.2
|
40.6
|
1.0
|
O
|
A:HOH932
|
2.2
|
80.9
|
1.0
|
O
|
A:HOH933
|
2.2
|
47.3
|
1.0
|
O
|
A:HOH930
|
2.2
|
62.8
|
1.0
|
O
|
A:HOH934
|
2.2
|
51.9
|
1.0
|
H1
|
A:HOH929
|
2.8
|
64.4
|
1.0
|
H1
|
A:HOH931
|
2.8
|
48.7
|
1.0
|
H1
|
A:HOH932
|
2.8
|
97.1
|
1.0
|
H1
|
A:HOH933
|
2.8
|
56.8
|
1.0
|
H1
|
A:HOH930
|
2.8
|
75.4
|
1.0
|
H1
|
A:HOH934
|
2.8
|
62.2
|
1.0
|
H41
|
A:C748
|
3.4
|
33.1
|
1.0
|
H41
|
A:C747
|
3.7
|
41.3
|
1.0
|
N4
|
A:C748
|
4.1
|
27.6
|
1.0
|
H41
|
A:C726
|
4.2
|
32.9
|
1.0
|
H42
|
A:C748
|
4.2
|
33.1
|
1.0
|
N4
|
A:C747
|
4.3
|
34.4
|
1.0
|
H42
|
A:C747
|
4.6
|
41.3
|
1.0
|
H42
|
A:C726
|
4.6
|
32.9
|
1.0
|
N4
|
A:C726
|
4.8
|
27.4
|
1.0
|
H5
|
A:C747
|
4.8
|
45.5
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 4r4v
Go back to
Magnesium Binding Sites List in 4r4v
Magnesium binding site 6 out
of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant
 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 Vs Ribozyme - G638A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg808
b:35.9
occ:1.00
|
O
|
A:HOH910
|
2.3
|
31.0
|
1.0
|
O
|
A:HOH909
|
2.7
|
33.4
|
1.0
|
N7
|
A:A656
|
3.9
|
32.9
|
1.0
|
OP2
|
A:A656
|
4.0
|
48.0
|
1.0
|
OP2
|
A:G655
|
4.0
|
30.0
|
1.0
|
H8
|
A:A656
|
4.2
|
41.5
|
1.0
|
H3'
|
A:G655
|
4.3
|
42.8
|
1.0
|
C8
|
A:A656
|
4.5
|
34.6
|
1.0
|
H62
|
A:A656
|
4.6
|
38.5
|
1.0
|
O5'
|
A:G655
|
4.6
|
32.5
|
1.0
|
H8
|
A:G655
|
4.6
|
40.8
|
1.0
|
OP2
|
A:G716
|
4.8
|
36.3
|
1.0
|
P
|
A:G655
|
4.8
|
36.9
|
1.0
|
H5'
|
A:G717
|
4.8
|
30.6
|
1.0
|
N7
|
A:G716
|
4.9
|
29.3
|
1.0
|
C8
|
A:G655
|
4.9
|
34.0
|
1.0
|
O5'
|
A:G717
|
5.0
|
20.9
|
1.0
|
H8
|
A:G716
|
5.0
|
35.5
|
1.0
|
N7
|
A:G655
|
5.0
|
34.7
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 4r4v
Go back to
Magnesium Binding Sites List in 4r4v
Magnesium binding site 7 out
of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant
 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 Vs Ribozyme - G638A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg812
b:47.6
occ:1.00
|
H41
|
A:C768
|
3.5
|
32.2
|
1.0
|
N4
|
A:C768
|
4.3
|
26.8
|
1.0
|
H42
|
A:C768
|
4.4
|
32.2
|
1.0
|
H5
|
A:C768
|
5.0
|
28.5
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 4r4v
Go back to
Magnesium Binding Sites List in 4r4v
Magnesium binding site 8 out
of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant
 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 Vs Ribozyme - G638A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg813
b:62.1
occ:1.00
|
H41
|
A:C785
|
3.9
|
69.0
|
1.0
|
N4
|
A:C785
|
4.6
|
57.5
|
1.0
|
H42
|
A:C785
|
4.9
|
69.0
|
1.0
|
H5
|
A:C785
|
4.9
|
72.7
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 4r4v
Go back to
Magnesium Binding Sites List in 4r4v
Magnesium binding site 9 out
of 9 in the Crystal Structure of the Vs Ribozyme - G638A Mutant
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of the Vs Ribozyme - G638A Mutant within 5.0Å range:
|
Reference:
N.B.Suslov,
S.Dasgupta,
H.Huang,
J.R.Fuller,
D.M.Lilley,
P.A.Rice,
J.A.Piccirilli.
Crystal Structure of the Varkud Satellite Ribozyme. Nat.Chem.Biol. V. 11 840 2015.
ISSN: ISSN 1552-4450
PubMed: 26414446
DOI: 10.1038/NCHEMBIO.1929
Page generated: Tue Aug 20 02:51:16 2024
|