Magnesium in PDB 430d: Structure of Sarcin/Ricin Loop From Rat 28S Rrna
Protein crystallography data
The structure of Structure of Sarcin/Ricin Loop From Rat 28S Rrna, PDB code: 430d
was solved by
C.C.Correll,
A.Munishkin,
Y.L.Chan,
Z.Ren,
I.G.Wool,
T.A.Steitz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.10
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.830,
56.830,
107.960,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
28 /
33
|
Other elements in 430d:
The structure of Structure of Sarcin/Ricin Loop From Rat 28S Rrna also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna
(pdb code 430d). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Structure of Sarcin/Ricin Loop From Rat 28S Rrna, PDB code: 430d:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 430d
Go back to
Magnesium Binding Sites List in 430d
Magnesium binding site 1 out
of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg31
b:56.5
occ:1.00
|
OP2
|
A:C23
|
3.2
|
71.6
|
1.0
|
OP1
|
A:C23
|
3.4
|
71.9
|
1.0
|
OP2
|
A:G24
|
3.6
|
72.8
|
1.0
|
P
|
A:C23
|
3.6
|
71.8
|
1.0
|
O5'
|
A:C23
|
3.9
|
72.6
|
1.0
|
|
Magnesium binding site 2 out
of 9 in 430d
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Magnesium Binding Sites List in 430d
Magnesium binding site 2 out
of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg32
b:67.5
occ:1.00
|
O
|
A:HOH107
|
2.2
|
63.8
|
1.0
|
N1
|
A:G16
|
3.6
|
67.1
|
1.0
|
N2
|
A:G16
|
3.7
|
66.8
|
1.0
|
C2
|
A:G16
|
4.2
|
66.9
|
1.0
|
C2
|
A:A17
|
4.4
|
67.9
|
1.0
|
O6
|
A:G16
|
4.6
|
67.2
|
1.0
|
C6
|
A:G16
|
4.6
|
66.5
|
1.0
|
N6
|
A:A15
|
4.7
|
66.4
|
1.0
|
N3
|
A:A17
|
4.9
|
68.2
|
1.0
|
N1
|
A:A17
|
5.0
|
67.6
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 430d
Go back to
Magnesium Binding Sites List in 430d
Magnesium binding site 3 out
of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg33
b:64.3
occ:1.00
|
OP1
|
A:G24
|
2.2
|
72.6
|
1.0
|
P
|
A:G24
|
2.7
|
72.6
|
1.0
|
O5'
|
A:G24
|
2.9
|
72.4
|
1.0
|
OP2
|
A:G24
|
2.9
|
72.8
|
1.0
|
C5'
|
A:G24
|
3.5
|
71.0
|
1.0
|
C3'
|
A:G24
|
3.9
|
69.1
|
1.0
|
OP2
|
A:C25
|
3.9
|
67.3
|
1.0
|
C4'
|
A:G24
|
4.2
|
70.0
|
1.0
|
O3'
|
A:G24
|
4.3
|
68.0
|
1.0
|
O3'
|
A:C23
|
4.3
|
73.2
|
1.0
|
P
|
A:C25
|
4.7
|
67.5
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 430d
Go back to
Magnesium Binding Sites List in 430d
Magnesium binding site 4 out
of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg34
b:71.5
occ:1.00
|
N4
|
A:C28
|
3.4
|
52.0
|
1.0
|
BR
|
A:CBV27
|
4.2
|
92.7
|
1.0
|
MG
|
A:MG36
|
4.3
|
70.5
|
1.0
|
C4
|
A:C28
|
4.6
|
51.9
|
1.0
|
O6
|
A:G2
|
4.6
|
46.3
|
1.0
|
N4
|
A:CBV27
|
4.6
|
51.9
|
1.0
|
C5
|
A:C28
|
4.9
|
52.1
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 430d
Go back to
Magnesium Binding Sites List in 430d
Magnesium binding site 5 out
of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg35
b:66.1
occ:1.00
|
OP2
|
A:A12
|
2.3
|
71.2
|
1.0
|
N4
|
A:C13
|
2.8
|
72.5
|
1.0
|
C5
|
A:C13
|
3.4
|
72.4
|
1.0
|
OP2
|
A:U11
|
3.5
|
67.8
|
1.0
|
C4
|
A:C13
|
3.5
|
72.4
|
1.0
|
O5'
|
A:U11
|
3.5
|
67.8
|
1.0
|
P
|
A:A12
|
3.6
|
72.3
|
1.0
|
N2
|
A:G19
|
3.8
|
57.3
|
1.0
|
P
|
A:U11
|
4.0
|
67.3
|
1.0
|
C3'
|
A:U11
|
4.1
|
69.8
|
1.0
|
O3'
|
A:U11
|
4.2
|
71.2
|
1.0
|
O5'
|
A:A12
|
4.2
|
72.0
|
1.0
|
N7
|
A:A12
|
4.5
|
73.1
|
1.0
|
O6
|
A:G14
|
4.5
|
68.3
|
1.0
|
C5'
|
A:U11
|
4.6
|
68.5
|
1.0
|
OP1
|
A:U11
|
4.7
|
67.5
|
1.0
|
C6
|
A:C13
|
4.7
|
72.0
|
1.0
|
C8
|
A:A12
|
4.7
|
72.8
|
1.0
|
N3
|
A:C13
|
4.8
|
72.3
|
1.0
|
OP1
|
A:A12
|
4.9
|
72.2
|
1.0
|
C2
|
A:G19
|
4.9
|
58.3
|
1.0
|
C4'
|
A:U11
|
5.0
|
69.2
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 430d
Go back to
Magnesium Binding Sites List in 430d
Magnesium binding site 6 out
of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg36
b:70.5
occ:1.00
|
N4
|
A:C29
|
3.2
|
50.1
|
1.0
|
N4
|
A:C28
|
4.0
|
52.0
|
1.0
|
C4
|
A:C29
|
4.1
|
50.5
|
1.0
|
C5
|
A:C29
|
4.1
|
50.2
|
1.0
|
MG
|
A:MG34
|
4.3
|
71.5
|
1.0
|
C5
|
A:C28
|
4.4
|
52.1
|
1.0
|
C4
|
A:C28
|
4.4
|
51.9
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 430d
Go back to
Magnesium Binding Sites List in 430d
Magnesium binding site 7 out
of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg37
b:66.5
occ:1.00
|
C8
|
A:G10
|
3.8
|
64.5
|
1.0
|
C2'
|
A:G10
|
4.2
|
65.0
|
1.0
|
C5'
|
A:G10
|
4.3
|
63.8
|
1.0
|
N7
|
A:G10
|
4.7
|
64.2
|
1.0
|
N9
|
A:G10
|
4.7
|
64.5
|
1.0
|
O4'
|
A:G10
|
4.8
|
64.8
|
1.0
|
C1'
|
A:G10
|
4.9
|
64.8
|
1.0
|
C4'
|
A:G10
|
4.9
|
64.7
|
1.0
|
C3'
|
A:G10
|
5.0
|
65.3
|
1.0
|
O2'
|
A:G10
|
5.0
|
65.3
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 430d
Go back to
Magnesium Binding Sites List in 430d
Magnesium binding site 8 out
of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg38
b:56.0
occ:1.00
|
N4
|
A:C25
|
3.4
|
59.3
|
1.0
|
N6
|
A:A26
|
3.8
|
53.5
|
1.0
|
C4
|
A:C25
|
4.3
|
60.4
|
1.0
|
C5
|
A:C25
|
4.6
|
60.2
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 430d
Go back to
Magnesium Binding Sites List in 430d
Magnesium binding site 9 out
of 9 in the Structure of Sarcin/Ricin Loop From Rat 28S Rrna
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Structure of Sarcin/Ricin Loop From Rat 28S Rrna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg39
b:68.9
occ:1.00
|
O2
|
A:CBV27
|
3.7
|
53.3
|
1.0
|
O2
|
A:U4
|
3.8
|
48.7
|
1.0
|
C2
|
A:CBV27
|
4.2
|
53.4
|
1.0
|
C1'
|
A:CBV27
|
4.4
|
55.9
|
1.0
|
N1
|
A:CBV27
|
4.6
|
54.5
|
1.0
|
O2'
|
A:U4
|
4.7
|
48.2
|
1.0
|
C2
|
A:A26
|
4.7
|
55.5
|
1.0
|
N2
|
A:G3
|
4.8
|
47.4
|
1.0
|
O4'
|
A:G5
|
4.9
|
52.1
|
1.0
|
C1'
|
A:G5
|
4.9
|
51.5
|
1.0
|
N3
|
A:CBV27
|
4.9
|
52.8
|
1.0
|
|
Reference:
C.C.Correll,
A.Munishkin,
Y.L.Chan,
Z.Ren,
I.G.Wool,
T.A.Steitz.
Crystal Structure of the Ribosomal Rna Domain Essential For Binding Elongation Factors. Proc.Natl.Acad.Sci.Usa V. 95 13436 1998.
ISSN: ISSN 0027-8424
PubMed: 9811818
DOI: 10.1073/PNAS.95.23.13436
Page generated: Thu Aug 15 14:12:25 2024
|