Magnesium in PDB 7of0: Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
Enzymatic activity of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
All present enzymatic activity of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).:
3.1.1.29;
Other elements in 7of0:
The structure of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 61 in 7of0
Go back to
Magnesium Binding Sites List in 7of0
Magnesium binding site 1 out
of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
![](/pictures/MG/pdb/of/7of0-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/of/7of0-MG-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3301
b:71.2
occ:1.00
|
OP1
|
A:A2866
|
2.8
|
59.4
|
1.0
|
OP2
|
A:U2864
|
3.0
|
87.7
|
1.0
|
C2
|
A:U2863
|
3.6
|
72.0
|
1.0
|
C2'
|
A:U2863
|
3.7
|
72.0
|
1.0
|
O2
|
A:U2863
|
3.8
|
72.0
|
1.0
|
N3
|
A:U2863
|
3.9
|
72.0
|
1.0
|
N1
|
A:U2863
|
4.0
|
72.0
|
1.0
|
OP2
|
A:C2867
|
4.1
|
56.4
|
1.0
|
P
|
A:A2866
|
4.1
|
59.4
|
1.0
|
C3'
|
A:U2863
|
4.3
|
72.0
|
1.0
|
P
|
A:U2864
|
4.4
|
87.7
|
1.0
|
C1'
|
A:U2863
|
4.4
|
72.0
|
1.0
|
C4
|
A:U2863
|
4.5
|
72.0
|
1.0
|
C6
|
A:U2863
|
4.5
|
72.0
|
1.0
|
OP2
|
A:A2866
|
4.6
|
59.4
|
1.0
|
O2'
|
A:U2863
|
4.6
|
72.0
|
1.0
|
N6
|
A:A2869
|
4.6
|
58.0
|
1.0
|
C5'
|
A:U2864
|
4.7
|
87.7
|
1.0
|
C5
|
A:U2863
|
4.7
|
72.0
|
1.0
|
O3'
|
A:U2863
|
4.7
|
72.0
|
1.0
|
O3'
|
A:C2865
|
4.9
|
81.6
|
1.0
|
|
Magnesium binding site 2 out
of 61 in 7of0
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Magnesium Binding Sites List in 7of0
Magnesium binding site 2 out
of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
![](/pictures/MG/pdb/of/7of0-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/of/7of0-MG-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3302
b:56.0
occ:1.00
|
O4
|
A:U1758
|
2.0
|
62.3
|
1.0
|
OP2
|
A:A1757
|
2.1
|
58.7
|
1.0
|
C4
|
A:U1758
|
3.1
|
62.3
|
1.0
|
P
|
A:A1757
|
3.5
|
58.7
|
1.0
|
O4
|
A:U1759
|
3.6
|
70.3
|
1.0
|
C5
|
A:U1758
|
3.8
|
62.3
|
1.0
|
O5'
|
A:A1756
|
3.9
|
54.0
|
1.0
|
N1
|
A:A1740
|
4.0
|
52.1
|
1.0
|
N6
|
A:A1739
|
4.1
|
61.3
|
1.0
|
OP1
|
A:A1757
|
4.2
|
58.7
|
1.0
|
N3
|
A:U1758
|
4.3
|
62.3
|
1.0
|
O3'
|
A:A1756
|
4.3
|
54.0
|
1.0
|
C3'
|
A:A1756
|
4.3
|
54.0
|
1.0
|
C2
|
A:A1740
|
4.5
|
52.1
|
1.0
|
OP2
|
A:A1756
|
4.5
|
54.0
|
1.0
|
O5'
|
A:A1757
|
4.5
|
58.7
|
1.0
|
P
|
A:A1756
|
4.6
|
54.0
|
1.0
|
C4
|
A:U1759
|
4.6
|
70.3
|
1.0
|
OP1
|
A:A1756
|
4.7
|
54.0
|
1.0
|
C5'
|
A:A1756
|
4.8
|
54.0
|
1.0
|
|
Magnesium binding site 3 out
of 61 in 7of0
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Magnesium Binding Sites List in 7of0
Magnesium binding site 3 out
of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
![](/pictures/MG/pdb/of/7of0-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/of/7of0-MG-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3303
b:48.9
occ:1.00
|
OP1
|
A:C1725
|
1.9
|
51.6
|
1.0
|
OP2
|
A:C1726
|
2.0
|
51.7
|
1.0
|
N7
|
A:A1723
|
2.2
|
48.2
|
1.0
|
C8
|
A:A1723
|
3.1
|
48.2
|
1.0
|
P
|
A:C1725
|
3.4
|
51.6
|
1.0
|
C5
|
A:A1723
|
3.4
|
48.2
|
1.0
|
P
|
A:C1726
|
3.4
|
51.7
|
1.0
|
N6
|
A:A1723
|
3.7
|
48.2
|
1.0
|
C6
|
A:A1723
|
4.0
|
48.2
|
1.0
|
N7
|
A:A1722
|
4.0
|
48.2
|
1.0
|
OP2
|
A:C1725
|
4.1
|
51.6
|
1.0
|
OP2
|
A:A1723
|
4.1
|
48.2
|
1.0
|
OP2
|
A:A1722
|
4.1
|
48.2
|
1.0
|
OP1
|
A:C1726
|
4.2
|
51.7
|
1.0
|
O5'
|
A:C1725
|
4.2
|
51.6
|
1.0
|
O3'
|
A:C1725
|
4.2
|
51.6
|
1.0
|
C8
|
A:A1722
|
4.3
|
48.2
|
1.0
|
O3'
|
A:A1724
|
4.3
|
50.2
|
1.0
|
N9
|
A:A1723
|
4.3
|
48.2
|
1.0
|
O5'
|
A:C1726
|
4.4
|
51.7
|
1.0
|
C5'
|
A:C1725
|
4.4
|
51.6
|
1.0
|
C4
|
A:A1723
|
4.5
|
48.2
|
1.0
|
C5
|
A:C1726
|
4.6
|
51.7
|
1.0
|
C3'
|
A:C1725
|
4.7
|
51.6
|
1.0
|
C5
|
A:A1722
|
4.7
|
48.2
|
1.0
|
O5'
|
A:A1722
|
4.9
|
48.2
|
1.0
|
|
Magnesium binding site 4 out
of 61 in 7of0
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Magnesium Binding Sites List in 7of0
Magnesium binding site 4 out
of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
![](/pictures/MG/pdb/of/7of0-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/of/7of0-MG-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3304
b:50.1
occ:1.00
|
OP2
|
A:U1778
|
2.3
|
46.8
|
1.0
|
OP2
|
A:G1776
|
3.1
|
39.6
|
1.0
|
P
|
A:U1778
|
3.8
|
46.8
|
1.0
|
O
|
F:GLY148
|
4.0
|
44.3
|
1.0
|
OP2
|
A:A1777
|
4.2
|
52.9
|
1.0
|
P
|
A:G1776
|
4.4
|
39.6
|
1.0
|
C5'
|
A:U1778
|
4.5
|
46.8
|
1.0
|
OP1
|
A:U1778
|
4.5
|
46.8
|
1.0
|
C
|
F:GLY148
|
4.5
|
44.3
|
1.0
|
O5'
|
A:U1778
|
4.5
|
46.8
|
1.0
|
C5'
|
A:A1777
|
4.6
|
52.9
|
1.0
|
CA
|
F:GLY148
|
4.6
|
44.3
|
1.0
|
CG1
|
F:VAL120
|
4.7
|
45.3
|
1.0
|
O
|
F:GLY149
|
4.7
|
43.1
|
1.0
|
O5'
|
A:G1776
|
4.7
|
39.6
|
1.0
|
OP2
|
A:A1775
|
4.7
|
52.5
|
1.0
|
O3'
|
A:A1777
|
4.8
|
52.9
|
1.0
|
N7
|
A:G1776
|
4.8
|
39.6
|
1.0
|
OP2
|
A:A1779
|
4.9
|
45.9
|
1.0
|
C8
|
A:G1776
|
4.9
|
39.6
|
1.0
|
|
Magnesium binding site 5 out
of 61 in 7of0
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Magnesium Binding Sites List in 7of0
Magnesium binding site 5 out
of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
![](/pictures/MG/pdb/of/7of0-MG-sphere_05.jpg) Mono view
![](/pictures/MG/pdb/of/7of0-MG-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3305
b:52.1
occ:1.00
|
OP2
|
A:A1815
|
2.1
|
47.7
|
1.0
|
OP1
|
A:A1814
|
2.1
|
53.9
|
1.0
|
P
|
A:A1815
|
3.5
|
47.7
|
1.0
|
P
|
A:A1814
|
3.5
|
53.9
|
1.0
|
O6
|
A:G1816
|
3.6
|
46.2
|
1.0
|
N7
|
A:G1816
|
3.8
|
46.2
|
1.0
|
O5'
|
A:A1814
|
4.2
|
53.9
|
1.0
|
OP1
|
A:A1815
|
4.2
|
47.7
|
1.0
|
O5'
|
A:A1815
|
4.2
|
47.7
|
1.0
|
OP2
|
A:A1814
|
4.3
|
53.9
|
1.0
|
N4
|
A:C1817
|
4.3
|
47.8
|
1.0
|
C6
|
A:G1816
|
4.4
|
46.2
|
1.0
|
N7
|
A:A1815
|
4.4
|
47.7
|
1.0
|
C5
|
A:G1816
|
4.5
|
46.2
|
1.0
|
O3'
|
A:A1814
|
4.5
|
53.9
|
1.0
|
O3'
|
A:C1813
|
4.6
|
70.8
|
1.0
|
C3'
|
A:A1814
|
4.6
|
53.9
|
1.0
|
C8
|
A:A1815
|
4.7
|
47.7
|
1.0
|
C5'
|
A:A1814
|
4.7
|
53.9
|
1.0
|
OP2
|
A:C1813
|
4.9
|
70.8
|
1.0
|
C8
|
A:G1816
|
5.0
|
46.2
|
1.0
|
|
Magnesium binding site 6 out
of 61 in 7of0
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Magnesium Binding Sites List in 7of0
Magnesium binding site 6 out
of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
![](/pictures/MG/pdb/of/7of0-MG-sphere_06.jpg) Mono view
![](/pictures/MG/pdb/of/7of0-MG-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3306
b:45.1
occ:1.00
|
OP1
|
A:A1779
|
2.0
|
45.9
|
1.0
|
O6
|
A:G1776
|
2.1
|
39.6
|
1.0
|
C6
|
A:G1776
|
3.2
|
39.6
|
1.0
|
P
|
A:A1779
|
3.4
|
45.9
|
1.0
|
C5
|
A:G1776
|
3.9
|
39.6
|
1.0
|
N7
|
A:G1776
|
4.0
|
39.6
|
1.0
|
O5'
|
A:A1779
|
4.0
|
45.9
|
1.0
|
OP2
|
A:A1779
|
4.2
|
45.9
|
1.0
|
N7
|
A:A1775
|
4.2
|
52.5
|
1.0
|
C5'
|
A:A1779
|
4.3
|
45.9
|
1.0
|
N1
|
A:G1776
|
4.3
|
39.6
|
1.0
|
O3'
|
A:U1778
|
4.4
|
46.8
|
1.0
|
OP2
|
A:A1775
|
4.4
|
52.5
|
1.0
|
N6
|
A:A1775
|
4.7
|
52.5
|
1.0
|
OP1
|
A:A1795
|
4.9
|
50.1
|
1.0
|
C5'
|
A:U1774
|
5.0
|
48.4
|
1.0
|
C5
|
A:A1775
|
5.0
|
52.5
|
1.0
|
|
Magnesium binding site 7 out
of 61 in 7of0
Go back to
Magnesium Binding Sites List in 7of0
Magnesium binding site 7 out
of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
![](/pictures/MG/pdb/of/7of0-MG-sphere_07.jpg) Mono view
![](/pictures/MG/pdb/of/7of0-MG-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3307
b:45.3
occ:1.00
|
OP2
|
A:G1918
|
2.0
|
46.8
|
1.0
|
P
|
A:G1918
|
3.3
|
46.8
|
1.0
|
O3'
|
A:A1917
|
3.7
|
46.4
|
1.0
|
OP2
|
A:C1919
|
3.8
|
48.4
|
1.0
|
O5'
|
A:G1918
|
4.1
|
46.8
|
1.0
|
O6
|
A:G1981
|
4.2
|
50.8
|
1.0
|
O4
|
A:U1920
|
4.2
|
48.7
|
1.0
|
O6
|
A:G1982
|
4.3
|
49.6
|
1.0
|
OP1
|
A:G1918
|
4.5
|
46.8
|
1.0
|
N4
|
A:C1922
|
4.8
|
51.3
|
1.0
|
|
Magnesium binding site 8 out
of 61 in 7of0
Go back to
Magnesium Binding Sites List in 7of0
Magnesium binding site 8 out
of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
![](/pictures/MG/pdb/of/7of0-MG-sphere_08.jpg) Mono view
![](/pictures/MG/pdb/of/7of0-MG-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3308
b:57.7
occ:1.00
|
OP2
|
A:U1950
|
1.9
|
61.0
|
1.0
|
OP1
|
A:A2503
|
1.9
|
61.0
|
1.0
|
OP2
|
A:A2504
|
2.1
|
57.9
|
1.0
|
P
|
A:U1950
|
3.1
|
61.0
|
1.0
|
P
|
A:A2504
|
3.2
|
57.9
|
1.0
|
P
|
A:A2503
|
3.4
|
61.0
|
1.0
|
OP1
|
A:A2504
|
3.5
|
57.9
|
1.0
|
OP1
|
A:U1950
|
3.6
|
61.0
|
1.0
|
O5'
|
A:U1950
|
4.0
|
61.0
|
1.0
|
OP2
|
A:A2503
|
4.1
|
61.0
|
1.0
|
O3'
|
A:A2503
|
4.2
|
61.0
|
1.0
|
O5'
|
A:A2503
|
4.2
|
61.0
|
1.0
|
O3'
|
A:C2502
|
4.3
|
64.0
|
1.0
|
O3'
|
A:G1949
|
4.3
|
59.1
|
1.0
|
O5'
|
A:A2504
|
4.4
|
57.9
|
1.0
|
C5'
|
A:A2503
|
4.4
|
61.0
|
1.0
|
OP2
|
A:C1951
|
4.4
|
61.0
|
1.0
|
C3'
|
A:A2503
|
4.5
|
61.0
|
1.0
|
C3'
|
A:G1949
|
4.7
|
59.1
|
1.0
|
C5'
|
A:U1950
|
4.7
|
61.0
|
1.0
|
|
Magnesium binding site 9 out
of 61 in 7of0
Go back to
Magnesium Binding Sites List in 7of0
Magnesium binding site 9 out
of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
![](/pictures/MG/pdb/of/7of0-MG-sphere_09.jpg) Mono view
![](/pictures/MG/pdb/of/7of0-MG-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3309
b:48.4
occ:1.00
|
OP2
|
A:G2011
|
2.0
|
46.5
|
1.0
|
P
|
A:G2011
|
3.3
|
46.5
|
1.0
|
O3'
|
A:U2010
|
3.6
|
49.7
|
1.0
|
OP2
|
A:G2009
|
4.0
|
45.0
|
1.0
|
OP1
|
A:G2011
|
4.2
|
46.5
|
1.0
|
O
|
F:GLY122
|
4.2
|
47.5
|
1.0
|
O
|
F:ALA118
|
4.3
|
45.6
|
1.0
|
OP1
|
A:G2008
|
4.3
|
49.7
|
1.0
|
O5'
|
A:G2011
|
4.4
|
46.5
|
1.0
|
O
|
F:GLY123
|
4.4
|
48.8
|
1.0
|
NZ
|
i:LYS112
|
4.5
|
46.2
|
1.0
|
C5'
|
A:G2011
|
4.6
|
46.5
|
1.0
|
O2'
|
A:U2010
|
4.6
|
49.7
|
1.0
|
C3'
|
A:U2010
|
4.7
|
49.7
|
1.0
|
CA
|
F:GLY124
|
4.8
|
50.1
|
1.0
|
C
|
F:GLY123
|
4.9
|
48.8
|
1.0
|
CA
|
F:ALA118
|
4.9
|
45.6
|
1.0
|
O
|
F:ARG117
|
5.0
|
45.7
|
1.0
|
|
Magnesium binding site 10 out
of 61 in 7of0
Go back to
Magnesium Binding Sites List in 7of0
Magnesium binding site 10 out
of 61 in the Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1).
![](/pictures/MG/pdb/of/7of0-MG-sphere_10.jpg) Mono view
![](/pictures/MG/pdb/of/7of0-MG-sphere_10_stereo.jpg) Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Structure of A Human Mitochondrial Ribosome Large Subunit Assembly Intermediate in Complex with MTERF4-NSUN4 (DATASET1). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3310
b:62.4
occ:1.00
|
OP1
|
A:A3076
|
2.0
|
67.8
|
1.0
|
OP2
|
A:A1993
|
2.2
|
57.1
|
1.0
|
OP2
|
A:A1994
|
2.3
|
65.0
|
1.0
|
P
|
A:A1993
|
3.3
|
57.1
|
1.0
|
P
|
A:A3076
|
3.4
|
67.8
|
1.0
|
O3'
|
A:C1992
|
3.5
|
57.8
|
1.0
|
P
|
A:A1994
|
3.7
|
65.0
|
1.0
|
O5'
|
A:A1993
|
3.9
|
57.1
|
1.0
|
O3'
|
A:G3075
|
4.1
|
66.0
|
1.0
|
O5'
|
A:A3076
|
4.2
|
67.8
|
1.0
|
C5'
|
A:A1993
|
4.4
|
57.1
|
1.0
|
OP2
|
A:A3076
|
4.4
|
67.8
|
1.0
|
OP1
|
A:A1994
|
4.4
|
65.0
|
1.0
|
C5'
|
A:A3076
|
4.4
|
67.8
|
1.0
|
O3'
|
A:A1993
|
4.5
|
57.1
|
1.0
|
OP1
|
A:A1993
|
4.6
|
57.1
|
1.0
|
O5'
|
A:A1994
|
4.8
|
65.0
|
1.0
|
C3'
|
A:A1993
|
4.8
|
57.1
|
1.0
|
C3'
|
A:C1992
|
4.9
|
57.8
|
1.0
|
O2'
|
A:C1992
|
4.9
|
57.8
|
1.0
|
|
Reference:
H.S.Hillen,
E.Lavdovskaia,
F.Nadler,
E.Hanitsch,
A.Linden,
K.E.Bohnsack,
H.Urlaub,
R.Richter-Dennerlein.
Structural Basis of Gtpase-Mediated Mitochondrial Ribosome Biogenesis and Recycling Nat Commun 2021.
ISSN: ESSN 2041-1723
Page generated: Mon Jul 12 14:52:56 2021
|