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Magnesium in PDB 1jj2: Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution

Protein crystallography data

The structure of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1jj2 was solved by D.J.Klein, T.M.Schmeing, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.660, 299.670, 573.770, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.2

Other elements in 1jj2:

The structure of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution also contains other interesting chemical elements:

Potassium (K) 2 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 86 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 117;

Binding sites:

The binding sites of Magnesium atom in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution (pdb code 1jj2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 117 binding sites of Magnesium where determined in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1jj2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 117 in 1jj2

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Magnesium binding site 1 out of 117 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8001

b:25.8
occ:1.00
 OP2 0:C2534 1.9 27.3 1.0
O 0:HOH7327 2.0 21.6 1.0
OP2 0:C2533 2.1 30.5 1.0
O 0:HOH8694 2.1 30.9 1.0
OP2 0:A2483 2.1 29.9 1.0
O 0:HOH3142 2.2 15.8 1.0
P 0:A2483 3.2 27.0 1.0
O3' 0:G2482 3.3 28.6 1.0
P 0:C2534 3.3 27.1 1.0
P 0:C2533 3.5 29.4 1.0
O3' 0:A2532 3.9 28.4 1.0
O2' 0:A2532 4.0 28.9 1.0
OP1 0:A2483 4.0 30.4 1.0
O 0:HOH9161 4.0 34.9 1.0
O 0:HOH3854 4.1 33.7 1.0
O3' 0:C2533 4.1 25.0 1.0
OP1 0:C2534 4.1 29.2 1.0
O2' 0:G2482 4.2 25.3 1.0
OP2 0:U2484 4.2 32.9 1.0
O5' 0:C2533 4.2 30.3 1.0
O5' 0:C2534 4.3 23.9 1.0
C3' 0:C2533 4.4 24.7 1.0
O5' 0:A2483 4.4 31.0 1.0
O 0:HOH7029 4.4 32.8 1.0
O 0:HOH5915 4.5 38.8 1.0
OP1 0:C2533 4.6 28.7 1.0
C3' 0:G2482 4.6 26.1 1.0
MG 0:MG8002 4.7 26.0 1.0
C5' 0:A2483 4.7 26.6 1.0
C5 0:C2534 4.8 28.9 1.0
C2' 0:G2482 4.9 23.9 1.0
C3' 0:A2532 4.9 27.4 1.0

Magnesium binding site 2 out of 117 in 1jj2

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Magnesium binding site 2 out of 117 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8002

b:26.0
occ:1.00
 OP1 0:A2483 1.9 30.4 1.0
O 0:HOH3854 1.9 33.7 1.0
O 0:HOH7305 2.1 20.8 1.0
O6 0:G627 2.1 26.5 1.0
OP1 0:C2534 2.2 29.2 1.0
O 0:HOH7306 2.2 24.7 1.0
P 0:A2483 3.1 27.0 1.0
C6 0:G627 3.3 26.1 1.0
P 0:C2534 3.4 27.1 1.0
OP2 0:A2483 3.5 29.9 1.0
O 0:HOH6646 3.8 39.6 1.0
O4 0:U626 3.8 25.2 1.0
OP2 0:C2534 3.9 27.3 1.0
N1 0:G627 3.9 25.4 1.0
O5' 0:A2483 4.0 31.0 1.0
O3' 0:C2533 4.1 25.0 1.0
O 0:HOH5414 4.3 28.0 1.0
O3' 0:G2482 4.3 28.6 1.0
O2' 0:U625 4.3 19.6 1.0
O 0:HOH8780 4.4 24.3 1.0
OP2 0:U2535 4.4 26.4 1.0
C5 0:U626 4.4 25.2 1.0
C4 0:U626 4.4 24.6 1.0
C5 0:G627 4.5 25.4 1.0
O 0:HOH3056 4.5 43.5 1.0
O5' 0:C2534 4.6 23.9 1.0
MG 0:MG8001 4.7 25.8 1.0
C3' 0:G2482 4.8 26.1 1.0
OP2 0:C2533 4.9 30.5 1.0
N7 0:G627 5.0 25.8 1.0
C5' 0:C2534 5.0 24.7 1.0

Magnesium binding site 3 out of 117 in 1jj2

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Magnesium binding site 3 out of 117 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8003

b:21.6
occ:1.00
 OP1 0:A2624 2.0 18.5 1.0
OP2 0:A876 2.1 20.0 1.0
O A:HOH8512 2.1 14.1 1.0
OP2 0:G877 2.1 19.4 1.0
O 0:HOH3193 2.2 21.5 1.0
O A:HOH8535 2.4 21.9 1.0
P 0:G877 3.4 19.3 1.0
P 0:A2624 3.4 21.2 1.0
P 0:A876 3.4 23.5 1.0
OP1 0:G877 3.8 19.9 1.0
O3' 0:G2623 4.0 17.2 1.0
O5' 0:A876 4.0 19.5 1.0
O3' 0:A875 4.0 20.7 1.0
O 0:HOH5818 4.1 29.7 1.0
O 0:HOH6706 4.1 32.3 1.0
OD1 A:ASN195 4.2 18.1 1.0
O3' 0:A876 4.2 19.6 1.0
C5' 0:A876 4.3 19.5 1.0
OP2 0:A2624 4.3 20.7 1.0
O A:ALA193 4.3 22.7 1.0
O A:HOH8624 4.3 28.9 1.0
O A:HOH8568 4.3 29.4 1.0
O 0:HOH8541 4.4 19.0 1.0
O5' 0:A2624 4.4 22.9 1.0
O5' 0:G877 4.6 19.8 1.0
C5' 0:A2624 4.6 23.3 1.0
OP1 0:A876 4.6 22.4 1.0
C3' 0:A876 4.7 21.2 1.0
O A:HOH8546 4.8 39.3 1.0
CG A:ASN195 4.9 17.4 1.0

Magnesium binding site 4 out of 117 in 1jj2

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Magnesium binding site 4 out of 117 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8004

b:21.9
occ:1.00
 O 0:HOH3309 1.9 12.7 1.0
OP1 0:A459 1.9 19.4 1.0
O 0:HOH8567 2.0 18.3 1.0
O 0:HOH9303 2.0 11.5 1.0
O 0:HOH7312 2.0 20.9 1.0
O6 0:G456 2.1 21.6 1.0
C6 0:G456 3.2 24.8 1.0
P 0:A459 3.2 23.2 1.0
O5' 0:A459 3.8 22.6 1.0
C5 0:G456 3.9 26.0 1.0
OP2 0:A459 3.9 21.5 1.0
N7 0:G456 4.0 23.3 1.0
C5' 0:A459 4.1 24.1 1.0
O 0:HOH5499 4.2 45.7 1.0
O 0:HOH3230 4.2 26.6 1.0
NZ C:LYS85 4.2 19.4 1.0
CE C:LYS85 4.3 19.6 1.0
O 0:HOH8853 4.3 20.0 1.0
N1 0:G456 4.3 25.4 1.0
O3' 0:G458 4.4 24.2 1.0
OP2 0:A455 4.4 24.2 1.0
OP1 0:A460 4.4 21.7 1.0
N7 0:A455 4.5 26.4 1.0
O 0:HOH3043 4.5 31.7 1.0
OP1 0:A477 4.6 22.3 1.0
O 0:HOH4938 4.7 25.5 1.0
CD C:LYS85 4.8 19.7 1.0
O 0:HOH7313 4.9 15.5 1.0
OP2 0:A477 5.0 19.7 1.0

Magnesium binding site 5 out of 117 in 1jj2

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Magnesium binding site 5 out of 117 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8005

b:24.4
occ:1.00
 OP1 0:U1838 1.9 22.8 1.0
O 0:HOH7328 2.0 11.9 1.0
O 0:HOH3139 2.0 15.6 1.0
OP1 0:A1836 2.0 21.7 1.0
O 0:HOH7329 2.1 23.6 1.0
OP2 0:A1839 2.1 17.4 1.0
P 0:U1838 3.4 21.1 1.0
P 0:A1836 3.5 21.3 1.0
P 0:A1839 3.6 20.6 1.0
O 0:HOH5036 3.9 29.2 1.0
O 0:HOH5095 4.0 27.9 1.0
OP2 0:U1838 4.1 21.4 1.0
O 0:HOH8528 4.1 15.2 1.0
O3' 0:U1838 4.2 21.6 1.0
O5' 0:A1836 4.2 26.6 1.0
C3' 0:G1837 4.2 24.2 1.0
O5' 0:U1838 4.2 21.9 1.0
OP2 0:A1836 4.3 23.1 1.0
O3' 0:G1837 4.3 21.4 1.0
C2' 0:U1835 4.3 22.5 1.0
O5' 0:A1839 4.3 19.8 1.0
O3' 0:U1835 4.4 22.7 1.0
O 0:HOH7403 4.4 25.2 1.0
O 0:HOH9032 4.4 28.4 1.0
O 0:HOH9157 4.4 22.7 1.0
C3' 0:U1838 4.4 19.8 1.0
C3' 0:U1835 4.5 21.2 1.0
OP2 0:G1837 4.5 23.8 1.0
C5' 0:U1838 4.5 19.4 1.0
OP1 0:A1839 4.6 24.5 1.0
O2' 0:U1835 4.7 24.4 1.0
N7 0:A1839 4.7 19.6 1.0
C8 0:A1839 4.8 21.0 1.0

Magnesium binding site 6 out of 117 in 1jj2

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Magnesium binding site 6 out of 117 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8006

b:27.1
occ:1.00
 OP2 0:C822 1.9 29.7 1.0
OP1 0:G854 1.9 25.8 1.0
O 0:HOH9335 1.9 23.1 1.0
OP2 0:U821 2.0 25.7 1.0
O 0:HOH3144 2.1 25.0 1.0
O 0:HOH3281 2.3 31.2 1.0
P 0:G854 3.2 27.9 1.0
P 0:C822 3.3 30.4 1.0
P 0:U821 3.4 25.5 1.0
OP2 0:G854 3.8 27.3 1.0
O5' 0:G854 3.8 24.5 1.0
NA 0:NA8327 3.9 38.7 1.0
O5' 0:U821 3.9 32.0 1.0
OP1 0:G856 4.0 28.0 1.0
O3' 0:U821 4.0 29.6 1.0
O 0:HOH9728 4.0 30.9 1.0
C3' 0:U821 4.1 29.4 1.0
OP1 0:C822 4.1 29.4 1.0
OP1 0:U855 4.2 27.7 1.0
C5' 0:G854 4.2 24.1 1.0
O3' 0:G820 4.3 28.4 1.0
O5' 0:C822 4.4 30.9 1.0
O 0:HOH4528 4.4 27.9 1.0
O3' 0:C853 4.4 26.8 1.0
OP1 0:U821 4.5 26.0 1.0
O 0:HOH9255 4.8 39.6 1.0
O 0:HOH8828 4.9 35.9 1.0
C5 0:C822 5.0 28.1 1.0

Magnesium binding site 7 out of 117 in 1jj2

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Magnesium binding site 7 out of 117 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8007

b:21.5
occ:1.00
 OP2 0:U832 2.0 24.0 1.0
OP1 0:A1839 2.0 24.5 1.0
O 0:HOH9884 2.1 23.6 1.0
O 0:HOH7317 2.2 12.3 1.0
O 0:HOH8528 2.2 15.2 1.0
OP2 0:A1840 2.2 18.9 1.0
P 0:A1839 3.3 20.6 1.0
P 0:U832 3.4 24.3 1.0
P 0:A1840 3.5 22.4 1.0
O 0:HOH5893 3.7 45.4 1.0
OP2 0:A1839 3.7 17.4 1.0
O 0:HOH8621 3.8 17.6 1.0
OP1 0:A1840 3.9 18.3 1.0
O 0:HOH9157 3.9 22.7 1.0
O5' 0:U832 4.1 24.1 1.0
OP1 0:U832 4.1 23.6 1.0
O3' 0:U1838 4.2 21.6 1.0
O3' 0:A1839 4.3 21.7 1.0
O 0:HOH7403 4.4 25.2 1.0
O5' 0:A1839 4.4 19.8 1.0
O 0:HOH7434 4.5 38.5 1.0
O3' 0:U831 4.5 23.3 1.0
C3' 0:A1839 4.6 20.3 1.0
O5' 0:A1840 4.7 20.3 1.0
C5' 0:A1839 4.7 20.1 1.0
C5' 0:U832 4.8 24.0 1.0
O 0:HOH7329 4.9 23.6 1.0
OP2 0:G833 4.9 24.3 1.0
C3' 0:U831 4.9 22.8 1.0

Magnesium binding site 8 out of 117 in 1jj2

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Magnesium binding site 8 out of 117 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8008

b:22.8
occ:1.00
 O 0:HOH7321 2.0 17.3 1.0
OP1 0:C2464 2.0 23.7 1.0
O 0:HOH7404 2.0 27.0 1.0
O 0:HOH3156 2.1 18.9 1.0
OP1 0:U919 2.2 19.9 1.0
OP1 0:A2465 2.2 25.5 1.0
P 0:U919 3.2 22.1 1.0
P 0:C2464 3.3 23.9 1.0
P 0:A2465 3.6 26.6 1.0
OP2 0:U919 3.6 24.1 1.0
O5' 0:U919 3.8 23.1 1.0
O5' 0:C2464 3.9 27.3 1.0
O 0:HOH9874 4.0 21.7 1.0
C5' 0:C2464 4.0 28.1 1.0
O 0:HOH8968 4.1 29.8 1.0
OP2 0:C2464 4.1 29.7 1.0
O 0:HOH5427 4.2 35.0 1.0
O5' 0:A2465 4.2 27.5 1.0
OP2 0:A2465 4.2 28.1 1.0
C5' 0:U919 4.3 22.3 1.0
O 0:HOH9066 4.4 30.0 1.0
O3' 0:A2463 4.4 27.4 1.0
OP1 0:G2466 4.5 26.8 1.0
O3' 0:G918 4.5 22.9 1.0
O 0:HOH9447 4.6 36.4 1.0
C3' 0:A2465 4.7 24.9 1.0
O3' 0:C2464 4.7 26.6 1.0
C5' 0:A2465 4.9 25.4 1.0
C2' 0:A2465 5.0 26.0 1.0
C3' 0:C2464 5.0 27.3 1.0

Magnesium binding site 9 out of 117 in 1jj2

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Magnesium binding site 9 out of 117 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8009

b:24.8
occ:1.00
 O 0:HOH7323 1.9 21.9 1.0
OP1 0:G2611 1.9 23.3 1.0
O 0:HOH3267 2.0 17.5 1.0
OP1 0:A2612 2.0 20.3 1.0
O 0:HOH6979 2.0 22.5 1.0
O 0:HOH7322 2.3 20.5 1.0
P 0:G2611 3.2 22.1 1.0
NA 0:NA8358 3.3 74.7 1.0
O3' 0:U2610 3.4 23.7 1.0
P 0:A2612 3.4 21.0 1.0
O 0:HOH8854 3.7 21.5 1.0
OP2 0:G2093 3.9 24.8 1.0
O5' 0:G2611 4.1 24.1 1.0
OP2 0:G2094 4.1 20.5 1.0
C5' 0:G2611 4.1 21.8 1.0
OP2 0:A2612 4.1 24.0 1.0
O 0:HOH8987 4.1 31.7 1.0
OP1 0:G2094 4.2 20.4 1.0
O3' 0:G2611 4.3 21.3 1.0
O 0:HOH8825 4.3 18.6 1.0
OP2 0:G2611 4.4 22.8 1.0
O5' 0:A2612 4.4 23.8 1.0
C3' 0:G2611 4.6 19.7 1.0
P 0:G2094 4.6 21.0 1.0
C3' 0:U2610 4.6 24.0 1.0
C4' 0:U2610 4.8 24.5 1.0
O 0:HOH7338 4.8 29.4 1.0
C4' 0:G2611 4.9 20.2 1.0

Magnesium binding site 10 out of 117 in 1jj2

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Magnesium binding site 10 out of 117 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg8010

b:24.3
occ:1.00
 OP1 0:G836 2.0 19.4 1.0
O 0:HOH3365 2.0 24.7 1.0
O B:HOH8526 2.0 17.9 1.0
OP1 0:U2615 2.1 17.4 1.0
OE1 B:GLN230 2.1 23.1 1.0
O 0:HOH8881 2.2 16.4 1.0
CD B:GLN230 3.3 22.3 1.0
P 0:G836 3.4 23.1 1.0
P 0:U2615 3.5 19.5 1.0
CG B:GLN230 3.9 19.7 1.0
CB B:GLN230 4.0 20.0 1.0
O 0:HOH4573 4.0 30.3 1.0
C5' 0:G836 4.1 24.0 1.0
O5' 0:G836 4.2 23.8 1.0
O 0:HOH8725 4.3 20.9 1.0
OP2 0:G836 4.3 21.8 1.0
OP2 0:U2615 4.3 22.7 1.0
O3' 0:U835 4.4 21.4 1.0
O 0:HOH6369 4.4 43.0 1.0
O3' 0:C2614 4.4 20.9 1.0
NE2 B:GLN230 4.4 20.1 1.0
O5' 0:U2615 4.4 20.9 1.0
C3' 0:U835 4.4 22.1 1.0
CA B:GLN230 4.4 21.0 1.0
OP2 0:G2616 4.6 23.0 1.0
O 0:HOH3519 4.6 37.0 1.0
O B:GLN230 4.6 21.3 1.0
C5' 0:U835 4.7 22.8 1.0
C5' 0:U2615 4.8 17.9 1.0
N2 0:G2616 4.8 26.0 1.0

Reference:

D.J.Klein, T.M.Schmeing, P.B.Moore, T.A.Steitz. The Kink-Turn: A New Rna Secondary Structure Motif. Embo J. V. 20 4214 2001.
ISSN: ISSN 0261-4189
PubMed: 11483524
DOI: 10.1093/EMBOJ/20.15.4214
Page generated: Tue Aug 13 06:37:13 2024

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