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Magnesium in PDB 1i94: Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3

Protein crystallography data

The structure of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3, PDB code: 1i94 was solved by M.Pioletti, F.Schluenzen, J.Harms, R.Zarivach, M.Gluehmann, H.Avila, H.Bartels, C.Jacobi, T.Hartsch, A.Yonath, F.Franceschi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 3.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 406.300, 406.300, 173.100, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.5

Other elements in 1i94:

The structure of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 also contains other interesting chemical elements:

Tungsten (W) 252 atoms
Zinc (Zn) 2 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 - 75;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 (pdb code 1i94). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 75 binding sites of Magnesium where determined in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3, PDB code: 1i94:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 75 in 1i94

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Magnesium binding site 1 out of 75 in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1

b:57.7
occ:1.00
C E:LYS121 2.1 45.6 1.0
N E:GLU122 2.2 53.4 1.0
CA E:LYS121 2.2 45.6 1.0
O E:THR120 2.3 34.4 1.0
N E:LYS121 2.4 45.6 1.0
C E:THR120 2.4 34.4 1.0
O E:LYS121 3.0 45.6 1.0
CA E:GLU122 3.3 53.4 1.0
CB E:GLU122 3.4 53.4 1.0
CA E:THR120 3.7 34.4 1.0
CB E:LYS121 3.8 45.6 1.0
CB E:THR120 3.8 34.4 1.0
O E:VAL90 4.4 30.0 1.0
C E:GLU122 4.5 53.4 1.0
O2' A:G7 4.5 40.4 1.0
OP1 A:G9 4.5 33.9 1.0
O E:GLU122 4.6 53.4 1.0
N E:THR120 4.8 34.4 1.0
OP2 A:G9 4.8 33.9 1.0

Magnesium binding site 2 out of 75 in 1i94

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Magnesium binding site 2 out of 75 in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1516

b:57.7
occ:1.00
OP2 A:U14 4.0 34.6 1.0
OP1 A:U13 4.2 53.6 1.0
OP2 A:A16 4.6 39.6 1.0
C5 A:U14 4.6 34.6 1.0
OP1 A:A16 4.6 39.6 1.0
OP2 A:G15 4.9 34.2 1.0

Magnesium binding site 3 out of 75 in 1i94

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Magnesium binding site 3 out of 75 in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1517

b:57.7
occ:1.00
OP1 A:G21 2.4 31.1 1.0
N6 A:A546 3.7 24.2 1.0
P A:G21 3.7 31.1 1.0
OP2 A:G21 4.0 31.1 1.0
N3 A:G550 4.1 34.9 1.0
N2 A:G550 4.1 34.9 1.0
N1 A:A556 4.2 51.2 1.0
O2' A:G550 4.4 34.9 1.0
C2 A:G550 4.6 34.9 1.0
N6 A:A556 4.6 51.2 1.0
O3' A:U20 4.7 29.3 1.0
O5' A:G21 4.8 31.1 1.0
C6 A:A546 4.8 24.2 1.0
O2' A:G551 4.9 46.8 1.0
C6 A:A556 4.9 51.2 1.0

Magnesium binding site 4 out of 75 in 1i94

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Magnesium binding site 4 out of 75 in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 within 5.0Å range:

Magnesium binding site 5 out of 75 in 1i94

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Magnesium binding site 5 out of 75 in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg136

b:57.7
occ:1.00
O L:LYS124 2.7 75.5 1.0
C L:LYS124 2.8 75.5 1.0
OP1 A:U37 2.9 46.4 1.0
N L:LYS124 2.9 75.5 1.0
CB L:LYS124 2.9 75.5 1.0
CA L:LYS124 2.9 75.5 1.0
O L:PRO125 3.3 94.1 1.0
N L:PRO125 3.7 94.1 1.0
C L:LYS123 3.7 76.1 1.0
C L:PRO125 4.2 94.1 1.0
P A:U37 4.2 46.4 1.0
C5' A:U37 4.2 46.4 1.0
O L:LYS123 4.4 76.1 1.0
CA L:PRO125 4.4 94.1 1.0
O3' A:C36 4.5 55.2 1.0
CA L:LYS123 4.5 76.1 1.0
O5' A:U37 4.7 46.4 1.0
CB L:LYS123 4.8 76.1 1.0

Magnesium binding site 6 out of 75 in 1i94

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Magnesium binding site 6 out of 75 in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1519

b:57.7
occ:1.00
O4 A:U45 3.8 39.3 1.0
N4 A:C390 4.5 52.4 1.0
O6 A:G391 4.7 59.8 1.0
N7 A:G44 4.7 55.2 1.0
O6 A:G44 4.7 55.2 1.0
C4 A:U45 4.9 39.3 1.0

Magnesium binding site 7 out of 75 in 1i94

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Magnesium binding site 7 out of 75 in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1520

b:57.7
occ:1.00
O6 A:G64 3.6 75.6 1.0
N7 A:A94 3.9 82.9 1.0
C6 A:G64 4.3 75.6 1.0
N6 A:A94 4.3 82.9 1.0
O6 A:G95 4.4 71.8 1.0
N7 A:G95 4.5 71.8 1.0
C5 A:A94 4.6 82.9 1.0
C8 A:A94 4.7 82.9 1.0
C6 A:A94 4.8 82.9 1.0
N1 A:G64 4.9 75.6 1.0
C5 A:G64 5.0 75.6 1.0

Magnesium binding site 8 out of 75 in 1i94

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Magnesium binding site 8 out of 75 in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1521

b:57.7
occ:1.00
OP2 A:G104 1.9 54.6 1.0
P A:G104 3.2 54.6 1.0
OP1 A:C103 3.7 48.7 1.0
OP1 A:G104 3.9 54.6 1.0
O5' A:G104 3.9 54.6 1.0
O5' A:C103 4.2 48.7 1.0
P A:C103 4.3 48.7 1.0
O3' A:C103 4.3 48.7 1.0
OP2 A:C103 4.5 48.7 1.0
C3' A:C103 4.6 48.7 1.0
C5' A:C103 4.7 48.7 1.0
N7 A:G105 4.7 48.1 1.0
C8 A:G104 4.7 54.6 1.0
N7 A:G104 4.8 54.6 1.0

Magnesium binding site 9 out of 75 in 1i94

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Magnesium binding site 9 out of 75 in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1522

b:57.7
occ:1.00
O3' A:C71 2.5 0.6 1.0
C4' A:C71 3.0 0.6 1.0
C3' A:C71 3.2 0.6 1.0
O2' A:C71 3.5 0.6 1.0
OP1 A:C72 3.7 0.4 1.0
C5' A:C71 3.7 0.6 1.0
P A:C72 3.8 0.4 1.0
C2' A:C71 3.9 0.6 1.0
O4' A:C71 4.2 0.6 1.0
O5' A:C72 4.6 0.4 1.0
C5' A:C72 4.6 0.4 1.0
C1' A:C71 4.6 0.6 1.0
OP2 A:C72 4.9 0.4 1.0
O5' A:C71 5.0 0.6 1.0

Magnesium binding site 10 out of 75 in 1i94

Go back to Magnesium Binding Sites List in 1i94
Magnesium binding site 10 out of 75 in the Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structures of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1523

b:57.7
occ:1.00
O3' A:G78 2.5 88.5 1.0
C4' A:U79 2.6 0.2 1.0
O2' A:G78 2.6 88.5 1.0
O4' A:U79 2.9 0.2 1.0
C5' A:U79 2.9 0.2 1.0
C2' A:G78 3.0 88.5 1.0
O5' A:U79 3.0 0.2 1.0
C3' A:G78 3.2 88.5 1.0
P A:U79 3.2 0.2 1.0
OP1 A:U79 3.5 0.2 1.0
C3' A:U79 4.0 0.2 1.0
C1' A:U79 4.1 0.2 1.0
O2' A:U79 4.3 0.2 1.0
C4' A:G78 4.4 88.5 1.0
O3' A:U79 4.4 0.2 1.0
C2' A:U79 4.4 0.2 1.0
C1' A:G78 4.5 88.5 1.0
OP2 A:U79 4.6 0.2 1.0

Reference:

M.Pioletti, F.Schlunzen, J.Harms, R.Zarivach, M.Gluhmann, H.Avila, A.Bashan, H.Bartels, T.Auerbach, C.Jacobi, T.Hartsch, A.Yonath, F.Franceschi. Crystal Structures of Complexes of the Small Ribosomal Subunit with Tetracycline, Edeine and IF3. Embo J. V. 20 1829 2001.
ISSN: ISSN 0261-4189
PubMed: 11296217
DOI: 10.1093/EMBOJ/20.8.1829
Page generated: Mon Dec 14 06:02:34 2020

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