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Magnesium in PDB 1i96: Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain)

Protein crystallography data

The structure of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain), PDB code: 1i96 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 / 4.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 407.500, 407.500, 174.800, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26.4

Other elements in 1i96:

The structure of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) also contains other interesting chemical elements:

Tungsten (W) 216 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 Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) (pdb code 1i96). 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 Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain), PDB code: 1i96:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 75 in 1i96

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Magnesium binding site 1 out of 75 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain)


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 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1

b:66.3
occ:1.00
CA E:LYS121 2.2 57.6 1.0
CA E:THR120 3.7 44.1 1.0
CA E:GLU122 4.2 62.2 1.0
OP1 A:G9 4.5 42.5 1.0
OP2 A:G9 4.6 42.5 1.0
O2' A:G7 4.9 49.0 1.0

Magnesium binding site 2 out of 75 in 1i96

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Magnesium binding site 2 out of 75 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain)


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 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1516

b:66.3
occ:1.00
OP2 A:U14 4.0 43.1 1.0
OP1 A:U13 4.3 62.2 1.0
OP1 A:A16 4.4 48.2 1.0
OP2 A:A16 4.4 48.2 1.0
OP2 A:G15 4.7 42.7 1.0
C5 A:U14 4.8 43.1 1.0
P A:A16 4.9 48.2 1.0

Magnesium binding site 3 out of 75 in 1i96

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Magnesium binding site 3 out of 75 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain)


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 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1517

b:66.3
occ:1.00
OP1 A:G21 2.1 39.6 1.0
P A:G21 3.4 39.6 1.0
OP2 A:G21 3.8 39.6 1.0
N1 A:A556 4.0 59.7 1.0
O2' A:G550 4.1 43.5 1.0
O3' A:U20 4.4 37.9 1.0
N6 A:A556 4.4 59.7 1.0
O5' A:G21 4.4 39.6 1.0
N6 A:A546 4.4 32.7 1.0
N3 A:G550 4.6 43.5 1.0
C6 A:A556 4.7 59.7 1.0
N2 A:G550 4.8 43.5 1.0
C5' A:G21 4.9 39.6 1.0
C2 A:A556 5.0 59.7 1.0

Magnesium binding site 4 out of 75 in 1i96

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Magnesium binding site 4 out of 75 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain)


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 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1518

b:66.3
occ:1.00
OP1 A:U30 4.9 52.9 1.0

Magnesium binding site 5 out of 75 in 1i96

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Magnesium binding site 5 out of 75 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain)


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 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1519

b:66.3
occ:1.00
CA L:LYS124 2.7 91.2 1.0
OP1 A:U37 3.3 55.0 1.0
CA L:PRO125 4.4 0.3 1.0
C5' A:U37 4.4 55.0 1.0
P A:U37 4.5 55.0 1.0
CA L:LYS123 4.5 84.8 1.0
O3' A:C36 4.5 63.8 1.0

Magnesium binding site 6 out of 75 in 1i96

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Magnesium binding site 6 out of 75 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain)


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 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1520

b:66.3
occ:1.00
O4 A:U45 3.4 47.9 1.0
O6 A:G391 4.5 68.4 1.0
O6 A:G44 4.5 63.8 1.0
C4 A:U45 4.6 47.9 1.0
N7 A:G44 4.7 63.8 1.0
N4 A:C390 4.8 61.0 1.0

Magnesium binding site 7 out of 75 in 1i96

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Magnesium binding site 7 out of 75 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain)


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 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1521

b:66.3
occ:1.00
O6 A:G64 3.9 84.2 1.0
N7 A:A94 4.1 91.4 1.0
N6 A:A94 4.6 91.4 1.0
C6 A:G64 4.6 84.2 1.0
O6 A:G95 4.7 80.3 1.0
C5 A:A94 4.8 91.4 1.0
N7 A:G95 4.9 80.3 1.0
C8 A:A94 4.9 91.4 1.0

Magnesium binding site 8 out of 75 in 1i96

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Magnesium binding site 8 out of 75 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain)


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 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1522

b:66.3
occ:1.00
OP2 A:G104 2.2 63.2 1.0
P A:G104 3.4 63.2 1.0
O5' A:G104 3.9 63.2 1.0
OP1 A:G104 3.9 63.2 1.0
OP1 A:C103 4.2 57.2 1.0
O5' A:C103 4.5 57.2 1.0
O3' A:C103 4.6 57.2 1.0
N7 A:G105 4.8 56.7 1.0
C8 A:G104 4.9 63.2 1.0
P A:C103 4.9 57.2 1.0
C3' A:C103 4.9 57.2 1.0
OP2 A:G105 5.0 56.7 1.0
C5' A:C103 5.0 57.2 1.0

Magnesium binding site 9 out of 75 in 1i96

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Magnesium binding site 9 out of 75 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain)


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 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1523

b:66.3
occ:1.00
O3' A:C71 2.6 0.2 1.0
O2' A:C71 3.0 0.2 1.0
C4' A:C71 3.1 0.2 1.0
C3' A:C71 3.2 0.2 1.0
C2' A:C71 3.6 0.2 1.0
OP1 A:C72 3.7 0.0 1.0
P A:C72 3.7 0.0 1.0
C5' A:C71 4.0 0.2 1.0
O4' A:C71 4.1 0.2 1.0
O5' A:C72 4.3 0.0 1.0
C1' A:C71 4.4 0.2 1.0
C5' A:C72 4.5 0.0 1.0
OP2 A:C72 4.9 0.0 1.0

Magnesium binding site 10 out of 75 in 1i96

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Magnesium binding site 10 out of 75 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with the Translation Initiation Factor IF3 (C-Terminal Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1524

b:66.3
occ:1.00
O3' A:G78 2.2 97.1 1.0
O2' A:G78 2.3 97.1 1.0
C2' A:G78 2.7 97.1 1.0
C4' A:U79 2.8 0.8 1.0
C5' A:U79 2.8 0.8 1.0
C3' A:G78 2.9 97.1 1.0
O4' A:U79 2.9 0.8 1.0
O5' A:U79 3.0 0.8 1.0
P A:U79 3.1 0.8 1.0
OP1 A:U79 3.5 0.8 1.0
C4' A:G78 4.1 97.1 1.0
C1' A:G78 4.2 97.1 1.0
C3' A:U79 4.3 0.8 1.0
C1' A:U79 4.3 0.8 1.0
OP2 A:U79 4.4 0.8 1.0
O4' A:G78 4.8 97.1 1.0
C2' A:U79 4.8 0.8 1.0
O3' A:U79 4.8 0.8 1.0
O2' A:U79 4.9 0.8 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 06:02:35 2020

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