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Magnesium in PDB 1hnz: Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B

Protein crystallography data

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B, PDB code: 1hnz was solved by D.E.Brodersen, W.M.Clemons Jr., A.P.Carter, R.Morgan-Warren, B.T.Wimberly, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.063, 402.063, 175.263, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 26.1

Other elements in 1hnz:

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B also contains other interesting chemical elements:

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 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 96;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B (pdb code 1hnz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 96 binding sites of Magnesium where determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B, PDB code: 1hnz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 96 in 1hnz

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Magnesium binding site 1 out of 96 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1545

b:58.2
occ:0.76
O2 A:C519 2.6 82.7 1.0
O4' A:A520 2.9 79.5 1.0
O2' A:C519 3.0 81.9 1.0
C4' A:A520 3.7 79.5 1.0
C2' A:C519 3.8 81.9 1.0
C2 A:C519 3.8 82.7 1.0
C1' A:A520 3.8 79.5 1.0
C5' A:A520 4.2 79.5 1.0
C1' A:C519 4.2 81.9 1.0
N1 A:C519 4.5 82.7 1.0
N9 A:A520 4.6 81.8 1.0
N3 A:C519 4.7 82.7 1.0
OP1 A:G517 4.9 98.5 1.0
O2' A:U516 4.9 85.9 1.0
C2' A:A520 4.9 79.5 1.0

Magnesium binding site 2 out of 96 in 1hnz

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Magnesium binding site 2 out of 96 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1546

b:58.2
occ:1.28
OP2 A:G945 2.2 78.8 1.0
OP1 A:G944 2.3 73.3 1.0
P A:G944 3.3 64.6 1.0
P A:G945 3.5 66.1 1.0
OP2 A:G944 3.7 73.3 1.0
O5' A:G944 3.7 64.6 1.0
OP1 A:G945 4.1 78.8 1.0
N7 A:A946 4.2 64.4 1.0
C5' A:G944 4.3 64.6 1.0
O6 A:G947 4.3 74.1 1.0
O5' A:G945 4.3 66.1 1.0
OP2 A:A946 4.5 64.4 1.0
O3' A:G944 4.6 64.6 1.0
O3' A:U943 4.7 61.9 1.0
C8 A:A946 4.8 64.4 1.0
C3' A:G944 4.8 64.6 1.0
O6 A:G1233 5.0 92.2 1.0
C5' A:G945 5.0 66.1 1.0

Magnesium binding site 3 out of 96 in 1hnz

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Magnesium binding site 3 out of 96 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1547

b:58.2
occ:1.33
OP1 A:G1224 2.1 84.5 1.0
P A:G1224 3.4 83.3 1.0
OP2 A:G1224 3.8 84.5 1.0
O2' A:C1223 3.9 88.2 1.0
N6 A:A977 4.2 0.7 1.0
C2' A:C1223 4.3 88.2 1.0
N7 A:A977 4.3 0.7 1.0
OP1 A:G951 4.3 75.6 1.0
O3' A:C1223 4.3 88.2 1.0
O5' A:G1224 4.4 83.3 1.0
OP2 A:U952 4.6 82.1 1.0
C3' A:C1223 4.8 88.2 1.0
C5 A:A977 5.0 0.7 1.0
C6 A:A977 5.0 0.7 1.0

Magnesium binding site 4 out of 96 in 1hnz

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Magnesium binding site 4 out of 96 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1548

b:58.2
occ:1.07
O4 A:U12 2.8 65.7 1.0
O6 A:G11 3.0 67.9 1.0
O6 A:G22 3.0 62.3 1.0
O6 A:G21 3.3 80.3 1.0
N4 A:C23 3.5 62.5 1.0
C6 A:G21 3.7 80.3 1.0
C4 A:U12 3.8 65.7 1.0
N3 A:U12 4.0 65.7 1.0
C6 A:G22 4.1 62.3 1.0
C6 A:G11 4.1 67.9 1.0
N1 A:G21 4.1 80.3 1.0
N7 A:G22 4.3 62.3 1.0
C5 A:G21 4.5 80.3 1.0
C4 A:C23 4.5 62.5 1.0
C5 A:G22 4.6 62.3 1.0
N3 A:C23 4.9 62.5 1.0
N1 A:G11 4.9 67.9 1.0
C5 A:G11 5.0 67.9 1.0

Magnesium binding site 5 out of 96 in 1hnz

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Magnesium binding site 5 out of 96 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1549

b:58.2
occ:0.81
O6 A:G742 3.0 75.4 1.0
O6 A:G741 3.2 72.1 1.0
O6 A:G664 3.4 71.5 1.0
N7 A:G741 3.8 72.1 1.0
C6 A:G742 3.9 75.4 1.0
C6 A:G741 4.0 72.1 1.0
N7 A:G742 4.2 75.4 1.0
C5 A:G741 4.2 72.1 1.0
C5 A:G742 4.3 75.4 1.0
C6 A:G664 4.4 71.5 1.0
N6 A:A663 4.6 74.2 1.0
N1 A:G664 4.7 71.5 1.0
C8 A:G741 5.0 72.1 1.0

Magnesium binding site 6 out of 96 in 1hnz

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Magnesium binding site 6 out of 96 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1550

b:58.2
occ:0.62
O4 A:U14 3.0 75.9 1.0
OP2 A:U17 3.2 64.7 1.0
C4 A:U14 3.9 75.9 1.0
OP1 A:U17 3.9 64.7 1.0
P A:U17 4.0 62.2 1.0
N3 A:U14 4.3 75.9 1.0

Magnesium binding site 7 out of 96 in 1hnz

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Magnesium binding site 7 out of 96 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1551

b:58.2
occ:1.18
O6 A:G377 3.4 80.3 1.0
O6 A:G376 3.9 85.6 1.0
N7 A:G376 4.1 85.6 1.0
N7 A:G377 4.2 80.3 1.0
C6 A:G377 4.3 80.3 1.0
C6 A:G376 4.4 85.6 1.0
C5 A:G376 4.5 85.6 1.0
C5 A:G377 4.6 80.3 1.0
MG A:MG1601 4.8 58.2 1.0

Magnesium binding site 8 out of 96 in 1hnz

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Magnesium binding site 8 out of 96 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1552

b:58.2
occ:0.92
OP2 A:C749 2.0 86.0 1.0
OP2 A:G750 2.1 79.8 1.0
P A:C749 3.3 85.9 1.0
P A:G750 3.6 84.7 1.0
OP1 A:C749 3.8 86.0 1.0
O2' A:C748 3.9 0.8 1.0
O5' A:C749 4.3 85.9 1.0
C3' A:C749 4.3 85.9 1.0
O3' A:C749 4.3 85.9 1.0
O3' A:C748 4.5 0.8 1.0
O5' A:G750 4.5 84.7 1.0
OP1 A:G750 4.5 79.8 1.0
N7 A:G750 4.7 79.8 1.0
C2' A:C748 4.9 0.8 1.0
C8 A:G750 5.0 79.8 1.0

Magnesium binding site 9 out of 96 in 1hnz

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Magnesium binding site 9 out of 96 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1553

b:58.2
occ:1.68
OP2 A:A766 2.2 50.0 1.0
N4 A:C811 3.2 64.1 1.0
O2 A:C812 3.4 59.8 1.0
P A:A766 3.7 61.6 1.0
N3 A:C811 3.7 64.1 1.0
C4 A:C811 3.9 64.1 1.0
N3 A:C812 4.0 59.8 1.0
C2 A:C812 4.1 59.8 1.0
O4 A:U813 4.3 66.7 1.0
O3' A:G765 4.3 58.7 1.0
O5' A:A766 4.4 61.6 1.0
C3' A:G765 4.5 58.7 1.0
OP1 A:A766 4.7 50.0 1.0
N6 A:A768 4.8 55.1 1.0
C2 A:C811 4.8 64.1 1.0
C2' A:G765 4.9 58.7 1.0
N7 A:A767 4.9 59.1 1.0
C4 A:U813 5.0 66.7 1.0

Magnesium binding site 10 out of 96 in 1hnz

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Magnesium binding site 10 out of 96 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with Hygromycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1554

b:58.2
occ:1.43
OP2 A:A768 2.3 55.1 1.0
P A:A768 3.8 62.2 1.0
OP2 A:A767 4.3 59.1 1.0
OP1 A:U804 4.3 76.6 1.0
O5' A:A768 4.4 62.2 1.0
O5' A:A767 4.5 74.7 1.0
N7 A:A768 4.5 55.1 1.0
OP2 A:C805 4.5 61.9 1.0
N7 A:G769 4.6 57.0 1.0
O3' A:A767 4.7 74.7 1.0
C3' A:A767 4.7 74.7 1.0
OP1 A:A768 4.7 55.1 1.0
P A:A767 4.7 74.7 1.0
C8 A:A768 4.8 55.1 1.0
OP1 A:A767 4.8 59.1 1.0
C5' A:U804 4.9 55.2 1.0

Reference:

D.E.Brodersen, W.M.Clemons Jr., A.P.Carter, R.J.Morgan-Warren, B.T.Wimberly, V.Ramakrishnan. The Structural Basis For the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit. Cell(Cambridge,Mass.) V. 103 1143 2000.
ISSN: ISSN 0092-8674
PubMed: 11163189
DOI: 10.1016/S0092-8674(00)00216-6
Page generated: Mon Dec 14 05:59:47 2020

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