Atomistry » Magnesium » PDB 1muh-1n6h » 1n32
Atomistry »
  Magnesium »
    PDB 1muh-1n6h »
      1n32 »

Magnesium in PDB 1n32: Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin

Protein crystallography data

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin, PDB code: 1n32 was solved by J.M.Ogle, F.V.Murphy Iv, M.J.Tarry, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 141.42 / 3.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.296, 400.296, 175.483, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 27

Other elements in 1n32:

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin 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 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 158;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin (pdb code 1n32). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 158 binding sites of Magnesium where determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin, PDB code: 1n32:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 158 in 1n32

Go back to Magnesium Binding Sites List in 1n32
Magnesium binding site 1 out of 158 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin


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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1546

b:24.8
occ:1.03
OP1 A:G944 2.0 56.2 1.0
OP2 A:G945 2.5 55.2 1.0
P A:G944 3.0 39.5 1.0
OP2 A:G944 3.2 56.2 1.0
O5' A:G944 3.7 42.7 1.0
P A:G945 3.8 52.4 1.0
C5' A:G944 4.2 42.7 1.0
OP1 A:G945 4.2 55.2 1.0
N7 A:A946 4.2 43.5 1.0
O3' A:U943 4.3 51.7 1.0
O6 A:G947 4.4 55.0 1.0
O6 A:G1233 4.5 67.1 1.0
O5' A:G945 4.7 38.5 1.0
OP2 A:A946 4.8 53.7 1.0
C8 A:A946 4.9 43.5 1.0
O3' A:G944 4.9 42.7 1.0

Magnesium binding site 2 out of 158 in 1n32

Go back to Magnesium Binding Sites List in 1n32
Magnesium binding site 2 out of 158 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin


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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1547

b:24.8
occ:0.91
OP1 A:G1224 1.8 64.0 1.0
P A:G1224 2.8 42.1 1.0
OP2 A:G1224 3.1 64.0 1.0
O2' A:C1223 3.5 60.4 1.0
O3' A:C1223 3.7 60.4 1.0
C2' A:C1223 3.9 60.4 1.0
O5' A:G1224 4.1 64.6 1.0
C3' A:C1223 4.3 60.4 1.0
OP2 A:U952 4.4 58.1 1.0
N6 A:A977 4.4 96.0 1.0
N7 A:A977 4.6 96.0 1.0
OP1 A:G951 4.7 52.9 1.0

Magnesium binding site 3 out of 158 in 1n32

Go back to Magnesium Binding Sites List in 1n32
Magnesium binding site 3 out of 158 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin


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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1548

b:24.8
occ:1.01
O6 A:G22 2.7 44.9 1.0
O4 A:U12 2.8 48.1 1.0
O6 A:G21 3.1 49.9 1.0
O6 A:G11 3.3 38.5 1.0
C6 A:G21 3.6 49.9 1.0
N4 A:C23 3.6 41.8 1.0
C4 A:U12 3.8 48.1 1.0
C6 A:G22 3.8 44.9 1.0
N3 A:U12 4.0 48.1 1.0
N1 A:G21 4.0 49.9 1.0
N7 A:G22 4.3 44.9 1.0
C6 A:G11 4.3 38.5 1.0
C5 A:G22 4.4 44.9 1.0
C5 A:G21 4.4 49.9 1.0
C4 A:C23 4.7 41.8 1.0
N7 A:G21 5.0 49.9 1.0
N1 A:G22 5.0 44.9 1.0

Magnesium binding site 4 out of 158 in 1n32

Go back to Magnesium Binding Sites List in 1n32
Magnesium binding site 4 out of 158 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin


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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1549

b:24.8
occ:0.62
O4 A:U14 3.2 38.8 1.0
OP2 A:U17 3.4 45.5 1.0
OP1 A:U17 4.1 45.5 1.0
C4 A:U14 4.1 38.8 1.0
P A:U17 4.3 45.5 1.0
N3 A:U14 4.4 38.8 1.0

Magnesium binding site 5 out of 158 in 1n32

Go back to Magnesium Binding Sites List in 1n32
Magnesium binding site 5 out of 158 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin


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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1550

b:24.8
occ:0.95
O6 A:G377 4.1 61.0 1.0
O6 A:G376 4.3 65.5 1.0
N7 A:G376 4.3 65.5 1.0
N7 A:G377 4.4 61.0 1.0
C6 A:G376 4.8 65.5 1.0
C5 A:G376 4.8 65.5 1.0
C6 A:G377 5.0 61.0 1.0

Magnesium binding site 6 out of 158 in 1n32

Go back to Magnesium Binding Sites List in 1n32
Magnesium binding site 6 out of 158 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin


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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1551

b:24.8
occ:0.75
OP2 A:G750 1.9 74.6 1.0
OP2 A:C749 2.5 86.0 1.0
O5' A:C749 3.1 48.1 1.0
P A:C749 3.2 78.7 1.0
P A:G750 3.4 75.2 1.0
C3' A:C749 3.7 48.1 1.0
OP1 A:C749 3.7 86.0 1.0
O3' A:C749 3.9 48.1 1.0
O5' A:G750 4.2 48.8 1.0
C5' A:C749 4.2 48.1 1.0
N7 A:G750 4.2 46.1 1.0
OP1 A:G750 4.4 74.6 1.0
C8 A:G750 4.5 46.1 1.0
C4' A:C749 4.5 48.1 1.0
O2' A:C748 4.6 96.6 1.0
C2' A:C749 4.7 48.1 1.0
O3' A:C748 4.7 96.6 1.0
C2' A:C748 4.8 96.6 1.0
C6 A:C749 4.9 54.2 1.0

Magnesium binding site 7 out of 158 in 1n32

Go back to Magnesium Binding Sites List in 1n32
Magnesium binding site 7 out of 158 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin


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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1552

b:24.8
occ:1.25
OP2 A:A766 2.1 25.6 1.0
P A:A766 3.6 35.3 1.0
O2 A:C812 3.7 33.3 1.0
N4 A:C811 4.0 32.0 1.0
N3 A:C811 4.1 32.0 1.0
N3 A:C812 4.1 33.3 1.0
O3' A:G765 4.2 45.9 1.0
C2 A:C812 4.3 33.3 1.0
O5' A:A766 4.3 33.0 1.0
C3' A:G765 4.4 45.9 1.0
C4 A:C811 4.5 32.0 1.0
OP1 A:A766 4.6 25.6 1.0
O4 A:U813 4.7 27.7 1.0
N6 A:A768 4.9 30.6 1.0
C2' A:G765 4.9 45.9 1.0

Magnesium binding site 8 out of 158 in 1n32

Go back to Magnesium Binding Sites List in 1n32
Magnesium binding site 8 out of 158 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin


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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1553

b:24.8
occ:1.01
OP2 A:A768 2.2 42.8 1.0
P A:A768 3.7 36.7 1.0
O5' A:A768 4.3 26.0 1.0
OP1 A:U804 4.3 55.8 1.0
N7 A:A768 4.3 30.6 1.0
OP2 A:A767 4.3 40.9 1.0
C8 A:A768 4.5 30.6 1.0
OP1 A:A768 4.5 42.8 1.0
O5' A:A767 4.5 38.8 1.0
O3' A:A767 4.6 38.8 1.0
N7 A:G769 4.7 23.5 1.0
C3' A:A767 4.7 38.8 1.0
OP2 A:C805 4.7 35.2 1.0
P A:A767 4.8 50.8 1.0
C5' A:U804 4.9 43.2 1.0

Magnesium binding site 9 out of 158 in 1n32

Go back to Magnesium Binding Sites List in 1n32
Magnesium binding site 9 out of 158 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin


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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1554

b:24.8
occ:0.94
O4 A:U772 4.0 53.5 1.0
OP1 A:G803 4.3 52.1 1.0
N7 A:G771 4.3 42.8 1.0
OP2 A:U804 4.7 55.8 1.0
O6 A:G771 4.8 42.8 1.0
C5 A:C770 4.8 26.9 1.0
N4 A:C770 4.9 26.9 1.0
C4 A:C770 5.0 26.9 1.0

Magnesium binding site 10 out of 158 in 1n32

Go back to Magnesium Binding Sites List in 1n32
Magnesium binding site 10 out of 158 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin


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 Bound to Codon and Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched at the First Codon Position at the A Site with Paromomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1555

b:24.8
occ:1.01
O6 A:G800 3.3 34.7 1.0
OP2 A:A780 3.4 55.6 1.0
N7 A:G800 3.5 34.7 1.0
N7 A:A780 4.0 52.6 1.0
C6 A:G800 4.0 34.7 1.0
C5 A:G800 4.1 34.7 1.0
C8 A:A780 4.3 52.6 1.0
OP2 A:C779 4.5 50.6 1.0
C8 A:G800 4.6 34.7 1.0
N7 A:G799 4.8 42.8 1.0
P A:A780 4.8 35.4 1.0
O5' A:C779 4.9 40.2 1.0
C8 A:G799 4.9 42.8 1.0

Reference:

J.M.Ogle, F.V.Murphy Iv, M.J.Tarry, V.Ramakrishnan. Selection of Trna By the Ribosome Requires A Transition From An Open to A Closed Form Cell(Cambridge,Mass.) V. 111 721 2002.
ISSN: ISSN 0092-8674
PubMed: 12464183
DOI: 10.1016/S0092-8674(02)01086-3
Page generated: Mon Dec 14 06:30:39 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy