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Magnesium in PDB 2uxb: Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit.

Protein crystallography data

The structure of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit., PDB code: 2uxb was solved by C.M.Dunham, M.Selmer, S.S.Phelps, A.C.Kelley, T.Suzuki, S.Joseph, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.88 / 3.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 401.950, 401.950, 174.086, 90.00, 90.00, 90.00
R / Rfree (%) 29.5 / 32.8

Other elements in 2uxb:

The structure of Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. also contains other interesting chemical elements:

Potassium (K) 10 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 - 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 - 131;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. (pdb code 2uxb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 131 binding sites of Magnesium where determined in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit., PDB code: 2uxb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 131 in 2uxb

Go back to Magnesium Binding Sites List in 2uxb
Magnesium binding site 1 out of 131 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit.


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 An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3002

b:79.4
occ:1.00
OP2 A:U17 2.9 43.4 1.0
OP1 A:U17 3.0 43.4 1.0
P A:U17 3.2 26.4 1.0
O3' A:A16 3.6 35.5 1.0
O4 A:U14 3.7 54.6 1.0
C4 A:U14 4.6 54.6 1.0
C3' A:A16 4.6 35.5 1.0
N3 A:U14 4.6 54.6 1.0
O5' A:U17 4.8 26.4 1.0
C5' A:A16 4.9 35.5 1.0

Magnesium binding site 2 out of 131 in 2uxb

Go back to Magnesium Binding Sites List in 2uxb
Magnesium binding site 2 out of 131 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit.


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 An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3003

b:0.0
occ:1.00
O6 A:G377 3.1 60.6 1.0
O6 A:G376 3.8 53.4 1.0
C6 A:G377 4.0 60.6 1.0
N7 A:G377 4.1 60.6 1.0
N7 A:G376 4.2 53.4 1.0
C6 A:G376 4.3 53.4 1.0
C5 A:G376 4.4 53.4 1.0
C5 A:G377 4.4 60.6 1.0

Magnesium binding site 3 out of 131 in 2uxb

Go back to Magnesium Binding Sites List in 2uxb
Magnesium binding site 3 out of 131 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit.


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 An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3004

b:89.8
occ:1.00
OP2 A:C749 2.2 63.0 1.0
OP2 A:G750 2.8 53.2 1.0
P A:C749 3.5 48.7 1.0
O3' A:C748 3.8 73.5 1.0
P A:G750 4.2 55.6 1.0
OP1 A:C749 4.4 63.0 1.0
O5' A:C749 4.6 48.7 1.0
C3' A:C749 4.8 48.7 1.0
O2' A:C748 4.9 73.5 1.0
O3' A:C749 4.9 48.7 1.0
OP1 A:G750 4.9 53.2 1.0

Magnesium binding site 4 out of 131 in 2uxb

Go back to Magnesium Binding Sites List in 2uxb
Magnesium binding site 4 out of 131 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit.


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 An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3005

b:95.6
occ:1.00
OP2 A:A766 2.5 18.0 1.0
N3 A:C811 3.3 37.0 1.0
N4 A:C811 3.6 37.0 1.0
O2 A:C812 3.7 29.8 1.0
C4 A:C811 3.9 37.0 1.0
N3 A:C812 4.0 29.8 1.0
P A:A766 4.0 30.6 1.0
C2 A:C812 4.2 29.8 1.0
C2 A:C811 4.3 37.0 1.0
O2 A:C811 4.4 37.0 1.0
N6 A:A768 4.6 33.4 1.0
OP1 A:A766 4.8 18.0 1.0
O5' A:A766 4.8 30.6 1.0
N7 A:A767 4.9 29.0 1.0
O4 A:U813 4.9 38.7 1.0
C4 A:C812 5.0 29.8 1.0

Magnesium binding site 5 out of 131 in 2uxb

Go back to Magnesium Binding Sites List in 2uxb
Magnesium binding site 5 out of 131 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit.


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 An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3006

b:92.5
occ:1.00
OP2 A:A768 3.1 33.4 1.0
OP1 A:U804 3.7 66.5 1.0
OP2 A:C805 4.3 26.4 1.0
P A:A768 4.5 26.6 1.0
O6 A:G769 4.8 16.4 1.0
N7 A:G769 4.8 16.4 1.0
OP2 A:A767 4.8 29.0 1.0
N7 A:A768 4.9 33.4 1.0

Magnesium binding site 6 out of 131 in 2uxb

Go back to Magnesium Binding Sites List in 2uxb
Magnesium binding site 6 out of 131 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit.


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 An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3007

b:89.9
occ:1.00
O4 A:U772 4.3 49.6 1.0
N7 A:G771 4.4 39.5 1.0
OP1 A:G803 4.5 44.2 1.0
O6 A:G771 4.5 39.5 1.0
N4 A:C770 4.7 32.1 1.0
OP2 A:U804 4.7 66.5 1.0
C5 A:C770 4.9 32.1 1.0
C4 A:C770 4.9 32.1 1.0

Magnesium binding site 7 out of 131 in 2uxb

Go back to Magnesium Binding Sites List in 2uxb
Magnesium binding site 7 out of 131 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit.


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 An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3008

b:0.4
occ:1.00
OP2 A:C779 3.6 40.7 1.0
N7 A:G800 3.7 47.5 1.0
OP2 A:A780 3.9 48.8 1.0
O6 A:G800 4.2 47.5 1.0
N7 A:A780 4.3 48.8 1.0
OP2 A:G800 4.3 47.5 1.0
P A:C779 4.4 41.3 1.0
OP1 A:C779 4.5 40.7 1.0
C5 A:G800 4.6 47.5 1.0
C8 A:G800 4.6 47.5 1.0
C8 A:A780 4.7 48.8 1.0
O5' A:C779 4.7 41.3 1.0
C6 A:G800 4.8 47.5 1.0
OP2 A:G799 4.9 46.1 1.0

Magnesium binding site 8 out of 131 in 2uxb

Go back to Magnesium Binding Sites List in 2uxb
Magnesium binding site 8 out of 131 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit.


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 An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3009

b:90.5
occ:1.00
OP1 A:C578 2.5 31.0 1.0
OP2 A:G576 3.5 41.6 1.0
P A:C578 4.0 20.4 1.0
O2' A:G575 4.0 29.8 1.0
OP1 A:U820 4.1 32.1 1.0
O3' A:G577 4.3 27.3 1.0
C5' A:G821 4.3 18.4 1.0
O3' A:G575 4.4 29.8 1.0
C4' A:G821 4.5 18.4 1.0
OP2 A:C817 4.5 15.2 1.0
P A:G576 4.5 23.4 1.0
OP2 A:C578 4.9 31.0 1.0
C5' A:C578 5.0 20.4 1.0
O5' A:C578 5.0 20.4 1.0

Magnesium binding site 9 out of 131 in 2uxb

Go back to Magnesium Binding Sites List in 2uxb
Magnesium binding site 9 out of 131 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit.


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 An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3010

b:0.6
occ:1.00
N7 A:G853 4.0 45.5 1.0
O6 A:G853 4.2 45.5 1.0
O6 A:G854 4.2 42.7 1.0
OP1 A:U871 4.4 49.8 1.0
N7 A:G854 4.5 42.7 1.0
C5 A:G853 4.6 45.5 1.0
C6 A:G853 4.7 45.5 1.0
MG G:MG3132 4.8 51.6 1.0
C8 A:G853 4.9 45.5 1.0
OP2 A:U871 4.9 49.8 1.0

Magnesium binding site 10 out of 131 in 2uxb

Go back to Magnesium Binding Sites List in 2uxb
Magnesium binding site 10 out of 131 in the Crystal Structure of An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit.


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 An Extended Trna Anticodon Stem Loop in Complex with Its Cognate Mrna Gggu in the Context of the Thermus Thermophilus 30S Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3011

b:0.9
occ:1.00
OP2 A:A509 2.5 75.6 1.0
OP2 A:A510 2.7 67.2 1.0
OP1 A:G506 3.4 66.4 1.0
P A:A509 3.9 43.0 1.0
P A:A510 4.0 80.3 1.0
OP2 A:C507 4.3 53.3 1.0
OP1 A:A510 4.4 67.2 1.0
OP1 A:A509 4.5 75.6 1.0
O3' A:C508 4.6 57.0 1.0
P A:G506 4.8 61.6 1.0
OP1 A:C507 4.8 53.3 1.0
O5' A:A510 4.9 80.3 1.0

Reference:

C.M.Dunham, M.Selmer, S.S.Phelps, A.C.Kelley, T.Suzuki, S.Joseph, V.Ramakrishnan. Structures of Trnas with An Expanded Anticodon Loop in the Decoding Center of the 30S Ribosomal Subunit. Rna V. 13 817 2007.
ISSN: ISSN 1355-8382
PubMed: 17416634
DOI: 10.1261/RNA.367307
Page generated: Mon Dec 14 07:39:55 2020

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