Magnesium in PDB 4x64: Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus

Protein crystallography data

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 4x64 was solved by H.Demirci, J.Chen, J.Choi, M.Soltis, J.D.Puglisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.88 / 3.35
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.496, 400.496, 175.534, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.5

Other elements in 4x64:

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus also contains other interesting chemical elements:

Potassium (K) 41 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 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 280; Page 29, Binding sites: 281 - 290; Page 30, Binding sites: 291 - 300; Page 31, Binding sites: 301 - 310; Page 32, Binding sites: 311 - 311;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus (pdb code 4x64). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 311 binding sites of Magnesium where determined in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 4x64:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 311 in 4x64

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Magnesium binding site 1 out of 311 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:86.8
occ:1.00
O4 A:U203 3.5 0.9 1.0
N3 A:U203 3.8 0.3 1.0
C4 A:U203 4.1 0.9 1.0
C2 A:U203 4.9 0.4 1.0

Magnesium binding site 2 out of 311 in 4x64

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Magnesium binding site 2 out of 311 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:63.7
occ:1.00
O A:HOH2008 2.1 49.4 1.0
O A:HOH2007 2.1 38.9 1.0
O A:HOH2006 2.1 29.7 1.0
N7 A:G376 4.0 64.5 1.0
O6 A:G377 4.3 61.3 1.0
O6 A:G376 4.6 53.6 1.0
C5 A:G376 4.7 61.9 1.0
C8 A:G376 4.8 65.9 1.0
N7 A:G377 4.8 65.8 1.0
C6 A:G376 5.0 61.8 1.0

Magnesium binding site 3 out of 311 in 4x64

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Magnesium binding site 3 out of 311 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:0.8
occ:1.00
O A:HOH2011 2.1 58.2 1.0
O A:HOH2010 2.1 75.9 1.0
O A:HOH2009 2.1 92.9 1.0
OP2 A:A753 3.4 66.9 1.0
N7 A:G650 3.8 77.6 1.0
O6 A:G650 3.9 77.3 1.0
P A:A753 4.5 63.8 1.0
C5 A:G650 4.6 77.9 1.0
C6 A:G650 4.6 77.0 1.0
N7 A:G649 4.7 84.4 1.0
OP1 A:A753 4.7 64.6 1.0
O6 A:G649 4.9 81.8 1.0
C8 A:G650 4.9 80.8 1.0

Magnesium binding site 4 out of 311 in 4x64

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Magnesium binding site 4 out of 311 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:0.2
occ:1.00
O A:HOH2013 2.1 39.0 1.0
O A:HOH2012 2.1 97.0 1.0
OP2 A:C749 2.9 0.1 1.0
OP2 A:G750 3.0 89.8 1.0
OP1 A:C749 3.4 0.9 1.0
P A:C749 3.7 0.6 1.0
O2' A:C748 4.4 0.6 1.0
P A:G750 4.4 90.1 1.0
O6 A:G752 4.8 94.8 1.0
OP2 A:A653 4.8 78.8 1.0
O3' A:C748 4.8 0.6 1.0
O5' A:C749 4.9 86.7 1.0

Magnesium binding site 5 out of 311 in 4x64

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Magnesium binding site 5 out of 311 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1611

b:66.4
occ:1.00
O2 A:U871 4.1 79.4 1.0
MG A:MG1781 4.1 75.6 1.0
OP2 A:G855 4.5 69.6 1.0
N3 A:G818 4.5 57.2 1.0
C4 A:G818 4.5 57.5 1.0
O4' A:G818 4.6 63.9 1.0
N9 A:G818 4.8 54.4 1.0
C2 A:G818 4.9 65.3 1.0
C5 A:G818 4.9 67.1 1.0

Magnesium binding site 6 out of 311 in 4x64

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Magnesium binding site 6 out of 311 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1612

b:54.2
occ:1.00
O A:HOH2015 2.1 0.9 1.0
O A:HOH2016 2.1 32.7 1.0
O A:HOH2017 2.1 39.0 1.0
O A:HOH2014 2.1 30.7 1.0
OP2 A:G117 2.8 68.7 1.0
OP2 A:G289 3.0 44.9 1.0
OP1 A:A116 3.3 46.2 1.0
P A:G117 3.7 65.3 1.0
OP1 A:G117 3.7 62.5 1.0
P A:G289 4.0 55.5 1.0
C3' A:A288 4.0 48.8 1.0
O5' A:A288 4.0 59.7 1.0
O4 A:U118 4.0 61.0 1.0
P A:A116 4.3 58.4 1.0
OP2 A:A116 4.3 71.8 1.0
O3' A:A288 4.4 53.7 1.0
OP1 A:G289 4.4 42.0 1.0
C8 A:A288 4.4 66.8 1.0
N7 A:G117 4.5 68.0 1.0
OP2 A:A288 4.5 73.1 1.0
C5 A:U118 4.5 57.4 1.0
C4 A:U118 4.7 58.1 1.0
O3' A:A116 4.7 58.0 1.0
P A:A288 4.8 71.0 1.0
C5' A:A116 4.8 47.1 1.0
O5' A:G117 4.8 69.5 1.0
C2' A:A288 4.8 46.8 1.0
C8 A:G117 4.9 62.3 1.0
N7 A:A288 4.9 67.0 1.0
C3' A:A116 4.9 50.9 1.0
C5' A:A288 5.0 57.0 1.0

Magnesium binding site 7 out of 311 in 4x64

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Magnesium binding site 7 out of 311 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1613

b:67.7
occ:1.00
OP2 A:C48 2.8 74.5 1.0
OP1 A:G115 3.4 68.1 1.0
OP1 A:A51 3.7 77.8 1.0
O23 A:PAR1603 3.9 0.7 1.0
P A:C48 3.9 66.0 1.0
C23 A:PAR1603 4.1 0.1 1.0
OP2 A:U49 4.2 85.5 1.0
OP1 A:C48 4.2 58.6 1.0
O3' A:U114 4.4 54.8 1.0
P A:G115 4.5 59.1 1.0
C5' A:G115 4.6 60.3 1.0
O2' A:C47 4.7 52.4 1.0
P A:A51 4.9 70.3 1.0
O3' A:C47 4.9 63.6 1.0
C13 A:PAR1603 5.0 0.1 1.0
O5' A:C48 5.0 58.1 1.0
O52 A:PAR1603 5.0 0.3 1.0

Magnesium binding site 8 out of 311 in 4x64

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Magnesium binding site 8 out of 311 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1614

b:89.1
occ:1.00
O A:HOH2019 2.1 43.9 1.0
O A:HOH2020 2.1 0.2 1.0
O A:HOH2021 2.1 58.1 1.0
O A:HOH2018 2.1 86.1 1.0
N7 A:G752 3.9 87.6 1.0
OP2 A:U751 4.0 83.0 1.0
OP2 A:U652 4.2 86.7 1.0
OP1 A:U751 4.4 90.1 1.0
C8 A:G752 4.5 79.7 1.0
P A:U751 4.6 85.0 1.0
OP1 A:C651 4.6 92.7 1.0
OP2 A:G752 4.8 75.2 1.0

Magnesium binding site 9 out of 311 in 4x64

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Magnesium binding site 9 out of 311 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1615

b:49.3
occ:1.00
O A:HOH2024 2.1 38.8 1.0
O A:HOH2022 2.1 27.8 1.0
O A:HOH2023 2.1 25.4 1.0
O6 A:G800 3.4 61.3 1.0
O A:HOH2132 3.6 53.9 1.0
N7 A:G799 3.8 66.0 1.0
O6 A:G799 4.0 65.3 1.0
C6 A:G800 4.2 56.5 1.0
N7 A:G798 4.5 47.3 1.0
C5 A:G799 4.6 60.2 1.0
OP2 A:A781 4.6 57.1 1.0
C6 A:G799 4.7 57.5 1.0
N1 A:G800 4.8 49.5 1.0
C8 A:G799 4.8 67.5 1.0
OP2 A:A780 4.8 60.1 1.0
O6 A:G798 4.8 50.4 1.0

Magnesium binding site 10 out of 311 in 4x64

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Magnesium binding site 10 out of 311 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1616

b:80.1
occ:1.00
O2 A:U1506 3.0 65.2 1.0
O2' A:U1506 3.5 66.6 1.0
OP2 A:G1508 3.5 67.0 1.0
C2 A:U1506 3.9 56.2 1.0
C1' A:U1506 4.2 56.2 1.0
OP1 A:U1522 4.3 51.3 1.0
C2' A:U1506 4.4 59.7 1.0
N1 A:U1506 4.4 50.8 1.0
OP2 A:U1522 4.5 55.6 1.0
MG A:MG1830 4.7 54.9 1.0
P A:G1508 4.7 57.0 1.0
O3' A:U1506 4.8 64.2 1.0
N3 A:U1506 4.8 54.8 1.0
P A:U1522 4.9 50.1 1.0
OP1 A:G1508 5.0 63.2 1.0

Reference:

J.Choi, K.W.Ieong, H.Demirci, J.Chen, A.Petrov, A.Prabhakar, S.E.O'leary, D.Dominissini, G.Rechavi, S.M.Soltis, M.Ehrenberg, J.D.Puglisi. N(6)-Methyladenosine in Mrna Disrupts Trna Selection and Translation-Elongation Dynamics. Nat.Struct.Mol.Biol. V. 23 110 2016.
ISSN: ESSN 1545-9985
PubMed: 26751643
DOI: 10.1038/NSMB.3148
Page generated: Mon Dec 14 19:44:36 2020

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