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Magnesium in PDB 4x66: 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: 4x66 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) 49.78 / 3.45
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 401.322, 401.322, 175.648, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.7

Other elements in 4x66:

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

Potassium (K) 46 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 301 in 4x66

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Magnesium binding site 1 out of 301 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:87.5
occ:1.00
O4 A:U203 3.4 0.9 1.0
N3 A:U203 3.6 0.3 1.0
C4 A:U203 3.9 0.3 1.0
C5 A:C201 4.2 89.0 1.0
N4 A:C201 4.3 90.4 1.0
OP2 A:G200 4.5 83.4 1.0
C2 A:U203 4.7 98.7 1.0
C4 A:C201 4.8 84.6 1.0
O2 A:U203 5.0 98.8 1.0

Magnesium binding site 2 out of 301 in 4x66

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Magnesium binding site 2 out of 301 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:67.0
occ:1.00
O A:HOH2009 2.1 19.8 1.0
O A:HOH2007 2.1 61.7 1.0
O A:HOH2008 2.1 62.6 1.0
MG A:MG1821 4.5 32.7 1.0
N7 A:G376 4.6 70.3 1.0
O6 A:G377 4.8 71.3 1.0
O6 A:G376 5.0 70.9 1.0

Magnesium binding site 3 out of 301 in 4x66

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Magnesium binding site 3 out of 301 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:96.6
occ:1.00
O A:HOH2012 2.1 43.2 1.0
O A:HOH2011 2.1 71.6 1.0
O A:HOH2010 2.1 81.7 1.0
OP2 A:A753 3.9 71.2 1.0
N7 A:G650 4.1 73.8 1.0
O6 A:G650 4.2 71.7 1.0
OP1 A:A753 4.6 70.6 1.0
P A:A753 4.7 70.6 1.0
N7 A:G649 4.7 75.3 1.0
C5 A:G650 4.9 73.7 1.0
C6 A:G650 4.9 72.7 1.0
O6 A:G649 4.9 80.8 1.0

Magnesium binding site 4 out of 301 in 4x66

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Magnesium binding site 4 out of 301 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:0.4
occ:1.00
O A:HOH2014 2.1 43.2 1.0
O A:HOH2013 2.1 88.7 1.0
OP2 A:G750 2.9 78.2 1.0
OP1 A:C749 3.1 0.0 1.0
OP2 A:C749 3.1 97.5 1.0
P A:C749 3.5 95.6 1.0
O2' A:C748 4.2 91.5 1.0
P A:G750 4.2 79.2 1.0
O3' A:C748 4.3 96.1 1.0
OP1 A:G750 4.7 80.2 1.0
O5' A:C749 4.9 82.6 1.0
O6 A:G752 5.0 84.9 1.0

Magnesium binding site 5 out of 301 in 4x66

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Magnesium binding site 5 out of 301 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:37.6
occ:1.00
N3 A:G818 4.3 57.5 1.0
O4' A:G818 4.5 57.3 1.0
C2 A:G818 4.8 57.7 1.0
C4 A:G818 4.8 57.4 1.0
C1' A:G818 4.9 57.1 1.0
N2 A:G818 5.0 57.8 1.0

Magnesium binding site 6 out of 301 in 4x66

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Magnesium binding site 6 out of 301 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:56.1
occ:1.00
O A:HOH2016 2.1 0.1 1.0
O A:HOH2018 2.1 50.6 1.0
O A:HOH2017 2.1 48.4 1.0
O A:HOH2015 2.1 32.0 1.0
OP2 A:G117 2.9 62.7 1.0
OP2 A:G289 3.0 58.3 1.0
OP1 A:A116 3.3 59.3 1.0
OP1 A:G117 3.8 63.0 1.0
P A:G117 3.8 63.4 1.0
O5' A:A288 4.0 57.6 1.0
P A:G289 4.1 58.3 1.0
C3' A:A288 4.1 57.7 1.0
P A:A116 4.3 59.6 1.0
OP2 A:A116 4.4 59.6 1.0
O4 A:U118 4.4 61.6 1.0
C8 A:A288 4.5 62.6 1.0
OP1 A:G289 4.5 58.6 1.0
O3' A:A288 4.5 57.9 1.0
OP2 A:A288 4.6 61.0 1.0
N7 A:G117 4.6 59.3 1.0
C5 A:U118 4.8 58.3 1.0
P A:A288 4.8 57.8 1.0
O3' A:A116 4.8 59.8 1.0
C5' A:A116 4.8 60.0 1.0
C8 A:G117 4.9 59.4 1.0
C5' A:A288 4.9 57.5 1.0
N7 A:A288 4.9 63.1 1.0
C2' A:A288 4.9 57.5 1.0
O5' A:G117 5.0 65.6 1.0
C3' A:A116 5.0 60.0 1.0
C4' A:A288 5.0 57.4 1.0

Magnesium binding site 7 out of 301 in 4x66

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Magnesium binding site 7 out of 301 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:49.8
occ:1.00
OP2 A:C48 2.8 66.2 1.0
OP1 A:A51 3.2 63.9 1.0
OP2 A:U49 3.8 74.4 1.0
OP1 A:G115 3.8 61.3 1.0
O23 A:PAR1603 3.9 0.2 1.0
P A:C48 4.2 62.4 1.0
C23 A:PAR1603 4.5 0.2 1.0
P A:A51 4.5 63.4 1.0
O2' A:C47 4.7 63.8 1.0
C5' A:A51 4.8 62.6 1.0
O5' A:A51 4.8 63.1 1.0
OP1 A:C48 4.8 62.5 1.0
O3' A:C47 4.9 63.0 1.0
C5' A:G115 4.9 60.9 1.0
O3' A:U114 4.9 61.8 1.0
P A:G115 5.0 61.2 1.0

Magnesium binding site 8 out of 301 in 4x66

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Magnesium binding site 8 out of 301 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:72.4
occ:1.00
O A:HOH2020 2.1 54.7 1.0
O A:HOH2022 2.1 58.8 1.0
O A:HOH2021 2.1 0.6 1.0
O A:HOH2019 2.1 58.9 1.0
OP2 A:U652 4.1 82.5 1.0
N7 A:G752 4.2 74.7 1.0
OP2 A:U751 4.3 82.5 1.0
OP1 A:C651 4.4 93.9 1.0
OP1 A:U751 4.5 87.1 1.0
OP2 A:G752 4.6 76.2 1.0
P A:U751 4.8 78.7 1.0
C8 A:G752 4.9 74.2 1.0

Magnesium binding site 9 out of 301 in 4x66

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Magnesium binding site 9 out of 301 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:34.5
occ:1.00
O A:HOH2025 2.1 37.9 1.0
O A:HOH2024 2.1 29.6 1.0
O A:HOH2023 2.1 59.0 1.0
O6 A:G800 3.5 63.2 1.0
O A:HOH2130 4.0 75.8 1.0
C6 A:G800 4.4 63.4 1.0
N7 A:G799 4.4 64.8 1.0
OP2 A:A781 4.5 62.0 1.0
O6 A:G799 4.6 67.9 1.0
OP2 A:A780 4.7 62.6 1.0
N1 A:G800 4.8 63.1 1.0
OP1 A:A781 4.9 61.3 1.0
N7 A:G798 5.0 65.1 1.0

Magnesium binding site 10 out of 301 in 4x66

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Magnesium binding site 10 out of 301 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:78.9
occ:1.00
O2 A:U1506 3.2 53.8 1.0
C2 A:U1506 3.8 53.9 1.0
OP1 A:U1522 3.9 54.9 1.0
O2' A:U1506 4.0 56.0 1.0
OP2 A:G1508 4.0 55.8 1.0
OP2 A:U1522 4.1 56.0 1.0
N3 A:U1506 4.4 54.3 1.0
N1 A:U1506 4.5 53.9 1.0
P A:U1522 4.5 55.6 1.0
C1' A:U1506 4.5 53.5 1.0
C2' A:U1506 4.9 54.0 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: Tue Aug 20 14:06:04 2024

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