Magnesium in PDB 5wnv: 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: 5wnv was solved by H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.80 / 3.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400.000, 400.000, 173.000, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.3

Other elements in 5wnv:

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

Potassium (K) 22 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 251 in 5wnv

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Magnesium binding site 1 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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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:Mg1601

b:0.8
occ:1.00
O6 A:G216 3.3 0.3 1.0
C6 A:U204 3.4 0.6 1.0
O2 A:U203 3.6 0.4 1.0
C1' A:U204 3.9 0.9 1.0
C6 A:G216 3.9 0.7 1.0
N1 A:U204 4.1 0.8 1.0
C5 A:U204 4.2 0.5 1.0
O4' A:U204 4.2 0.3 1.0
N1 A:G216 4.5 1.0 1.0
C5 A:G216 4.7 0.1 1.0
C2 A:U203 4.7 0.9 1.0

Magnesium binding site 2 out of 251 in 5wnv

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Magnesium binding site 2 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


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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:Mg1602

b:1.0
occ:1.00
O A:HOH2060 2.1 0.7 1.0
O A:HOH2035 2.1 0.6 1.0
O A:HOH2029 2.1 71.5 1.0
O6 A:G377 4.6 0.7 1.0
N7 A:G376 4.6 0.9 1.0
N7 A:G377 4.8 0.5 1.0
O6 A:G376 4.9 0.8 1.0

Magnesium binding site 3 out of 251 in 5wnv

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Magnesium binding site 3 out of 251 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:Mg1603

b:0.9
occ:1.00
O A:HOH2107 2.1 0.8 1.0
O A:HOH2067 2.1 0.6 1.0
O A:HOH2017 2.1 97.5 1.0
OP2 A:A753 3.7 0.1 1.0
N7 A:G650 3.8 0.9 1.0
O6 A:G650 4.0 0.0 1.0
N7 A:G649 4.3 0.8 1.0
O6 A:G649 4.5 0.6 1.0
C5 A:G650 4.6 0.1 1.0
OP1 A:A753 4.6 89.1 1.0
P A:A753 4.6 100.0 1.0
C6 A:G650 4.7 0.1 1.0
C5 A:G649 4.8 0.6 1.0
C8 A:G650 4.9 0.7 1.0
C6 A:G649 4.9 0.6 1.0

Magnesium binding site 4 out of 251 in 5wnv

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Magnesium binding site 4 out of 251 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:Mg1604

b:0.5
occ:1.00
O A:HOH1926 2.1 0.1 1.0
O A:HOH1975 2.1 0.3 1.0
OP2 A:C749 3.0 0.5 1.0
OP2 A:G750 3.1 0.3 1.0
OP1 A:C749 3.3 0.9 1.0
P A:C749 3.6 0.3 1.0
P A:G750 4.4 0.8 1.0
O2' A:C748 4.5 0.9 1.0
O3' A:C748 4.6 0.3 1.0
O6 A:G752 4.8 0.6 1.0
O5' A:C749 4.9 0.5 1.0
OP2 A:A653 4.9 0.6 1.0
OP1 A:G750 5.0 1.0 1.0

Magnesium binding site 5 out of 251 in 5wnv

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Magnesium binding site 5 out of 251 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:Mg1605

b:0.6
occ:1.00
O A:HOH1906 2.1 0.5 1.0
O A:HOH1907 2.1 70.3 1.0
O A:HOH1910 2.1 0.5 1.0
O A:HOH1911 2.1 0.1 1.0
OP2 A:G117 2.8 71.0 1.0
OP2 A:G289 3.3 98.3 1.0
OP1 A:A116 3.6 83.3 1.0
P A:G117 3.7 0.4 1.0
OP1 A:G117 3.7 0.2 1.0
O5' A:A288 4.2 88.1 1.0
C8 A:A288 4.2 0.1 1.0
OP2 A:A288 4.2 65.7 1.0
O4 A:U118 4.2 84.4 1.0
C3' A:A288 4.4 0.8 1.0
N7 A:A288 4.4 0.9 1.0
P A:G289 4.5 92.3 1.0
C5 A:U118 4.5 89.7 1.0
P A:A116 4.6 1.0 1.0
O5' A:G117 4.6 0.6 1.0
OP2 A:A116 4.7 0.9 1.0
P A:A288 4.8 86.7 1.0
C4 A:U118 4.8 93.9 1.0
N7 A:G117 4.8 0.8 1.0
O3' A:A288 4.9 0.3 1.0
N9 A:A288 4.9 0.8 1.0
O3' A:A116 4.9 0.2 1.0
C5' A:A116 4.9 89.0 1.0
C8 A:G117 5.0 0.7 1.0
OP1 A:G289 5.0 66.4 1.0

Magnesium binding site 6 out of 251 in 5wnv

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Magnesium binding site 6 out of 251 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:Mg1606

b:0.7
occ:1.00
OP2 A:C48 3.0 0.9 1.0
OP2 A:U49 3.2 0.8 1.0
OP1 A:A51 3.3 0.8 1.0
OP1 A:G115 3.7 0.7 1.0
O3' A:C47 4.1 0.1 1.0
P A:C48 4.2 0.6 1.0
P A:A51 4.5 0.6 1.0
P A:U49 4.6 0.1 1.0
O2' A:C47 4.6 0.3 1.0
C5' A:C48 4.9 84.1 1.0
P A:G115 4.9 98.9 1.0
O5' A:C48 4.9 91.9 1.0
C5' A:A51 5.0 0.4 1.0
O3' A:U114 5.0 0.4 1.0
O5' A:A51 5.0 97.3 1.0

Magnesium binding site 7 out of 251 in 5wnv

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Magnesium binding site 7 out of 251 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:Mg1607

b:0.7
occ:1.00
O A:HOH1951 2.1 0.6 1.0
O A:HOH2025 2.1 0.7 1.0
O A:HOH2021 2.1 0.8 1.0
O A:HOH2073 2.1 94.8 1.0
N7 A:G752 3.7 0.1 1.0
OP2 A:U751 4.1 0.6 1.0
OP2 A:U652 4.1 0.1 1.0
C8 A:G752 4.4 0.2 1.0
OP1 A:U751 4.5 0.8 1.0
OP2 A:G752 4.7 0.3 1.0
P A:U751 4.7 0.5 1.0
C5 A:G752 4.7 0.4 1.0
OP1 A:C651 4.8 0.1 1.0
O6 A:G752 4.9 0.6 1.0

Magnesium binding site 8 out of 251 in 5wnv

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Magnesium binding site 8 out of 251 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:Mg1608

b:94.8
occ:1.00
O A:HOH1962 2.1 0.3 1.0
O A:HOH2092 2.1 0.6 1.0
O A:HOH2106 2.1 82.8 1.0
O6 A:G800 3.7 98.1 1.0
O A:HOH2005 3.8 0.3 1.0
N7 A:G799 4.1 90.6 1.0
O6 A:G799 4.4 0.1 1.0
C6 A:G800 4.4 0.6 1.0
OP2 A:A781 4.7 93.6 1.0
N7 A:G798 4.8 95.2 1.0
N1 A:G800 4.9 81.6 1.0
O6 A:G798 4.9 0.9 1.0
C5 A:G799 4.9 92.0 1.0
OP1 A:A781 5.0 0.9 1.0

Magnesium binding site 9 out of 251 in 5wnv

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Magnesium binding site 9 out of 251 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:Mg1609

b:0.3
occ:1.00
O2 A:U1506 3.1 1.0 1.0
OP1 A:U1522 3.8 82.3 1.0
C2 A:U1506 3.8 88.1 1.0
OP2 A:U1522 4.1 0.3 1.0
O2' A:U1506 4.2 0.5 1.0
P A:U1522 4.4 93.6 1.0
OP2 A:G1508 4.5 0.9 1.0
C1' A:U1506 4.5 99.7 1.0
N1 A:U1506 4.5 84.8 1.0
N3 A:U1506 4.6 83.1 1.0
MG A:MG1788 5.0 91.2 1.0
C2' A:U1506 5.0 98.3 1.0

Magnesium binding site 10 out of 251 in 5wnv

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Magnesium binding site 10 out of 251 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:Mg1610

b:71.3
occ:1.00
O A:HOH1912 2.1 0.5 1.0
O A:HOH1914 2.1 76.2 1.0
OP1 A:G1505 2.9 0.6 1.0
OP1 A:G1508 2.9 88.6 1.0
OP1 A:A1500 3.0 84.1 1.0
O3' A:A1507 3.0 83.5 1.0
O5' A:G1505 3.2 0.9 1.0
OP1 A:G1504 3.3 92.0 1.0
C5' A:G1505 3.6 0.7 1.0
P A:G1508 3.6 91.2 1.0
P A:G1505 3.6 89.0 1.0
C3' A:G1504 3.9 0.2 1.0
O5' A:G1504 4.0 0.1 1.0
O2' A:U1506 4.1 0.5 1.0
O3' A:G1504 4.1 0.2 1.0
P A:G1504 4.2 94.4 1.0
C5' A:G1508 4.2 87.2 1.0
P A:A1500 4.2 84.6 1.0
C3' A:A1507 4.2 83.5 1.0
O5' A:G1508 4.4 93.1 1.0
OP2 A:C1501 4.4 85.4 1.0
C4' A:A1507 4.5 84.5 1.0
O2' A:A1507 4.5 84.3 1.0
OP2 A:A1500 4.6 85.4 1.0
C2' A:U1506 4.6 98.3 1.0
MG A:MG1721 4.7 58.5 1.0
C2' A:G1504 4.8 0.5 1.0
OP2 A:G1508 4.8 0.9 1.0
OP2 A:G1504 4.8 0.2 1.0
O2' A:G1504 4.9 0.8 1.0
C4' A:G1504 5.0 87.7 1.0
C5' A:A1507 5.0 0.3 1.0
OP2 A:G1505 5.0 98.5 1.0

Reference:

J.Choi, G.Indrisiunaite, H.Demirci, K.W.Ieong, J.Wang, A.Petrov, A.Prabhakar, G.Rechavi, D.Dominissini, C.He, M.Ehrenberg, J.D.Puglisi. 2'-O-Methylation in Mrna Disrupts Trna Decoding During Translation Elongation. Nat. Struct. Mol. Biol. V. 25 208 2018.
ISSN: ESSN 1545-9985
PubMed: 29459784
DOI: 10.1038/S41594-018-0030-Z
Page generated: Mon Dec 14 21:24:08 2020

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