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

Resolution Low / High (Å) 29.98 / 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 (%) 19.1 / 22.4

Other elements in 5wnp:

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 253 in 5wnp

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Magnesium binding site 1 out of 253 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:0.0
occ:1.00
O2 A:U203 3.1 0.0 1.0
C6 A:U204 3.4 0.3 1.0
O6 A:G216 3.7 0.3 1.0
C5 A:U204 4.0 0.3 1.0
C1' A:U204 4.3 0.4 1.0
N1 A:U204 4.3 0.4 1.0
C6 A:G216 4.3 0.9 1.0
C2 A:U203 4.3 0.5 1.0
O4' A:U204 4.7 0.2 1.0
N4 A:C201 4.9 0.4 1.0
N1 A:G216 4.9 0.6 1.0

Magnesium binding site 2 out of 253 in 5wnp

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Magnesium binding site 2 out of 253 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:Mg1602

b:0.6
occ:1.00
O A:HOH2017 2.1 0.2 1.0
O A:HOH2087 2.1 0.3 1.0
O A:HOH2000 2.1 97.4 1.0
N7 A:G376 4.1 0.5 1.0
O6 A:G376 4.6 0.1 1.0
O6 A:G377 4.6 0.8 1.0
N7 A:G377 4.8 0.4 1.0
C5 A:G376 4.9 0.5 1.0
MG A:MG1777 4.9 91.7 1.0
C8 A:G376 5.0 0.4 1.0

Magnesium binding site 3 out of 253 in 5wnp

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Magnesium binding site 3 out of 253 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:0.3
occ:1.00
O A:HOH2114 2.1 0.2 1.0
O A:HOH2060 2.1 0.6 1.0
O A:HOH2075 2.1 0.4 1.0
OP2 A:A753 3.5 0.4 1.0
N7 A:G650 4.2 0.7 1.0
O6 A:G650 4.3 0.9 1.0
P A:A753 4.4 0.4 1.0
OP1 A:A753 4.4 0.6 1.0
N7 A:G649 4.7 0.6 1.0
C5 A:G650 5.0 0.5 1.0
C6 A:G650 5.0 0.3 1.0

Magnesium binding site 4 out of 253 in 5wnp

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Magnesium binding site 4 out of 253 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:0.3
occ:1.00
O A:HOH1950 2.1 0.8 1.0
O A:HOH2007 2.1 0.2 1.0
OP2 A:G750 3.0 0.5 1.0
OP2 A:C749 3.1 0.7 1.0
OP1 A:C749 3.2 0.6 1.0
P A:C749 3.6 0.9 1.0
P A:G750 4.3 0.3 1.0
O2' A:C748 4.4 0.2 1.0
O3' A:C748 4.5 0.5 1.0
OP1 A:G750 4.7 0.9 1.0
O6 A:G752 4.8 0.7 1.0
OP2 A:A653 4.8 0.4 1.0
O5' A:C749 5.0 0.4 1.0

Magnesium binding site 5 out of 253 in 5wnp

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Magnesium binding site 5 out of 253 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:0.7
occ:1.00
O A:HOH1906 2.1 0.8 1.0
O A:HOH1907 2.1 93.5 1.0
O A:HOH1910 2.1 0.4 1.0
O A:HOH1912 2.1 0.5 1.0
OP2 A:G117 2.8 99.3 1.0
OP2 A:G289 3.3 0.6 1.0
OP1 A:A116 3.5 0.6 1.0
OP1 A:G117 3.8 0.9 1.0
P A:G117 3.8 0.6 1.0
C8 A:A288 3.9 0.6 1.0
O5' A:A288 4.1 0.6 1.0
O4 A:U118 4.2 0.9 1.0
N7 A:A288 4.2 0.6 1.0
OP2 A:A288 4.2 0.5 1.0
C3' A:A288 4.3 0.7 1.0
C5 A:U118 4.4 0.4 1.0
P A:G289 4.5 0.5 1.0
P A:A116 4.5 0.0 1.0
OP2 A:A116 4.6 0.5 1.0
C4 A:U118 4.7 0.1 1.0
N9 A:A288 4.7 0.4 1.0
P A:A288 4.8 0.4 1.0
O3' A:A288 4.8 0.6 1.0
O5' A:G117 4.8 0.1 1.0
N7 A:G117 4.9 0.1 1.0
O3' A:A116 4.9 0.2 1.0
C2' A:A288 4.9 0.1 1.0
C5' A:A116 4.9 0.3 1.0

Magnesium binding site 6 out of 253 in 5wnp

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Magnesium binding site 6 out of 253 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:0.3
occ:1.00
OP2 A:C48 3.0 0.9 1.0
OP1 A:G115 3.1 0.0 1.0
OP1 A:A51 3.5 0.5 1.0
OP2 A:U49 3.7 0.5 1.0
O3' A:U114 4.1 0.7 1.0
P A:G115 4.2 1.0 1.0
C5' A:G115 4.4 0.4 1.0
P A:C48 4.4 0.8 1.0
P A:A51 4.6 0.0 1.0
O5' A:A51 4.7 0.4 1.0
C5' A:A51 4.7 0.1 1.0
O5' A:G115 4.8 0.9 1.0
O3' A:C47 4.8 0.1 1.0

Magnesium binding site 7 out of 253 in 5wnp

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Magnesium binding site 7 out of 253 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:0.8
occ:1.00
O A:HOH1999 2.1 0.9 1.0
O A:HOH1991 2.1 0.8 1.0
O A:HOH2047 2.1 0.7 1.0
O A:HOH2096 2.1 0.2 1.0
N7 A:G752 3.7 0.4 1.0
OP2 A:U751 4.0 0.7 1.0
OP2 A:U652 4.1 0.0 1.0
OP1 A:U751 4.3 0.2 1.0
C8 A:G752 4.4 0.3 1.0
P A:U751 4.5 0.3 1.0
OP1 A:C651 4.6 0.2 1.0
C5 A:G752 4.7 0.5 1.0
OP2 A:G752 4.8 0.6 1.0
O6 A:G752 4.8 0.7 1.0

Magnesium binding site 8 out of 253 in 5wnp

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Magnesium binding site 8 out of 253 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:0.7
occ:1.00
O A:HOH2089 2.1 0.5 1.0
O A:HOH2010 2.1 0.0 1.0
O A:HOH2108 2.1 0.7 1.0
O6 A:G800 3.5 0.7 1.0
O A:HOH1979 3.8 0.1 1.0
N7 A:G799 4.1 0.2 1.0
C6 A:G800 4.2 0.1 1.0
O6 A:G799 4.2 0.5 1.0
OP2 A:A781 4.5 0.4 1.0
N1 A:G800 4.6 0.0 1.0
OP1 A:A781 4.8 0.8 1.0
N7 A:G798 4.9 0.8 1.0
C5 A:G799 4.9 0.2 1.0
O6 A:G798 4.9 0.5 1.0
C6 A:G799 4.9 0.4 1.0

Magnesium binding site 9 out of 253 in 5wnp

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Magnesium binding site 9 out of 253 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:0.6
occ:1.00
O2 A:U1506 3.0 0.5 1.0
OP1 A:U1522 3.3 0.2 1.0
C2 A:U1506 4.1 0.6 1.0
MG A:MG1788 4.3 0.8 1.0
P A:U1522 4.3 0.1 1.0
CE K:LYS123 4.6 0.4 1.0
NZ K:LYS123 4.6 0.8 1.0
OP2 A:U1522 4.6 0.9 1.0
O5' A:U1522 4.7 0.2 1.0
N3 A:U1506 4.7 0.5 1.0
OP2 A:G1523 5.0 0.4 1.0

Magnesium binding site 10 out of 253 in 5wnp

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Magnesium binding site 10 out of 253 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:0.9
occ:1.00
O A:HOH1925 2.1 0.2 1.0
O A:HOH1915 2.1 0.8 1.0
OP1 A:G1508 3.0 0.2 1.0
OP1 A:G1505 3.0 0.0 1.0
OP1 A:A1500 3.0 0.6 1.0
O3' A:A1507 3.0 0.4 1.0
O5' A:G1505 3.4 0.7 1.0
OP1 A:G1504 3.5 0.8 1.0
P A:G1508 3.6 0.0 1.0
C5' A:G1505 3.6 0.4 1.0
P A:G1505 3.7 0.9 1.0
O5' A:G1504 3.9 0.9 1.0
C3' A:G1504 4.0 0.8 1.0
C5' A:G1508 4.2 0.0 1.0
C3' A:A1507 4.2 0.7 1.0
P A:A1500 4.2 0.2 1.0
P A:G1504 4.2 0.3 1.0
O3' A:G1504 4.2 0.2 1.0
O2' A:U1506 4.2 0.3 1.0
O5' A:G1508 4.4 0.8 1.0
O2' A:A1507 4.4 0.8 1.0
C4' A:A1507 4.5 0.3 1.0
OP2 A:C1501 4.5 0.3 1.0
MG A:MG1722 4.5 86.3 1.0
OP2 A:A1500 4.6 0.2 1.0
C2' A:U1506 4.7 0.6 1.0
OP2 A:G1504 4.8 0.9 1.0
OP2 A:G1508 4.8 0.3 1.0
C2' A:G1504 4.9 0.6 1.0
C5' A:A1507 5.0 0.4 1.0
C4' A:G1504 5.0 0.0 1.0
C2' A:A1507 5.0 0.4 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 Sep 30 06:38:18 2024

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