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Magnesium in PDB 4dr3: Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound

Protein crystallography data

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound, PDB code: 4dr3 was solved by H.Demirci, F.Murphy Iv, E.Murphy, S.T.Gregory, A.E.Dahlberg, G.Jogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.55 / 3.35
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 404.041, 404.041, 173.527, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.6

Other elements in 4dr3:

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 264 in 4dr3

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Magnesium binding site 1 out of 264 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:0.1
occ:1.00
O A:HOH1901 2.1 0.5 1.0
O A:HOH1904 2.1 0.1 1.0
O A:HOH1903 2.1 77.3 1.0
O A:HOH1902 2.1 93.7 1.0
O6 A:G377 3.1 0.3 1.0
O6 A:G376 3.4 0.4 1.0
N7 A:G376 3.7 0.6 1.0
C6 A:G376 4.1 0.6 1.0
C6 A:G377 4.1 0.1 1.0
C5 A:G376 4.2 0.7 1.0
N7 A:G377 4.3 0.3 1.0
C5 A:G377 4.6 0.7 1.0
C8 A:G376 4.8 0.8 1.0
O4 A:U387 4.8 0.2 1.0
O4 A:U375 5.0 0.4 1.0

Magnesium binding site 2 out of 264 in 4dr3

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Magnesium binding site 2 out of 264 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:0.3
occ:1.00
O A:HOH1906 2.1 0.6 1.0
O A:HOH1907 2.1 78.2 1.0
O A:HOH1905 2.1 0.2 1.0
O6 A:G650 3.6 0.6 1.0
N7 A:G650 3.8 0.1 1.0
O6 A:G649 3.9 1.0 1.0
N7 A:G649 4.1 0.1 1.0
OP2 A:A753 4.2 1.0 1.0
C6 A:G650 4.4 0.2 1.0
C5 A:G650 4.5 0.9 1.0
C6 A:G649 4.5 0.8 1.0
C5 A:G649 4.6 0.8 1.0
C8 A:G650 5.0 0.6 1.0

Magnesium binding site 3 out of 264 in 4dr3

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Magnesium binding site 3 out of 264 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:0.4
occ:1.00
O A:HOH1908 2.1 0.2 1.0
O A:HOH1909 2.1 0.4 1.0
OP2 A:G750 2.8 1.0 1.0
OP2 A:C749 3.0 0.2 1.0
OP1 A:C749 3.0 1.0 1.0
P A:C749 3.5 0.6 1.0
P A:G750 4.2 0.3 1.0
O2' A:C748 4.4 0.1 1.0
O3' A:C748 4.4 0.4 1.0
O5' A:C749 4.8 91.5 1.0
OP1 A:G750 4.9 0.1 1.0

Magnesium binding site 4 out of 264 in 4dr3

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Magnesium binding site 4 out of 264 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:0.4
occ:1.00
OP2 A:G654 2.7 99.0 1.0
P A:G654 4.2 0.5 1.0
N6 A:A655 4.2 97.7 1.0
N7 A:A655 4.3 94.8 1.0
N4 A:C656 4.4 0.5 1.0
O5' A:G654 4.7 97.7 1.0
C3' A:A653 5.0 0.9 1.0
C5' A:A653 5.0 98.8 1.0
C5 A:A655 5.0 90.9 1.0

Magnesium binding site 5 out of 264 in 4dr3

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Magnesium binding site 5 out of 264 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:97.2
occ:1.00
O A:HOH1911 2.1 0.2 1.0
O A:HOH1913 2.1 53.5 1.0
O A:HOH1910 2.1 67.0 1.0
O A:HOH1912 2.1 73.7 1.0
OP2 A:G117 2.5 0.4 1.0
OP2 A:G289 2.8 98.5 1.0
OP1 A:A116 3.6 77.2 1.0
P A:G117 3.8 0.8 1.0
O4 A:U118 3.9 88.8 1.0
P A:G289 3.9 90.8 1.0
OP2 A:A116 4.1 0.8 1.0
OP1 A:G289 4.1 80.2 1.0
C3' A:A288 4.2 78.5 1.0
O3' A:A116 4.2 80.7 1.0
O5' A:A288 4.2 95.5 1.0
N7 A:G117 4.2 0.6 1.0
C5 A:U118 4.3 82.3 1.0
P A:A116 4.3 90.3 1.0
C8 A:A288 4.3 99.2 1.0
O3' A:A288 4.4 83.7 1.0
C4 A:U118 4.5 86.5 1.0
OP2 A:A288 4.5 0.4 1.0
C3' A:A116 4.5 81.3 1.0
N7 A:A288 4.6 0.7 1.0
O5' A:G117 4.7 95.8 1.0
C8 A:G117 4.8 0.4 1.0
OP1 A:G117 4.8 0.6 1.0
P A:A288 4.8 0.0 1.0
C2' A:A288 4.9 78.0 1.0
N9 A:A288 4.9 86.8 1.0
C5' A:A116 4.9 86.0 1.0

Magnesium binding site 6 out of 264 in 4dr3

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Magnesium binding site 6 out of 264 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:91.5
occ:1.00
OP2 A:C48 2.6 0.1 1.0
OP1 A:G115 2.9 0.4 1.0
O5' A:C48 3.4 0.5 1.0
P A:C48 3.4 0.6 1.0
O3' A:C47 3.7 0.1 1.0
OP2 A:U49 3.7 0.6 1.0
O3' A:U114 4.0 0.2 1.0
P A:G115 4.1 0.1 1.0
OP1 A:A51 4.2 0.5 1.0
O2' A:C47 4.5 0.8 1.0
C5' A:C48 4.6 0.1 1.0
C3' A:C47 4.8 0.8 1.0
OP1 A:C48 4.9 1.0 1.0
C5' A:G115 5.0 0.8 1.0

Magnesium binding site 7 out of 264 in 4dr3

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Magnesium binding site 7 out of 264 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:0.1
occ:1.00
O A:HOH1916 2.1 0.5 1.0
O A:HOH1917 2.1 0.2 1.0
O A:HOH1915 2.1 0.6 1.0
O A:HOH1914 2.1 0.9 1.0
OP2 A:U751 4.0 0.8 1.0
N7 A:G752 4.0 0.8 1.0
OP2 A:U652 4.2 0.3 1.0
C8 A:G752 4.5 95.7 1.0
OP1 A:C651 4.7 0.7 1.0
OP2 A:G752 4.7 0.7 1.0
OP1 A:U751 4.7 0.4 1.0
P A:U751 4.8 0.4 1.0

Magnesium binding site 8 out of 264 in 4dr3

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Magnesium binding site 8 out of 264 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:0.6
occ:1.00
O A:HOH1920 2.1 97.1 1.0
O A:HOH1919 2.1 84.6 1.0
O A:HOH1918 2.1 94.7 1.0
O6 A:G800 3.5 0.7 1.0
O6 A:G799 3.8 0.1 1.0
O A:HOH2043 4.1 98.2 1.0
OP2 A:A781 4.1 0.0 1.0
C6 A:G800 4.1 0.8 1.0
N7 A:G799 4.2 0.3 1.0
N1 A:G800 4.4 1.0 1.0
O6 A:G798 4.6 0.6 1.0
C6 A:G799 4.7 96.6 1.0
N7 A:G798 4.8 96.5 1.0
C5 A:G799 4.8 99.1 1.0

Magnesium binding site 9 out of 264 in 4dr3

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Magnesium binding site 9 out of 264 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:0.1
occ:1.00
O2' A:C795 3.2 0.9 1.0
O2 A:U1506 3.6 0.3 1.0
O3' A:C795 3.6 0.9 1.0
O4' A:U1506 4.0 0.4 1.0
C1' A:U1506 4.1 0.3 1.0
OP1 A:C796 4.2 0.1 1.0
O3' A:U1506 4.3 0.2 1.0
C2' A:C795 4.3 0.4 1.0
C3' A:C795 4.4 0.6 1.0
C2 A:U1506 4.5 0.6 1.0
OP1 A:A1507 4.6 0.7 1.0
C4' A:U1506 4.6 0.6 1.0
P A:C796 4.6 0.3 1.0
N1 A:U1506 4.8 0.5 1.0
C4' A:C795 4.9 0.2 1.0
C3' A:U1506 5.0 0.6 1.0

Magnesium binding site 10 out of 264 in 4dr3

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Magnesium binding site 10 out of 264 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound


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 the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Streptomycin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1611

b:74.8
occ:1.00
O A:HOH1921 2.1 0.8 1.0
O A:HOH1922 2.1 92.8 1.0
OP1 A:A1500 2.6 99.5 1.0
OP1 A:G1508 2.6 100.0 1.0
OP1 A:G1505 2.8 0.5 1.0
O3' A:A1507 3.1 97.7 1.0
P A:G1508 3.5 0.3 1.0
O5' A:G1505 3.5 0.0 1.0
OP2 A:G1504 3.6 99.2 1.0
P A:G1505 3.7 0.4 1.0
C3' A:G1504 3.7 0.3 1.0
P A:A1500 3.8 0.4 1.0
C5' A:G1508 3.9 96.8 1.0
C5' A:G1505 4.0 0.1 1.0
OP2 A:C1501 4.1 0.8 1.0
O3' A:G1504 4.2 1.0 1.0
O5' A:G1508 4.2 0.3 1.0
OP2 A:A1500 4.3 0.2 1.0
O2' A:U1506 4.3 0.4 1.0
P A:G1504 4.4 0.7 1.0
C3' A:A1507 4.4 97.3 1.0
MG A:MG1735 4.5 83.0 1.0
OP1 A:G1504 4.5 0.5 1.0
C5' A:G1504 4.5 0.1 1.0
O5' A:A1500 4.5 99.5 1.0
C4' A:G1504 4.5 0.0 1.0
O2' A:A1507 4.7 0.0 1.0
OP2 A:G1508 4.7 1.0 1.0
C2' A:G1504 4.7 0.6 1.0
C4' A:A1507 4.9 0.5 1.0
C2' A:U1506 4.9 0.8 1.0
O5' A:G1504 5.0 0.5 1.0
C5' A:A1500 5.0 98.4 1.0

Reference:

H.Demirci, F.Murphy, E.Murphy, S.T.Gregory, A.E.Dahlberg, G.Jogl. A Structural Basis For Streptomycin-Induced Misreading of the Genetic Code. Nat Commun V. 4 1355 2013.
ISSN: ESSN 2041-1723
PubMed: 23322043
DOI: 10.1038/NCOMMS2346
Page generated: Thu Aug 15 17:20:56 2024

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