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Magnesium in PDB 4dv0: Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G

Protein crystallography data

The structure of Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G, PDB code: 4dv0 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) 34.82 / 3.85
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.108, 402.108, 173.997, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 20.6

Other elements in 4dv0:

The structure of Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 277 in 4dv0

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Magnesium binding site 1 out of 277 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G


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 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:0.7
occ:1.00
O A:HOH1902 2.1 0.0 1.0
O A:HOH1901 2.1 0.1 1.0
O A:HOH1903 2.1 68.9 1.0
O6 A:G377 4.3 0.5 1.0
N7 A:G377 4.6 0.4 1.0
N7 A:G376 4.8 0.9 1.0
CG2 P:THR67 4.8 0.4 1.0

Magnesium binding site 2 out of 277 in 4dv0

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Magnesium binding site 2 out of 277 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G


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 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:0.8
occ:1.00
O A:HOH1904 2.1 0.9 1.0
O A:HOH1905 2.1 76.3 1.0
O A:HOH1906 2.1 0.8 1.0
O6 A:G650 3.4 0.6 1.0
OP2 A:A753 3.4 0.8 1.0
P A:A753 4.2 0.3 1.0
OP1 A:A753 4.3 0.8 1.0
O5' A:A753 4.5 0.6 1.0
C6 A:G650 4.5 0.3 1.0

Magnesium binding site 3 out of 277 in 4dv0

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Magnesium binding site 3 out of 277 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G


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 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:0.7
occ:1.00
O A:HOH1907 2.1 0.3 1.0
O A:HOH1908 2.1 98.4 1.0
OP2 A:C749 2.9 0.6 1.0
OP1 A:C749 3.0 0.8 1.0
OP2 A:G750 3.1 0.3 1.0
P A:C749 3.4 0.8 1.0
O2' A:C748 4.2 0.5 1.0
MG A:MG1765 4.3 0.7 1.0
O3' A:C748 4.3 0.9 1.0
P A:G750 4.5 0.2 1.0
O5' A:C749 4.7 0.9 1.0
OP2 A:A653 4.8 0.4 1.0
C3' A:C749 5.0 0.6 1.0

Magnesium binding site 4 out of 277 in 4dv0

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Magnesium binding site 4 out of 277 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G


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 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:0.6
occ:1.00
O A:HOH2104 2.9 0.2 1.0
O6 A:G741 3.3 0.7 1.0
N7 A:G741 3.7 0.2 1.0
O6 A:G742 3.9 0.4 1.0
C6 A:G741 4.0 0.2 1.0
O6 A:G664 4.1 0.3 1.0
C5 A:G741 4.2 0.4 1.0
O A:HOH2103 4.3 0.7 1.0
N7 A:G742 4.6 0.9 1.0
MG A:MG1780 4.6 0.1 1.0
C6 A:G742 4.7 0.0 1.0
O4 A:U740 4.8 0.5 1.0
C8 A:G741 4.9 0.0 1.0
C5 A:G742 4.9 0.4 1.0

Magnesium binding site 5 out of 277 in 4dv0

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Magnesium binding site 5 out of 277 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G


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 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:0.8
occ:1.00
O A:HOH1912 2.1 0.5 1.0
O A:HOH1910 2.1 0.2 1.0
O A:HOH1911 2.1 91.1 1.0
O A:HOH1909 2.1 87.1 1.0
OP2 A:G117 2.6 0.7 1.0
OP2 A:G289 3.0 0.8 1.0
P A:G117 3.5 0.2 1.0
OP1 A:G117 3.6 0.2 1.0
OP1 A:A116 3.8 0.5 1.0
OP2 A:A116 3.9 0.5 1.0
O3' A:A116 4.0 0.1 1.0
P A:G289 4.1 0.6 1.0
O4 A:U118 4.1 0.7 1.0
OP2 A:A288 4.2 0.6 1.0
O5' A:A288 4.3 0.3 1.0
C8 A:A288 4.3 0.8 1.0
P A:A116 4.3 0.0 1.0
OP1 A:G289 4.4 0.5 1.0
C3' A:A288 4.5 0.6 1.0
C3' A:A116 4.5 0.8 1.0
N7 A:A288 4.5 0.3 1.0
C5 A:U118 4.6 0.9 1.0
N7 A:G117 4.6 0.4 1.0
P A:A288 4.7 0.1 1.0
O3' A:A288 4.7 0.9 1.0
C4 A:U118 4.7 0.1 1.0
O5' A:G117 4.9 0.1 1.0
C8 A:G117 5.0 0.6 1.0

Magnesium binding site 6 out of 277 in 4dv0

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Magnesium binding site 6 out of 277 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G


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 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:0.9
occ:1.00
O A:HOH1914 2.1 0.9 1.0
O A:HOH1916 2.1 0.3 1.0
O A:HOH1913 2.1 0.3 1.0
O A:HOH1915 2.1 0.8 1.0
OP1 A:C651 4.0 0.8 1.0
N7 A:G752 4.2 0.9 1.0
OP2 A:U751 4.3 0.0 1.0
OP2 A:U652 4.4 1.0 1.0
OP1 A:U751 4.6 0.2 1.0
OP2 A:G752 4.6 0.9 1.0
C8 A:G752 4.6 0.4 1.0
MG A:MG1765 4.6 0.7 1.0
P A:U751 4.9 0.7 1.0
P A:C651 4.9 0.2 1.0

Magnesium binding site 7 out of 277 in 4dv0

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Magnesium binding site 7 out of 277 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G


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 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:0.6
occ:1.00
O A:HOH1917 2.1 72.5 1.0
O A:HOH1918 2.1 0.0 1.0
O A:HOH1919 2.1 0.6 1.0
O6 A:G800 4.3 0.6 1.0
OP1 A:A781 4.4 0.9 1.0
O6 A:G799 4.9 0.5 1.0
O A:HOH2020 5.0 0.6 1.0

Magnesium binding site 8 out of 277 in 4dv0

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Magnesium binding site 8 out of 277 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G


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 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:0.7
occ:1.00
O3' A:C795 3.3 0.3 1.0
O2' A:C795 3.4 0.3 1.0
OP1 A:C796 3.5 0.5 1.0
O2 A:U1506 3.7 0.6 1.0
O4' A:U1506 3.9 0.8 1.0
C1' A:U1506 4.0 0.3 1.0
P A:C796 4.0 0.0 1.0
C3' A:C795 4.3 0.1 1.0
C2 A:U1506 4.4 0.2 1.0
C2' A:C795 4.4 0.8 1.0
O3' A:U1506 4.5 0.3 1.0
C4' A:U1506 4.6 0.2 1.0
N1 A:U1506 4.6 0.3 1.0
C5' A:C796 4.9 0.4 1.0
C4' A:C795 4.9 0.5 1.0
O5' A:C796 5.0 0.4 1.0

Magnesium binding site 9 out of 277 in 4dv0

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Magnesium binding site 9 out of 277 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G


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 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:0.8
occ:1.00
O A:HOH1920 2.1 0.3 1.0
O A:HOH1921 2.1 83.9 1.0
OP1 A:A1500 2.6 0.5 1.0
OP1 A:G1508 2.6 0.8 1.0
O3' A:A1507 2.7 0.7 1.0
OP1 A:G1505 2.8 0.9 1.0
P A:G1508 3.2 0.1 1.0
C5' A:G1508 3.5 0.6 1.0
O5' A:G1508 3.8 0.5 1.0
P A:A1500 3.8 0.7 1.0
C3' A:G1504 3.9 0.9 1.0
C3' A:A1507 4.0 0.4 1.0
OP2 A:C1501 4.0 0.9 1.0
P A:G1505 4.0 0.5 1.0
O2' A:A1507 4.1 0.7 1.0
OP1 A:G1504 4.1 0.6 1.0
O5' A:G1504 4.2 0.5 1.0
O5' A:G1505 4.3 0.1 1.0
C5' A:G1505 4.3 0.7 1.0
OP2 A:A1500 4.3 0.4 1.0
C4' A:A1507 4.4 0.2 1.0
O5' A:A1500 4.4 0.8 1.0
C2' A:G1504 4.5 0.3 1.0
MG A:MG1714 4.5 0.7 1.0
OP2 A:G1508 4.5 0.5 1.0
O3' A:G1504 4.5 0.6 1.0
O2' A:G1504 4.5 0.2 1.0
O2' A:U1506 4.6 0.6 1.0
C2' A:A1507 4.6 0.9 1.0
C5' A:A1500 4.6 0.3 1.0
P A:G1504 4.6 0.1 1.0
C4' A:G1508 4.8 0.8 1.0

Magnesium binding site 10 out of 277 in 4dv0

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Magnesium binding site 10 out of 277 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G


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 30S Ribosomal Subunit with A 16S Rrna Mutation, U20G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:0.8
occ:1.00
O A:HOH1924 2.1 0.1 1.0
O A:HOH1923 2.1 0.4 1.0
O A:HOH1925 2.1 0.0 1.0
O A:HOH1922 2.1 89.5 1.0
O6 A:G1525 3.9 0.1 1.0
N7 A:G1525 3.9 0.1 1.0
O6 A:G1526 4.1 0.0 1.0
N4 A:C1524 4.5 1.0 1.0
C5 A:C1524 4.5 1.0 1.0
C6 A:G1525 4.6 0.8 1.0
C5 A:G1525 4.7 0.9 1.0
C4 A:C1524 4.7 0.4 1.0
N7 A:G1526 4.7 0.8 1.0
C6 A:G1526 5.0 0.8 1.0
C8 A:G1525 5.0 0.5 1.0

Reference:

H.Demirci, F.Murphy Iv, E.Murphy, S.T.Gregory, A.E.Dahlberg, G.Jogl. A Structural Basis For Streptomycin Resistance To Be Published.
Page generated: Fri Aug 16 04:28:20 2024

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