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Magnesium in PDB 4duz: Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin

Protein crystallography data

The structure of Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin, PDB code: 4duz 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) 34.56 / 3.65
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.524, 402.524, 173.978, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 21.6

Other elements in 4duz:

The structure of Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 267 in 4duz

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Magnesium binding site 1 out of 267 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin


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, U13C, Bound with Streptomycin 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:HOH1901 2.1 0.1 1.0
O A:HOH1903 2.1 95.7 1.0
O A:HOH1902 2.1 89.3 1.0
O6 A:G377 3.0 0.2 1.0
O6 A:G376 3.3 0.7 1.0
N7 A:G376 3.8 0.7 1.0
C6 A:G376 3.9 0.1 1.0
C6 A:G377 4.0 0.4 1.0
C5 A:G376 4.1 0.6 1.0
C5 A:G377 4.7 0.5 1.0
N7 A:G377 4.7 0.2 1.0
C8 A:G376 4.9 0.1 1.0
N1 A:G377 4.9 0.6 1.0
O4 A:U387 4.9 0.2 1.0
O4 A:U375 4.9 0.7 1.0

Magnesium binding site 2 out of 267 in 4duz

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Magnesium binding site 2 out of 267 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin


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, U13C, Bound with Streptomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:0.4
occ:1.00
O A:HOH1906 2.1 77.2 1.0
O A:HOH1905 2.1 0.1 1.0
O A:HOH1907 2.1 0.1 1.0
O6 A:G650 3.6 0.2 1.0
OP2 A:A753 3.8 0.1 1.0
O6 A:G649 4.1 0.5 1.0
N7 A:G650 4.1 0.9 1.0
OP1 A:A753 4.4 0.4 1.0
C6 A:G650 4.5 0.7 1.0
P A:A753 4.5 1.0 1.0
C5 A:G650 4.7 0.9 1.0
N7 A:G649 4.8 0.7 1.0
C6 A:G649 4.8 0.7 1.0
O5' A:A753 4.9 0.2 1.0
N4 A:C651 5.0 98.7 1.0

Magnesium binding site 3 out of 267 in 4duz

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Magnesium binding site 3 out of 267 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin


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, U13C, Bound with Streptomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:0.8
occ:1.00
OP2 A:G654 2.8 0.3 1.0
N6 A:A655 4.1 96.1 1.0
P A:G654 4.2 0.2 1.0
C5' A:A653 4.5 0.0 1.0
N7 A:A655 4.6 0.0 1.0
C3' A:A653 4.6 0.7 1.0
C4' A:A653 4.8 0.4 1.0
O3' A:A653 4.8 0.7 1.0
N4 A:C656 4.9 0.9 1.0
O5' A:A653 4.9 0.5 1.0
O5' A:G654 4.9 0.0 1.0
C6 A:A655 5.0 0.8 1.0

Magnesium binding site 4 out of 267 in 4duz

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Magnesium binding site 4 out of 267 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin


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, U13C, Bound with Streptomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:0.7
occ:1.00
O A:HOH1911 2.0 76.9 1.0
O A:HOH1909 2.1 0.9 1.0
O A:HOH1910 2.1 98.2 1.0
O A:HOH1908 2.1 92.4 1.0
OP2 A:G117 2.3 0.8 1.0
OP2 A:G289 2.7 0.1 1.0
P A:G117 3.6 0.6 1.0
OP2 A:A116 3.7 0.4 1.0
O4 A:U118 3.8 0.6 1.0
OP1 A:A116 3.8 0.7 1.0
P A:G289 3.8 0.2 1.0
O3' A:A116 4.1 0.7 1.0
C3' A:A288 4.1 98.1 1.0
OP1 A:G289 4.2 98.5 1.0
P A:A116 4.2 0.9 1.0
O5' A:A288 4.2 0.2 1.0
O3' A:A288 4.4 98.9 1.0
C5 A:U118 4.4 0.3 1.0
C8 A:A288 4.5 0.5 1.0
C4 A:U118 4.5 0.6 1.0
N7 A:G117 4.5 0.7 1.0
OP2 A:A288 4.5 0.9 1.0
OP1 A:G117 4.5 0.6 1.0
C3' A:A116 4.6 0.4 1.0
O5' A:G117 4.6 0.5 1.0
N7 A:A288 4.9 0.9 1.0
P A:A288 4.9 0.8 1.0
C2' A:A288 4.9 95.6 1.0
O5' A:A116 5.0 91.6 1.0

Magnesium binding site 5 out of 267 in 4duz

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Magnesium binding site 5 out of 267 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin


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, U13C, Bound with Streptomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:0.9
occ:1.00
OP2 A:C48 2.7 0.2 1.0
MG A:MG1807 2.8 99.8 1.0
O2' A:C47 3.7 1.0 1.0
P A:C48 3.8 0.8 1.0
O3' A:C47 3.9 0.7 1.0
O3' A:U114 4.1 0.6 1.0
OP1 A:G115 4.2 0.5 1.0
OP1 A:A51 4.3 0.0 1.0
C3' A:C47 4.4 0.8 1.0
C2' A:C47 4.5 0.8 1.0
O5' A:C48 4.6 0.1 1.0
P A:G115 4.9 0.6 1.0
C4' A:U114 5.0 0.3 1.0
OP2 A:A51 5.0 0.8 1.0

Magnesium binding site 6 out of 267 in 4duz

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Magnesium binding site 6 out of 267 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin


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, U13C, Bound with Streptomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:0.2
occ:1.00
O A:HOH1914 2.1 95.7 1.0
O A:HOH1915 2.1 0.2 1.0
O A:HOH1913 2.1 0.2 1.0
O A:HOH1912 2.1 0.4 1.0
OP2 A:U652 3.6 0.2 1.0
N7 A:G752 4.0 0.3 1.0
OP1 A:C651 4.3 0.3 1.0
OP2 A:C651 4.7 0.4 1.0
OP2 A:U751 4.7 0.6 1.0
C8 A:G752 4.7 0.3 1.0
P A:C651 4.9 1.0 1.0

Magnesium binding site 7 out of 267 in 4duz

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Magnesium binding site 7 out of 267 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin


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, U13C, Bound with Streptomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:0.4
occ:1.00
O A:HOH1918 2.1 0.8 1.0
O A:HOH1917 2.1 87.1 1.0
O A:HOH1916 2.1 95.0 1.0
O6 A:G800 3.4 0.1 1.0
O6 A:G799 3.4 0.0 1.0
O A:HOH2014 4.0 0.2 1.0
C6 A:G800 4.1 0.2 1.0
N7 A:G799 4.3 0.9 1.0
C6 A:G799 4.4 0.1 1.0
OP1 A:A781 4.4 0.9 1.0
N1 A:G800 4.5 1.0 1.0
OP2 A:A781 4.7 0.3 1.0
O6 A:G798 4.7 0.3 1.0
C5 A:G799 4.8 1.0 1.0
N7 A:G798 4.8 0.6 1.0

Magnesium binding site 8 out of 267 in 4duz

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Magnesium binding site 8 out of 267 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin


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, U13C, Bound with Streptomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:0.4
occ:1.00
O A:HOH1920 2.1 47.8 1.0
O A:HOH1919 2.1 95.2 1.0
OP1 A:G1505 2.6 0.8 1.0
OP1 A:G1508 2.7 0.9 1.0
OP1 A:A1500 2.9 0.4 1.0
O3' A:A1507 3.4 0.4 1.0
C5' A:A1500 3.5 0.9 1.0
OP2 A:C1501 3.6 1.0 1.0
C3' A:G1504 3.6 0.1 1.0
P A:G1508 3.6 0.7 1.0
P A:A1500 3.6 0.7 1.0
P A:G1505 3.7 0.6 1.0
C5' A:G1508 3.7 0.0 1.0
OP2 A:A1500 3.9 0.7 1.0
O5' A:G1505 3.9 0.1 1.0
O5' A:A1500 3.9 0.9 1.0
C2' A:G1504 4.1 1.0 1.0
O2' A:G1504 4.1 0.5 1.0
O3' A:G1504 4.1 0.1 1.0
C5' A:G1505 4.2 0.3 1.0
O5' A:G1508 4.2 0.1 1.0
O5' A:G1504 4.4 0.0 1.0
O2' A:A1507 4.5 0.6 1.0
OP1 A:G1504 4.6 1.0 1.0
C3' A:A1507 4.7 0.2 1.0
C4' A:G1504 4.8 0.5 1.0
P A:C1501 4.8 0.6 1.0
P A:G1504 4.8 0.8 1.0
OP2 A:G1504 4.8 0.5 1.0
MG A:MG1709 4.8 0.1 1.0
C5' A:G1504 4.9 0.6 1.0
OP2 A:G1508 4.9 0.3 1.0
C4' A:A1500 4.9 0.5 1.0
C4' A:G1508 5.0 0.8 1.0
O2' A:U1506 5.0 0.5 1.0

Magnesium binding site 9 out of 267 in 4duz

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Magnesium binding site 9 out of 267 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin


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, U13C, Bound with Streptomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:0.8
occ:1.00
O A:HOH1922 2.1 0.7 1.0
O A:HOH1921 2.1 89.9 1.0
O6 A:G1526 3.6 0.4 1.0
O6 A:G1525 4.5 0.2 1.0
C6 A:G1526 4.7 0.3 1.0
N7 A:G1525 4.8 0.0 1.0
N4 A:C1509 5.0 1.0 1.0

Magnesium binding site 10 out of 267 in 4duz

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Magnesium binding site 10 out of 267 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, U13C, Bound with Streptomycin


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, U13C, Bound with Streptomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1611

b:0.0
occ:1.00
O A:HOH1926 2.1 79.4 1.0
O A:HOH1923 2.1 0.2 1.0
O A:HOH1924 2.1 0.7 1.0
O A:HOH1925 2.1 0.8 1.0
O A:HOH1927 2.1 93.6 1.0
OP1 A:C620 3.4 0.7 1.0
OP2 A:G617 4.1 0.8 1.0
OP1 A:A621 4.5 0.4 1.0
OP2 A:A621 4.5 0.9 1.0
N7 A:G617 4.5 0.6 1.0
C5' A:C620 4.5 0.1 1.0
P A:C620 4.8 0.2 1.0
P A:A621 4.9 0.7 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: Thu Aug 15 19:39:03 2024

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