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Magnesium in PDB 4dr1: Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8)

Protein crystallography data

The structure of Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8), PDB code: 4dr1 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) 34.64 / 3.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 403.038, 403.038, 174.361, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 20.7

Other elements in 4dr1:

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

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 254 in 4dr1

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Magnesium binding site 1 out of 254 in the Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8)


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 Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:0.6
occ:1.00
O2 A:C381 3.0 0.6 1.0
O4 A:U65 3.2 0.7 1.0
N3 A:C381 3.6 0.9 1.0
C2 A:C381 3.7 0.3 1.0
C4 A:U65 4.2 0.1 1.0
C4 A:C381 4.8 0.2 1.0
C5 A:U65 5.0 0.8 1.0

Magnesium binding site 2 out of 254 in 4dr1

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Magnesium binding site 2 out of 254 in the Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8)


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 Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:0.1
occ:1.00
O A:HOH1903 2.1 77.0 1.0
O A:HOH1902 2.1 0.7 1.0
O A:HOH1901 2.1 100.0 1.0
O6 A:G377 3.7 0.9 1.0
N7 A:G377 4.2 0.3 1.0
N7 A:G376 4.3 0.3 1.0
MG A:MG1836 4.5 0.3 1.0
C6 A:G377 4.6 0.1 1.0
C5 A:G377 4.8 0.8 1.0
C5 A:G376 4.9 0.5 1.0
C8 A:G376 4.9 0.9 1.0

Magnesium binding site 3 out of 254 in 4dr1

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Magnesium binding site 3 out of 254 in the Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8)


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 Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:0.8
occ:1.00
O A:HOH1906 2.1 83.7 1.0
O A:HOH1904 2.1 0.7 1.0
O A:HOH1905 2.1 0.4 1.0
O6 A:G650 3.5 0.6 1.0
N7 A:G650 3.9 0.9 1.0
OP2 A:A753 4.1 0.2 1.0
O6 A:G649 4.2 0.8 1.0
N7 A:G649 4.2 0.5 1.0
C6 A:G650 4.4 0.6 1.0
C5 A:G650 4.5 0.7 1.0
OP1 A:A753 4.6 0.1 1.0
C6 A:G649 4.7 0.4 1.0
C5 A:G649 4.7 0.8 1.0
P A:A753 4.8 0.9 1.0

Magnesium binding site 4 out of 254 in 4dr1

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Magnesium binding site 4 out of 254 in the Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8)


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 Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:0.5
occ:1.00
O A:HOH1907 2.1 0.2 1.0
O A:HOH1908 2.1 0.8 1.0
OP2 A:G750 2.7 0.7 1.0
OP2 A:C749 2.9 0.0 1.0
OP1 A:C749 3.3 0.0 1.0
P A:C749 3.6 0.8 1.0
P A:G750 4.1 0.4 1.0
O2' A:C748 4.4 0.8 1.0
MG A:MG1819 4.5 0.8 1.0
O5' A:C749 4.6 0.0 1.0
O6 A:G752 4.7 0.3 1.0
OP1 A:G750 4.8 0.1 1.0
O3' A:C748 4.8 0.4 1.0

Magnesium binding site 5 out of 254 in 4dr1

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Magnesium binding site 5 out of 254 in the Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8)


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 Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:0.7
occ:1.00
O6 A:G741 3.1 1.0 1.0
O6 A:G664 3.4 0.0 1.0
O6 A:G742 3.5 0.5 1.0
N7 A:G741 3.6 0.9 1.0
C6 A:G741 3.9 0.1 1.0
C5 A:G741 4.1 0.7 1.0
C6 A:G742 4.3 0.5 1.0
C6 A:G664 4.5 0.4 1.0
O6 A:G666 4.5 1.0 1.0
O4 A:U740 4.6 0.2 1.0
N1 A:G664 4.7 0.3 1.0
N7 A:G742 4.7 0.4 1.0
C5 A:G742 4.8 0.1 1.0
C8 A:G741 4.8 0.4 1.0
C4 A:U740 5.0 0.0 1.0

Magnesium binding site 6 out of 254 in 4dr1

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Magnesium binding site 6 out of 254 in the Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8)


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 Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:0.7
occ:1.00
O A:HOH1912 2.1 0.3 1.0
O A:HOH1911 2.1 91.0 1.0
O A:HOH1910 2.1 0.4 1.0
O A:HOH1909 2.1 73.9 1.0
OP2 A:G117 2.6 0.8 1.0
OP2 A:G289 3.1 0.3 1.0
P A:G117 3.3 0.9 1.0
OP1 A:G117 3.3 0.5 1.0
OP1 A:A116 3.6 0.4 1.0
O3' A:A116 3.8 0.3 1.0
OP2 A:A116 4.0 0.7 1.0
O4 A:U118 4.1 0.4 1.0
P A:G289 4.2 0.1 1.0
O5' A:A288 4.2 0.4 1.0
OP2 A:A288 4.3 1.0 1.0
P A:A116 4.3 0.6 1.0
C3' A:A116 4.4 0.9 1.0
OP1 A:G289 4.4 94.5 1.0
C3' A:A288 4.4 100.0 1.0
C8 A:A288 4.5 0.9 1.0
C5 A:U118 4.5 0.8 1.0
N7 A:G117 4.6 0.3 1.0
C4 A:U118 4.7 0.0 1.0
P A:A288 4.7 0.7 1.0
O3' A:A288 4.8 0.8 1.0
O5' A:G117 4.8 0.6 1.0
N7 A:A288 4.8 0.3 1.0
C8 A:G117 4.9 0.7 1.0
C5' A:A116 5.0 0.9 1.0

Magnesium binding site 7 out of 254 in 4dr1

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Magnesium binding site 7 out of 254 in the Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8)


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 Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:0.6
occ:1.00
OP2 A:C48 2.6 0.3 1.0
OP1 A:G115 2.9 0.6 1.0
OP2 A:U49 3.6 0.5 1.0
P A:C48 3.7 0.5 1.0
O5' A:C48 3.8 0.3 1.0
O3' A:U114 3.9 0.8 1.0
P A:G115 4.0 0.1 1.0
OP1 A:A51 4.1 0.8 1.0
C5' A:G115 4.4 0.7 1.0
O3' A:C47 4.5 0.4 1.0
O5' A:G115 4.7 0.9 1.0
O2' A:C47 4.9 0.7 1.0
C5' A:C48 5.0 0.6 1.0
OP1 A:C48 5.0 0.4 1.0

Magnesium binding site 8 out of 254 in 4dr1

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Magnesium binding site 8 out of 254 in the Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8)


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 Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:0.6
occ:1.00
O A:HOH1914 2.1 0.5 1.0
O A:HOH1915 2.1 0.0 1.0
O A:HOH1913 2.1 1.0 1.0
O A:HOH1916 2.1 0.9 1.0
N7 A:G752 4.2 0.9 1.0
OP2 A:G752 4.3 0.4 1.0
OP1 A:C651 4.3 0.7 1.0
OP2 A:C651 4.5 0.5 1.0
OP2 A:U652 4.6 0.0 1.0
C8 A:G752 4.6 0.5 1.0
MG A:MG1819 4.6 0.8 1.0
OP2 A:U751 4.7 0.0 1.0
P A:C651 4.9 0.6 1.0
OP1 A:U751 5.0 0.4 1.0

Magnesium binding site 9 out of 254 in 4dr1

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Magnesium binding site 9 out of 254 in the Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8)


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 Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:0.2
occ:1.00
O A:HOH1918 2.1 99.6 1.0
O A:HOH1919 2.1 94.5 1.0
O A:HOH1917 2.1 0.4 1.0
O6 A:G800 3.6 0.0 1.0
O6 A:G799 3.6 0.8 1.0
N7 A:G799 4.1 0.3 1.0
C6 A:G800 4.2 0.6 1.0
OP2 A:A781 4.2 0.1 1.0
O A:HOH2040 4.3 0.9 1.0
O6 A:G798 4.4 0.4 1.0
N1 A:G800 4.4 0.2 1.0
C6 A:G799 4.5 0.1 1.0
OP1 A:A781 4.7 0.7 1.0
C5 A:G799 4.7 0.5 1.0
N7 A:G798 4.9 0.8 1.0

Magnesium binding site 10 out of 254 in 4dr1

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Magnesium binding site 10 out of 254 in the Crystal Structure of the Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8)


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 Apo 30S Ribosomal Subunit From Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:0.3
occ:1.00
O2' A:C795 3.4 0.1 1.0
O3' A:C795 3.5 0.3 1.0
O2 A:U1506 3.5 0.1 1.0
O4' A:U1506 3.6 0.8 1.0
OP1 A:C796 3.6 0.9 1.0
C1' A:U1506 3.9 0.2 1.0
P A:C796 4.2 0.3 1.0
C2 A:U1506 4.3 0.4 1.0
C4' A:U1506 4.3 0.2 1.0
O3' A:U1506 4.4 0.2 1.0
C2' A:C795 4.5 0.0 1.0
C3' A:C795 4.5 0.5 1.0
N1 A:U1506 4.5 0.1 1.0
C5' A:C796 4.7 0.2 1.0
C3' A:U1506 4.9 0.8 1.0
O5' A:C796 5.0 0.2 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 17:20:31 2024

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