Atomistry » Magnesium » PDB 4dob-4dv6 » 4dv4
Atomistry »
  Magnesium »
    PDB 4dob-4dv6 »
      4dv4 »

Magnesium in PDB 4dv4: Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G

Protein crystallography data

The structure of Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G, PDB code: 4dv4 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) 34.66 / 3.65
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.638, 402.638, 174.747, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 20.8

Other elements in 4dv4:

The structure of Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 287 in 4dv4

Go back to Magnesium Binding Sites List in 4dv4
Magnesium binding site 1 out of 287 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G


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, A914G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:0.4
occ:1.00
O2 A:C381 3.3 0.7 1.0
O4 A:U65 3.5 0.4 1.0
C2 A:C381 4.2 0.8 1.0
N3 A:C381 4.3 0.2 1.0
C4 A:U65 4.6 0.1 1.0

Magnesium binding site 2 out of 287 in 4dv4

Go back to Magnesium Binding Sites List in 4dv4
Magnesium binding site 2 out of 287 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G


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, A914G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1602

b:0.6
occ:1.00
O A:HOH1903 2.1 91.6 1.0
O A:HOH1902 2.1 0.0 1.0
O A:HOH1901 2.1 92.2 1.0
O6 A:G377 3.7 1.0 1.0
N7 A:G376 4.2 0.8 1.0
MG A:MG1775 4.3 0.7 1.0
N7 A:G377 4.5 0.5 1.0
O6 A:G376 4.7 0.8 1.0
C6 A:G377 4.7 0.0 1.0
C5 A:G376 4.8 0.1 1.0
C8 A:G376 4.9 0.3 1.0
C6 A:G376 5.0 0.0 1.0

Magnesium binding site 3 out of 287 in 4dv4

Go back to Magnesium Binding Sites List in 4dv4
Magnesium binding site 3 out of 287 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G


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, A914G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:0.6
occ:1.00
O A:HOH1905 2.1 0.7 1.0
O A:HOH1904 2.1 0.5 1.0
O A:HOH1906 2.1 1.0 1.0
O6 A:G650 3.2 0.1 1.0
O6 A:G649 3.8 1.0 1.0
N7 A:G649 4.1 0.1 1.0
N7 A:G650 4.2 0.5 1.0
OP2 A:A753 4.3 0.3 1.0
C6 A:G650 4.3 0.6 1.0
C6 A:G649 4.4 0.5 1.0
C5 A:G649 4.5 0.9 1.0
C5 A:G650 4.6 0.4 1.0
OP1 A:A753 4.9 0.5 1.0
P A:A753 5.0 0.5 1.0

Magnesium binding site 4 out of 287 in 4dv4

Go back to Magnesium Binding Sites List in 4dv4
Magnesium binding site 4 out of 287 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G


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, A914G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1604

b:0.3
occ:1.00
O A:HOH1907 2.1 0.3 1.0
O A:HOH1908 2.1 83.3 1.0
OP2 A:C749 2.9 0.7 1.0
OP2 A:G750 3.8 0.8 1.0
O2' A:C748 3.8 0.6 1.0
OP1 A:C749 3.9 0.6 1.0
P A:C749 3.9 0.1 1.0
OP2 A:A653 3.9 0.1 1.0
O3' A:C748 4.8 0.1 1.0
O6 A:G752 5.0 0.5 1.0
C2' A:C748 5.0 0.7 1.0

Magnesium binding site 5 out of 287 in 4dv4

Go back to Magnesium Binding Sites List in 4dv4
Magnesium binding site 5 out of 287 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G


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, A914G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1605

b:0.4
occ:1.00
O A:HOH2099 2.9 0.2 1.0
O A:HOH2100 3.0 0.5 1.0
O A:HOH2101 3.0 0.4 1.0
O6 A:G742 3.0 0.5 1.0
O6 A:G741 3.5 0.9 1.0
MG A:MG1779 3.7 0.1 1.0
N7 A:G741 3.7 0.2 1.0
O6 A:G664 3.8 0.1 1.0
C6 A:G742 3.9 0.9 1.0
N7 A:G742 4.2 0.2 1.0
C6 A:G741 4.2 0.2 1.0
C5 A:G741 4.2 0.8 1.0
C5 A:G742 4.3 0.8 1.0
N6 A:A663 4.6 0.2 1.0
C6 A:G664 4.7 0.1 1.0
N1 A:G664 4.8 0.7 1.0
C8 A:G741 4.8 0.1 1.0
N1 A:G742 5.0 0.6 1.0
O6 A:G666 5.0 0.1 1.0

Magnesium binding site 6 out of 287 in 4dv4

Go back to Magnesium Binding Sites List in 4dv4
Magnesium binding site 6 out of 287 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G


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, A914G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1606

b:0.1
occ:1.00
O A:HOH1912 2.1 0.1 1.0
O A:HOH1910 2.1 0.7 1.0
O A:HOH1909 2.1 73.2 1.0
O A:HOH1911 2.1 72.0 1.0
OP2 A:G117 2.6 0.3 1.0
OP2 A:G289 3.0 0.8 1.0
P A:G117 3.3 0.9 1.0
OP1 A:G117 3.4 0.9 1.0
OP1 A:A116 3.6 0.3 1.0
OP2 A:A116 3.9 0.0 1.0
O3' A:A116 4.0 0.2 1.0
O4 A:U118 4.1 0.1 1.0
P A:G289 4.1 0.9 1.0
O5' A:A288 4.2 0.8 1.0
P A:A116 4.2 0.7 1.0
OP2 A:A288 4.3 0.7 1.0
C3' A:A288 4.4 0.9 1.0
OP1 A:G289 4.4 0.0 1.0
C3' A:A116 4.4 0.6 1.0
C5 A:U118 4.5 0.9 1.0
C8 A:A288 4.5 0.1 1.0
N7 A:G117 4.6 0.8 1.0
O3' A:A288 4.7 0.3 1.0
P A:A288 4.7 0.2 1.0
C4 A:U118 4.7 0.4 1.0
O5' A:G117 4.8 0.4 1.0
N7 A:A288 4.8 0.9 1.0
C8 A:G117 4.9 0.5 1.0

Magnesium binding site 7 out of 287 in 4dv4

Go back to Magnesium Binding Sites List in 4dv4
Magnesium binding site 7 out of 287 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G


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, A914G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1607

b:0.0
occ:1.00
O A:HOH1915 2.1 68.4 1.0
O A:HOH1914 2.1 0.5 1.0
O A:HOH1916 2.1 0.4 1.0
O A:HOH1913 2.1 0.3 1.0
OP1 A:C651 3.7 0.4 1.0
OP2 A:C651 4.2 0.5 1.0
OP2 A:U652 4.3 0.5 1.0
P A:C651 4.4 0.8 1.0
MG A:MG1765 4.7 0.7 1.0
N7 A:G752 4.8 0.3 1.0
OP2 A:U751 5.0 0.7 1.0

Magnesium binding site 8 out of 287 in 4dv4

Go back to Magnesium Binding Sites List in 4dv4
Magnesium binding site 8 out of 287 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G


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, A914G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1608

b:99.3
occ:1.00
O A:HOH1918 2.1 82.7 1.0
O A:HOH1919 2.1 89.2 1.0
O A:HOH1917 2.1 85.5 1.0
O6 A:G800 4.3 0.3 1.0
O6 A:G798 4.7 0.0 1.0
O6 A:G799 4.7 0.8 1.0
O A:HOH2018 4.8 94.0 1.0
OP2 A:A781 4.9 0.9 1.0
N7 A:G798 4.9 1.0 1.0

Magnesium binding site 9 out of 287 in 4dv4

Go back to Magnesium Binding Sites List in 4dv4
Magnesium binding site 9 out of 287 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G


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, A914G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1609

b:0.0
occ:1.00
O2 A:U1506 3.4 0.5 1.0
O3' A:C795 3.5 0.0 1.0
OP1 A:C796 3.6 0.5 1.0
O2' A:C795 3.6 0.1 1.0
O4' A:U1506 3.6 0.6 1.0
C1' A:U1506 3.8 0.4 1.0
C2 A:U1506 4.2 0.1 1.0
P A:C796 4.3 0.2 1.0
C4' A:U1506 4.3 0.5 1.0
O3' A:U1506 4.4 0.5 1.0
N1 A:U1506 4.5 0.3 1.0
C3' A:C795 4.6 0.9 1.0
C2' A:C795 4.6 0.8 1.0
OP1 A:A1507 4.7 0.9 1.0
C3' A:U1506 4.9 0.1 1.0

Magnesium binding site 10 out of 287 in 4dv4

Go back to Magnesium Binding Sites List in 4dv4
Magnesium binding site 10 out of 287 in the Crystal Structure of the Thermus Thermophilus 30S Ribosomal Subunit with A 16S Rrna Mutation, A914G


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, A914G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1610

b:0.5
occ:1.00
O A:HOH1920 2.1 0.5 1.0
O A:HOH1921 2.1 71.4 1.0
OP1 A:A1500 2.6 0.3 1.0
O3' A:A1507 2.7 0.6 1.0
OP1 A:G1508 2.7 0.7 1.0
OP1 A:G1505 2.8 0.1 1.0
P A:G1508 3.2 0.4 1.0
C5' A:G1508 3.5 0.2 1.0
O2' A:A1507 3.7 0.3 1.0
OP2 A:C1501 3.8 0.6 1.0
OP1 A:G1504 3.8 0.5 1.0
P A:A1500 3.8 1.0 1.0
O5' A:G1508 3.8 0.4 1.0
C3' A:A1507 3.9 0.8 1.0
C3' A:G1504 4.0 0.0 1.0
O5' A:G1504 4.1 0.5 1.0
P A:G1505 4.2 0.1 1.0
OP2 A:A1500 4.3 0.1 1.0
P A:G1504 4.3 0.1 1.0
C4' A:A1507 4.4 0.7 1.0
C2' A:A1507 4.4 1.0 1.0
C5' A:G1505 4.4 0.9 1.0
O5' A:A1500 4.4 0.6 1.0
O2' A:U1506 4.5 0.6 1.0
OP2 A:G1508 4.6 0.8 1.0
C2' A:G1504 4.6 0.8 1.0
O3' A:G1504 4.6 0.6 1.0
MG A:MG1715 4.6 88.4 1.0
C5' A:A1500 4.6 0.3 1.0
OP2 A:G1504 4.7 0.3 1.0
O2' A:G1504 4.7 0.6 1.0
O5' A:G1505 4.7 0.2 1.0
C4' A:G1508 4.8 0.1 1.0
P A:C1501 4.9 0.2 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 12:30:10 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy