Atomistry » Magnesium » PDB 4doa-4dv5 » 4duz
Atomistry »
  Magnesium »
    PDB 4doa-4dv5 »
      4duz »

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

Go back to Magnesium Binding Sites List in 4duz
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

Go back to Magnesium Binding Sites List in 4duz
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

Go back to Magnesium Binding Sites List in 4duz
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

Go back to Magnesium Binding Sites List in 4duz
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

Go back to Magnesium Binding Sites List in 4duz
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

Go back to Magnesium Binding Sites List in 4duz
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

Go back to Magnesium Binding Sites List in 4duz
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

Go back to Magnesium Binding Sites List in 4duz
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

Go back to Magnesium Binding Sites List in 4duz
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

Go back to Magnesium Binding Sites List in 4duz
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

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy