Atomistry » Magnesium » PDB 3osu-3p0f » 3oto
Atomistry »
  Magnesium »
    PDB 3osu-3p0f »
      3oto »

Magnesium in PDB 3oto: Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)

Protein crystallography data

The structure of Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8), PDB code: 3oto was solved by H.Demirci, F.Murphy Iv, R.Belardinelli, A.C.Kelley, V.Ramakrishnan, 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) 29.84 / 3.69
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 402.089, 402.089, 173.254, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 23.1

Other elements in 3oto:

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

Potassium (K) 42 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 94;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) (pdb code 3oto). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 94 binding sites of Magnesium where determined in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8), PDB code: 3oto:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 94 in 3oto

Go back to Magnesium Binding Sites List in 3oto
Magnesium binding site 1 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of 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 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1545

b:75.1
occ:1.00
O2 A:C701 3.0 0.4 1.0
OP2 A:A702 3.4 0.1 1.0
O6 A:G703 3.5 0.3 1.0
C1' A:C701 4.1 0.0 1.0
C2 A:C701 4.2 0.5 1.0
C6 A:G703 4.2 0.4 1.0
OP1 A:A702 4.2 0.2 1.0
P A:A702 4.3 0.5 1.0
N1 A:C701 4.6 0.6 1.0
O2' A:C701 4.6 0.2 1.0
N1 A:G703 4.8 0.5 1.0
O4' A:C701 4.8 0.1 1.0
C5 A:G703 4.9 0.3 1.0
O3' A:C701 5.0 0.5 1.0
C2' A:C701 5.0 0.8 1.0

Magnesium binding site 2 out of 94 in 3oto

Go back to Magnesium Binding Sites List in 3oto
Magnesium binding site 2 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of 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 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1546

b:76.2
occ:1.00
O6 A:G258 3.4 0.7 1.0
O6 A:G259 3.5 0.5 1.0
OP2 A:G265 4.0 87.3 1.0
C6 A:G258 4.2 0.4 1.0
N7 A:G258 4.2 0.4 1.0
OP2 A:G266 4.3 88.2 1.0
C5 A:G258 4.5 0.4 1.0
C6 A:G259 4.7 0.4 1.0
OP1 A:G265 4.8 93.5 1.0
N4 A:C267 4.8 77.0 1.0
P A:G265 4.8 90.4 1.0

Magnesium binding site 3 out of 94 in 3oto

Go back to Magnesium Binding Sites List in 3oto
Magnesium binding site 3 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of 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 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1547

b:86.1
occ:1.00
N7 A:G724 3.7 83.2 1.0
OP2 A:G724 3.7 0.2 1.0
N7 A:G725 3.9 77.1 1.0
O6 A:G725 4.1 73.3 1.0
O6 A:G724 4.2 84.6 1.0
C5 A:G724 4.2 79.3 1.0
C8 A:G724 4.4 82.8 1.0
C6 A:G724 4.4 78.6 1.0
C5 A:G725 4.7 75.4 1.0
C6 A:G725 4.8 72.2 1.0
P A:G724 4.8 0.1 1.0
C8 A:G725 4.9 81.8 1.0
OP2 A:G725 4.9 0.8 1.0
OP1 A:G724 4.9 0.5 1.0

Magnesium binding site 4 out of 94 in 3oto

Go back to Magnesium Binding Sites List in 3oto
Magnesium binding site 4 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of 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 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1548

b:81.9
occ:1.00
OP1 A:G438 3.5 0.2 1.0
OP2 A:G492 4.0 0.5 1.0
OP2 A:G438 4.1 0.4 1.0
P A:G438 4.2 0.0 1.0
O6 A:G494 4.2 0.8 1.0
N7 A:G494 4.5 0.1 1.0
O5' A:G438 4.6 0.9 1.0
C6 A:G494 4.9 0.5 1.0
P A:G492 5.0 0.5 1.0

Magnesium binding site 5 out of 94 in 3oto

Go back to Magnesium Binding Sites List in 3oto
Magnesium binding site 5 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of 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 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1549

b:59.4
occ:1.00
O6 A:G309 3.4 89.4 1.0
N7 A:G309 3.6 82.7 1.0
C6 A:G309 3.9 82.6 1.0
C5 A:G309 4.1 82.8 1.0
C5 A:C308 4.1 67.7 1.0
O6 A:G310 4.1 73.4 1.0
N4 A:C308 4.2 71.5 1.0
OP2 A:C307 4.3 0.1 1.0
C4 A:C308 4.4 68.2 1.0
OP2 A:C308 4.4 0.0 1.0
C8 A:G309 4.7 81.1 1.0
N7 A:G310 4.9 72.1 1.0
C6 A:C308 4.9 67.8 1.0

Magnesium binding site 6 out of 94 in 3oto

Go back to Magnesium Binding Sites List in 3oto
Magnesium binding site 6 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of 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 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1550

b:52.5
occ:1.00
O6 A:G22 2.9 77.5 1.0
O4 A:U12 2.9 89.7 1.0
O6 A:G11 3.2 86.1 1.0
O6 A:G21 3.4 82.6 1.0
N4 A:C23 3.6 79.3 1.0
C6 A:G21 3.8 76.0 1.0
C6 A:G22 4.0 72.3 1.0
C4 A:U12 4.0 89.4 1.0
N1 A:G21 4.3 72.8 1.0
N3 A:U12 4.3 82.7 1.0
C6 A:G11 4.3 78.4 1.0
N7 A:G22 4.4 71.6 1.0
C5 A:G21 4.5 67.9 1.0
C5 A:G22 4.6 67.5 1.0
C4 A:C23 4.8 76.2 1.0
N7 A:G21 4.9 67.5 1.0

Magnesium binding site 7 out of 94 in 3oto

Go back to Magnesium Binding Sites List in 3oto
Magnesium binding site 7 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of 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 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1551

b:50.3
occ:1.00
K A:K1637 3.9 0.7 1.0
O6 A:G475 4.1 0.8 1.0
O6 A:G476 4.2 0.1 1.0
C6 A:G475 4.6 0.1 1.0
N7 A:G476 4.7 0.7 1.0
N7 A:G475 4.7 0.8 1.0
C5 A:G475 4.9 0.2 1.0
C6 A:G476 5.0 0.7 1.0

Magnesium binding site 8 out of 94 in 3oto

Go back to Magnesium Binding Sites List in 3oto
Magnesium binding site 8 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of 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 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1552

b:80.8
occ:1.00
O3' A:A665 2.7 79.2 1.0
OP2 A:G667 3.4 94.2 1.0
O5' A:G666 3.4 67.2 1.0
P A:G666 3.4 80.0 1.0
OP1 A:G666 3.5 81.7 1.0
O2' A:A665 3.5 75.0 1.0
C3' A:A665 3.9 78.2 1.0
C2' A:A665 4.3 75.8 1.0
C4' A:A665 4.3 82.9 1.0
C8 A:G666 4.5 83.5 1.0
C5' A:G666 4.5 69.6 1.0
N7 A:G666 4.6 88.4 1.0
C3' A:G666 4.8 76.5 1.0
P A:G667 4.8 0.4 1.0
O5' A:A665 4.8 90.4 1.0
OP2 A:G666 4.8 77.3 1.0
N7 A:G667 5.0 85.9 1.0

Magnesium binding site 9 out of 94 in 3oto

Go back to Magnesium Binding Sites List in 3oto
Magnesium binding site 9 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of 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 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1553

b:94.6
occ:1.00
O6 A:G890 2.9 98.6 1.0
OP2 A:G906 3.6 83.0 1.0
C6 A:G890 4.0 98.8 1.0
OP1 A:C883 4.7 76.3 1.0
N1 A:G890 4.7 95.7 1.0
OP1 A:U905 4.7 92.6 1.0
P A:G906 4.9 84.7 1.0
OP2 A:U905 4.9 89.8 1.0
C5 A:G890 5.0 97.4 1.0

Magnesium binding site 10 out of 94 in 3oto

Go back to Magnesium Binding Sites List in 3oto
Magnesium binding site 10 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of 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 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1554

b:59.8
occ:1.00
O6 A:G741 3.2 80.6 1.0
O6 A:G664 3.4 89.2 1.0
N7 A:G741 3.5 82.2 1.0
O6 A:G742 3.7 90.9 1.0
C6 A:G741 3.9 80.0 1.0
C5 A:G741 4.0 78.7 1.0
C6 A:G664 4.3 87.6 1.0
O6 A:G666 4.4 85.2 1.0
C6 A:G742 4.4 85.7 1.0
N1 A:G664 4.4 84.0 1.0
N7 A:G742 4.5 75.4 1.0
C8 A:G741 4.6 82.5 1.0
C5 A:G742 4.7 79.4 1.0
N6 A:A663 4.7 85.6 1.0
O4 A:U740 4.8 84.9 1.0

Reference:

H.Demirci, F.Murphy, R.Belardinelli, A.C.Kelley, V.Ramakrishnan, S.T.Gregory, A.E.Dahlberg, G.Jogl. Modification of 16S Ribosomal Rna By the Ksga Methyltransferase Restructures the 30S Subunit to Optimize Ribosome Function. Rna V. 16 2319 2010.
ISSN: ISSN 1355-8382
PubMed: 20962038
DOI: 10.1261/RNA.2357210
Page generated: Mon Dec 14 08:36:57 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy