Atomistry » Magnesium » PDB 3oto-3p0x » 3owz
Atomistry »
  Magnesium »
    PDB 3oto-3p0x »
      3owz »

Magnesium in PDB 3owz: Crystal Structure of Glycine Riboswitch, Soaked in Iridium

Protein crystallography data

The structure of Crystal Structure of Glycine Riboswitch, Soaked in Iridium, PDB code: 3owz was solved by L.Huang, A.Serganov, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.95
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.610, 82.610, 149.550, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 23.4

Other elements in 3owz:

The structure of Crystal Structure of Glycine Riboswitch, Soaked in Iridium also contains other interesting chemical elements:

Iridium (Ir) 23 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium (pdb code 3owz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium, PDB code: 3owz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 3owz

Go back to Magnesium Binding Sites List in 3owz
Magnesium binding site 1 out of 16 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium


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 Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:56.9
occ:1.00
OP2 A:G35 1.8 52.4 1.0
OP1 A:A34 2.0 50.9 1.0
O A:HOH119 2.2 56.5 1.0
O A:HOH121 2.2 57.2 1.0
O A:HOH120 2.2 57.1 1.0
O A:HOH122 2.2 57.5 1.0
P A:G35 3.2 53.1 1.0
P A:A34 3.4 50.2 1.0
O5' A:A34 3.8 50.5 1.0
O5' A:G35 3.9 53.5 1.0
OP1 A:G35 4.0 52.8 1.0
C5' A:A34 4.1 51.9 1.0
O3' A:A34 4.3 52.9 1.0
O3' A:A33 4.4 49.1 1.0
OP2 A:A34 4.4 50.3 1.0
CA A:GLY89 4.5 50.5 1.0
C3' A:A34 4.5 52.8 1.0
C4' A:A33 4.6 47.9 1.0
N7 A:G35 4.6 55.0 1.0
C8 A:G35 4.6 55.0 1.0
O2' A:A81 4.9 44.2 1.0
N7 A:G36 4.9 52.7 1.0
C4' A:A34 4.9 52.3 1.0
C3' A:A33 5.0 48.2 1.0

Magnesium binding site 2 out of 16 in 3owz

Go back to Magnesium Binding Sites List in 3owz
Magnesium binding site 2 out of 16 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium


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 Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:30.9
occ:1.00
OP2 A:A33 1.9 46.9 1.0
O A:HOH124 2.2 30.4 1.0
O A:HOH126 2.2 31.0 1.0
O A:HOH125 2.2 31.0 1.0
O A:HOH123 2.2 30.8 1.0
O2' A:G32 2.4 44.1 1.0
C2' A:G32 3.3 44.2 1.0
P A:A33 3.3 46.9 1.0
OXT A:GLY89 3.4 50.5 1.0
OP2 A:C66 3.5 46.6 1.0
C3' A:G32 3.6 44.6 1.0
O3' A:G32 3.8 45.8 1.0
C5' A:A33 4.1 47.1 1.0
O5' A:A33 4.2 46.5 1.0
O4 A:U67 4.3 44.0 1.0
O4 A:U69 4.4 54.9 1.0
OP1 A:A33 4.4 46.7 1.0
N4 A:C68 4.4 47.5 1.0
O3' A:A65 4.5 45.9 1.0
C5 A:U67 4.5 44.3 1.0
C A:GLY89 4.5 50.5 1.0
P A:C66 4.6 47.0 1.0
C1' A:G32 4.7 43.6 1.0
C4' A:A65 4.7 45.4 1.0
C4 A:U67 4.7 44.2 1.0
C5' A:A65 4.7 45.0 1.0
O A:GLY89 4.8 50.5 1.0
C3' A:A65 4.9 45.4 1.0
OP2 A:U67 5.0 44.7 1.0

Magnesium binding site 3 out of 16 in 3owz

Go back to Magnesium Binding Sites List in 3owz
Magnesium binding site 3 out of 16 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium


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 Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:44.2
occ:1.00
OP2 A:A75 1.9 36.2 1.0
O A:HOH127 2.2 44.0 1.0
O A:HOH129 2.2 44.6 1.0
O A:HOH128 2.2 44.7 1.0
O A:HOH130 2.2 44.1 1.0
O A:HOH131 2.2 45.0 1.0
P A:A75 3.3 36.1 1.0
O5' A:A75 3.8 35.5 1.0
N7 A:A75 3.8 32.9 1.0
O A:HOH133 3.9 51.7 1.0
C8 A:A75 4.0 32.5 1.0
O3' A:C74 4.1 35.8 1.0
C3' A:C74 4.3 35.9 1.0
OP1 A:A75 4.4 36.4 1.0
OP2 A:C74 4.6 35.5 1.0
OP1 A:U23 4.7 47.3 1.0
O5' A:C74 4.7 36.5 1.0
P A:C74 5.0 36.0 1.0

Magnesium binding site 4 out of 16 in 3owz

Go back to Magnesium Binding Sites List in 3owz
Magnesium binding site 4 out of 16 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium


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 Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:51.4
occ:1.00
OP1 A:C74 2.0 35.7 1.0
OP1 A:A75 2.0 36.4 1.0
O A:HOH132 2.2 50.7 1.0
O A:HOH134 2.2 51.4 1.0
O A:HOH133 2.2 51.7 1.0
OP2 A:A76 2.2 33.6 1.0
P A:A75 3.2 36.1 1.0
P A:C74 3.3 36.0 1.0
OP2 A:A75 3.6 36.2 1.0
P A:A76 3.7 34.2 1.0
O5' A:C74 3.8 36.5 1.0
C5' A:C74 3.8 36.5 1.0
N7 A:A76 4.1 36.3 1.0
O5' A:A75 4.1 35.5 1.0
N6 A:A77 4.3 43.6 1.0
C3' A:A75 4.3 33.8 1.0
O3' A:G73 4.3 36.6 1.0
OP2 A:C74 4.3 35.5 1.0
O3' A:A75 4.4 34.5 1.0
O3' A:C74 4.4 35.8 1.0
N7 A:A77 4.4 43.0 1.0
C8 A:A76 4.5 36.4 1.0
O5' A:A76 4.5 34.8 1.0
OP1 A:A76 4.7 34.1 1.0
N6 A:A78 4.7 45.1 1.0
C5' A:A75 4.8 34.4 1.0
C4' A:C74 4.8 36.3 1.0
O A:HOH128 4.9 44.7 1.0
O A:HOH129 4.9 44.6 1.0
C3' A:C74 4.9 35.9 1.0

Magnesium binding site 5 out of 16 in 3owz

Go back to Magnesium Binding Sites List in 3owz
Magnesium binding site 5 out of 16 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium


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 Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:62.8
occ:1.00
O A:HOH138 2.2 62.7 1.0
O A:HOH136 2.2 63.0 1.0
O A:HOH135 2.2 63.1 1.0
O A:HOH137 2.2 63.1 1.0
OP2 A:C70 2.3 54.4 1.0
OP2 A:A71 2.9 50.9 1.0
P A:C70 3.4 54.0 1.0
O3' A:U69 3.5 53.9 1.0
O6 A:G72 3.6 28.9 1.0
O2' A:U69 3.8 54.6 1.0
N7 A:G72 4.3 29.2 1.0
N7 A:A71 4.3 45.0 1.0
OP1 A:C70 4.4 53.5 1.0
P A:A71 4.4 51.4 1.0
C3' A:U69 4.5 54.1 1.0
C6 A:G72 4.5 28.8 1.0
O5' A:C70 4.6 53.4 1.0
C2' A:U69 4.7 54.5 1.0
N5 A:IRI221 4.7 39.2 0.8
C5 A:G72 4.8 28.8 1.0
C8 A:A71 4.8 45.3 1.0
N4 A:C31 4.9 39.3 1.0
O5' A:A71 5.0 50.0 1.0

Magnesium binding site 6 out of 16 in 3owz

Go back to Magnesium Binding Sites List in 3owz
Magnesium binding site 6 out of 16 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium


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 Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg106

b:62.9
occ:1.00
O B:HOH117 2.2 62.7 1.0
O A:HOH140 2.2 62.4 1.0
O A:HOH139 2.2 63.1 1.0
O B:HOH119 2.2 62.8 1.0
O B:HOH120 2.2 62.8 1.0
O B:HOH118 2.2 63.0 1.0
OP1 B:A33 3.5 34.3 1.0
OP1 A:A33 4.3 46.7 1.0
OP1 B:C66 4.7 48.4 1.0
OP1 A:C66 4.8 47.6 1.0
O3' B:A65 4.9 48.7 1.0
P B:A33 5.0 34.2 1.0

Magnesium binding site 7 out of 16 in 3owz

Go back to Magnesium Binding Sites List in 3owz
Magnesium binding site 7 out of 16 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium


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 Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg109

b:33.1
occ:1.00
OP1 B:G25 2.1 65.5 1.0
O B:HOH125 2.2 32.4 1.0
O B:HOH121 2.2 33.3 1.0
O B:HOH124 2.2 32.8 1.0
O B:HOH122 2.2 33.1 1.0
O B:HOH123 2.2 32.3 1.0
P B:G25 3.5 65.7 1.0
OP2 B:G73 4.0 37.4 1.0
O B:HOH139 4.0 41.6 1.0
OP2 B:G25 4.1 65.8 1.0
O5' B:G25 4.2 65.8 1.0
C5' B:G25 4.2 66.0 1.0
OP1 B:G73 4.2 36.9 1.0
O3' B:C24 4.6 66.6 1.0
P B:G73 4.6 37.1 1.0
OP1 B:G72 4.6 37.3 1.0

Magnesium binding site 8 out of 16 in 3owz

Go back to Magnesium Binding Sites List in 3owz
Magnesium binding site 8 out of 16 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium


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 Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg110

b:39.4
occ:1.00
OP1 B:A34 1.9 36.6 1.0
OP2 B:G35 2.1 39.5 1.0
O B:HOH128 2.2 39.4 1.0
O B:HOH129 2.2 39.9 1.0
O B:HOH126 2.2 41.0 1.0
O B:HOH127 2.2 40.5 1.0
P B:A34 3.3 36.0 1.0
P B:G35 3.5 40.1 1.0
O5' B:A34 3.8 36.5 1.0
OP2 B:A34 4.2 36.8 1.0
C4' B:A33 4.3 34.2 1.0
O3' B:A33 4.3 35.5 1.0
O5' B:G35 4.3 40.4 1.0
OP1 B:G35 4.3 40.4 1.0
C5' B:A34 4.3 37.4 1.0
CA B:GLY89 4.3 39.9 1.0
O3' B:A34 4.5 39.4 1.0
N7 B:G35 4.6 41.1 1.0
OXT B:GLY89 4.7 39.9 1.0
N7 B:G36 4.7 42.4 1.0
C3' B:A33 4.7 34.4 1.0
C5' B:A33 4.8 33.8 1.0
C3' B:A34 4.8 38.3 1.0
C8 B:G35 4.9 41.0 1.0
O6 B:G36 5.0 42.5 1.0

Magnesium binding site 9 out of 16 in 3owz

Go back to Magnesium Binding Sites List in 3owz
Magnesium binding site 9 out of 16 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium


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 Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg111

b:61.8
occ:1.00
O B:HOH135 2.2 61.6 1.0
O B:HOH131 2.2 61.8 1.0
O B:HOH133 2.2 62.0 1.0
O B:HOH134 2.2 62.1 1.0
O B:HOH132 2.2 61.5 1.0
O B:HOH130 2.2 61.9 1.0
O6 B:G50 3.7 82.9 1.0
C6 B:G50 4.8 83.1 1.0
N7 B:G50 4.9 83.3 1.0
O6 B:G49 4.9 83.5 1.0
N4 B:C48 4.9 87.2 1.0

Magnesium binding site 10 out of 16 in 3owz

Go back to Magnesium Binding Sites List in 3owz
Magnesium binding site 10 out of 16 in the Crystal Structure of Glycine Riboswitch, Soaked in Iridium


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 Glycine Riboswitch, Soaked in Iridium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg112

b:41.7
occ:1.00
O B:HOH137 2.2 42.1 1.0
O B:HOH139 2.2 41.6 1.0
O B:HOH138 2.2 41.7 1.0
O B:HOH136 2.2 41.9 1.0
O B:HOH140 2.2 41.8 1.0
OP1 B:C24 2.3 73.9 1.0
P B:C24 3.8 74.2 1.0
OP1 B:G73 4.1 36.9 1.0
OP2 B:G25 4.4 65.8 1.0
C5' B:C24 4.4 70.3 1.0
N1 B:A77 4.4 48.0 1.0
O5' B:C24 4.4 72.7 1.0
OP2 B:C74 4.5 41.9 1.0
O B:HOH125 4.6 32.4 1.0
OP2 B:C24 4.6 74.5 1.0
O3' B:U23 4.7 75.7 1.0
OP1 B:C74 4.8 42.4 1.0
C2 B:A77 4.8 48.2 1.0

Reference:

L.Huang, A.Serganov, D.J.Patel. Structural Insights Into Ligand Recognition By A Sensing Domain of the Cooperative Glycine Riboswitch. Mol.Cell V. 40 774 2010.
ISSN: ISSN 1097-2765
PubMed: 21145485
DOI: 10.1016/J.MOLCEL.2010.11.026
Page generated: Thu Aug 15 08:32:25 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