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Magnesium in PDB 5t3k: Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside

Protein crystallography data

The structure of Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside, PDB code: 5t3k was solved by T.Hermann, M.A.Boerneke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.02 / 2.14
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 31.553, 86.956, 32.564, 90.00, 94.14, 90.00
R / Rfree (%) 19.7 / 24.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside (pdb code 5t3k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside, PDB code: 5t3k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5t3k

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Magnesium binding site 1 out of 10 in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:39.9
occ:1.00
 OP2 A:G4 3.2 30.6 1.0
OP1 A:U3 3.8 38.9 1.0
O A:HOH207 3.9 32.8 1.0
OP1 A:G4 3.9 34.4 1.0
P A:G4 4.0 37.9 1.0
P A:U3 4.5 35.8 1.0
OP2 A:U3 4.6 38.6 1.0
O5' A:U3 4.6 33.6 1.0
O3' A:U3 4.6 28.1 1.0
C5' A:U3 4.9 32.5 1.0

Magnesium binding site 2 out of 10 in 5t3k

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Magnesium binding site 2 out of 10 in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:37.3
occ:1.00
 N7 A:G4 2.3 29.9 1.0
O A:HOH207 3.0 32.8 1.0
C8 A:G4 3.3 27.6 1.0
C5 A:G4 3.3 28.8 1.0
O6 A:G4 3.6 25.3 1.0
C5 A:U3 3.7 32.8 1.0
C4 A:U3 3.8 29.7 1.0
C6 A:G4 3.8 25.9 1.0
O4 A:U3 4.1 31.3 1.0
C6 A:U3 4.1 30.1 1.0
N3 A:U3 4.3 30.0 1.0
OP2 A:G4 4.3 30.6 1.0
N9 A:G4 4.5 29.1 1.0
C4 A:G4 4.5 25.3 1.0
N1 A:U3 4.6 33.4 1.0
C2 A:U3 4.7 31.0 1.0
O6 A:G5 4.9 28.3 1.0
N7 A:G5 4.9 23.6 1.0

Magnesium binding site 3 out of 10 in 5t3k

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Magnesium binding site 3 out of 10 in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:38.0
occ:1.00
 O B:HOH203 2.9 28.5 1.0
N7 B:G24 3.0 27.0 1.0
C5 B:C23 3.6 32.2 1.0
C22 B:75B25 3.6 29.8 1.0
O6 B:G24 3.7 20.3 1.0
N4 B:C23 3.8 27.5 1.0
C4 B:C23 3.8 29.2 1.0
C5 B:G24 3.9 23.8 1.0
SE1 B:75B25 3.9 33.3 1.0
C8 B:G24 4.0 27.9 1.0
C6 B:G24 4.2 26.3 1.0
C6 B:C23 4.4 29.9 1.0
C33 B:75B25 4.4 25.5 1.0
O B:HOH202 4.6 32.7 1.0
O A:HOH220 4.6 35.7 1.0
N3 B:C23 4.8 23.3 1.0
O A:HOH209 4.8 32.1 1.0
OP2 B:G24 4.9 40.1 1.0

Magnesium binding site 4 out of 10 in 5t3k

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Magnesium binding site 4 out of 10 in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:38.6
occ:1.00
 O B:HOH205 2.6 33.1 1.0
O B:HOH207 2.8 27.5 1.0
N7 B:A27 2.8 31.3 1.0
C5 B:C26 3.4 26.2 1.0
O B:HOH209 3.6 29.3 1.0
O B:HOH201 3.6 37.1 1.0
C8 B:A27 3.8 26.0 1.0
N4 B:C26 3.8 23.0 1.0
N6 B:A27 3.8 28.6 1.0
C4 B:C26 3.8 27.1 1.0
C5 B:A27 3.8 26.8 1.0
N4 B:C28 3.9 35.7 1.0
C6 B:C26 4.2 27.9 1.0
O A:HOH214 4.2 34.1 1.0
C6 B:A27 4.3 27.1 1.0
C4 B:C28 4.6 30.3 1.0
C5 B:C28 4.6 33.6 1.0
OP2 B:C26 4.7 24.7 1.0
O B:HOH210 4.8 37.4 1.0
N3 B:C26 4.8 27.6 1.0
OP2 B:A27 5.0 38.3 1.0
N9 B:A27 5.0 32.0 1.0

Magnesium binding site 5 out of 10 in 5t3k

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Magnesium binding site 5 out of 10 in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:41.0
occ:1.00
 N7 C:G4 2.5 25.3 1.0
C8 C:G4 3.5 27.8 1.0
C5 C:G4 3.5 26.7 1.0
O6 C:G4 3.6 29.7 1.0
C5 C:U3 3.7 23.4 1.0
C4 C:U3 3.9 26.6 1.0
C6 C:G4 3.9 28.2 1.0
O4 C:U3 4.0 30.2 1.0
C6 C:U3 4.3 26.3 1.0
OP2 C:G4 4.5 26.2 1.0
N7 C:G5 4.5 24.9 1.0
N3 C:U3 4.6 24.5 1.0
N9 C:G4 4.7 29.2 1.0
C4 C:G4 4.7 28.8 1.0
N1 C:U3 5.0 27.5 1.0

Magnesium binding site 6 out of 10 in 5t3k

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Magnesium binding site 6 out of 10 in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg102

b:37.2
occ:1.00
 N7 C:G1 2.1 33.8 1.0
C5 C:G1 3.0 29.5 1.0
O6 C:G1 3.0 29.3 1.0
C8 C:G1 3.2 33.5 1.0
C6 C:G1 3.4 27.6 1.0
C4 C:G1 4.2 30.8 1.0
N9 C:G1 4.3 35.8 1.0
N7 C:G2 4.4 24.3 1.0
O6 C:G2 4.7 22.1 1.0
N1 C:G1 4.8 28.3 1.0
O5' C:G1 4.9 45.4 1.0

Magnesium binding site 7 out of 10 in 5t3k

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Magnesium binding site 7 out of 10 in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg103

b:42.1
occ:1.00
 OP2 C:C12 2.2 32.9 1.0
C5 C:C12 3.6 28.2 1.0
P C:C12 3.7 34.4 1.0
O C:HOH207 3.8 37.7 1.0
O5' C:U11 3.9 34.7 1.0
OP2 C:U11 3.9 29.8 1.0
C6 C:C12 4.0 27.9 1.0
C3' C:U11 4.1 27.8 1.0
O5' C:C12 4.2 33.0 1.0
P C:U11 4.3 32.3 1.0
O3' C:U11 4.4 29.5 1.0
OP1 C:U11 4.6 32.7 1.0
C6 C:U11 4.6 30.9 1.0
OP1 C:C12 4.8 32.1 1.0
O C:HOH205 4.8 27.6 1.0
C2' C:U11 4.8 31.6 1.0
C4 C:C12 4.9 29.1 1.0
C5 C:U11 4.9 36.2 1.0

Magnesium binding site 8 out of 10 in 5t3k

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Magnesium binding site 8 out of 10 in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg104

b:35.3
occ:1.00
 OP1 C:G4 2.9 25.5 1.0
O3' C:U3 3.0 26.0 1.0
P C:G4 3.6 24.7 1.0
C3' C:U3 4.2 26.4 1.0
C4' C:U3 4.4 22.0 1.0
O2' C:U3 4.5 21.8 1.0
O5' C:G4 4.7 27.6 1.0
C5' C:G4 4.7 24.5 1.0
OP2 C:G4 4.7 26.2 1.0
C5' C:U3 4.8 24.5 1.0
C2' C:U3 5.0 26.0 1.0

Magnesium binding site 9 out of 10 in 5t3k

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Magnesium binding site 9 out of 10 in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:31.4
occ:1.00
 O C:HOH213 2.8 32.4 1.0
N7 D:G24 3.0 31.3 1.0
O D:HOH208 3.2 34.8 1.0
C22 D:75B25 3.2 33.7 1.0
SE1 D:75B25 3.4 38.0 1.0
O6 D:G24 3.8 32.9 1.0
C5 D:G24 3.9 33.0 1.0
C5 D:C23 3.9 33.2 1.0
C8 D:G24 4.0 29.3 1.0
N4 D:C23 4.1 32.4 1.0
C6 D:G24 4.2 30.7 1.0
C4 D:C23 4.2 33.0 1.0
C33 D:75B25 4.2 32.3 1.0
C6 D:C23 4.7 29.8 1.0
OP2 D:G24 4.7 38.6 1.0
C55 D:75B25 4.7 27.9 1.0
C44 D:75B25 5.0 27.0 1.0

Magnesium binding site 10 out of 10 in 5t3k

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Magnesium binding site 10 out of 10 in the Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Fluorescence Detection of Rna-Ligand Binding and Crystal Structure Determination of Ribosomal Decoding Site Rna Using A Heavy Atom Containing Fluorescent Ribonucleoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg102

b:34.4
occ:1.00
 O D:HOH205 2.7 31.5 1.0
N7 D:A27 2.7 29.0 1.0
N4 D:C28 3.5 24.3 1.0
C5 D:C26 3.5 31.3 1.0
N6 D:A27 3.6 30.5 1.0
C8 D:A27 3.7 26.8 1.0
C5 D:A27 3.7 27.1 1.0
N4 D:C26 3.7 23.9 1.0
C4 D:C26 3.8 31.3 1.0
C6 D:A27 4.1 27.3 1.0
O6 C:G7 4.2 31.9 1.0
C6 D:C26 4.3 31.4 1.0
O D:HOH201 4.3 36.8 1.0
C4 D:C28 4.3 28.9 1.0
N3 D:C26 4.6 28.3 1.0
OP2 D:A27 4.7 33.8 1.0
C5 D:C28 4.7 28.5 1.0
N9 D:A27 4.9 31.1 1.0
C4 D:A27 4.9 28.0 1.0
OP2 D:C26 5.0 35.3 1.0

Reference:

A.Nuthanakanti, M.A.Boerneke, T.Hermann, S.G.Srivatsan. Structure of the Ribosomal Rna Decoding Site Containing A Selenium-Modified Responsive Fluorescent Ribonucleoside Probe. Angew. Chem. Int. Ed. Engl. V. 56 2640 2017.
ISSN: ESSN 1521-3773
PubMed: 28156044
DOI: 10.1002/ANIE.201611700
Page generated: Mon Sep 30 04:43:46 2024

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