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Magnesium in PDB 8hzk: A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak

Protein crystallography data

The structure of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak, PDB code: 8hzk was solved by K.Y.Huang, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.11 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.893, 44.022, 58.304, 90, 112.94, 90
R / Rfree (%) 20.3 / 24

Other elements in 8hzk:

The structure of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak also contains other interesting chemical elements:

Iridium (Ir) 14 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak (pdb code 8hzk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak, PDB code: 8hzk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8hzk

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Magnesium binding site 1 out of 8 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg110

b:26.1
occ:1.00
 O A:HOH251 1.7 29.9 1.0
O A:HOH265 1.8 24.9 1.0
O A:HOH237 1.9 35.5 1.0
O A:HOH250 2.2 30.3 1.0
O A:HOH261 3.9 14.0 1.0
O6 A:G24 4.2 27.5 1.0
N7 A:G24 4.3 32.3 1.0
O6 A:G20 4.6 28.9 1.0
OP1 A:A23 4.7 37.0 1.0
C6 A:G24 5.0 25.2 1.0

Magnesium binding site 2 out of 8 in 8hzk

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Magnesium binding site 2 out of 8 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg111

b:20.4
occ:1.00
 O A:HOH264 1.8 38.9 1.0
O A:HOH263 1.8 27.5 1.0
O A:HOH244 2.0 35.7 1.0
OP1 A:A4 3.6 29.9 1.0
O3' A:A3 4.8 32.3 1.0
P A:A4 4.9 28.6 1.0

Magnesium binding site 3 out of 8 in 8hzk

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Magnesium binding site 3 out of 8 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg112

b:9.8
occ:1.00
 O A:HOH255 1.6 21.0 1.0
O A:HOH262 1.8 39.5 1.0
O A:HOH260 1.9 30.6 1.0
OP1 A:G28 4.4 30.9 1.0
OP2 A:A29 4.4 20.4 1.0
OP2 A:G28 4.7 17.1 1.0
P A:G28 5.0 24.4 1.0

Magnesium binding site 4 out of 8 in 8hzk

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Magnesium binding site 4 out of 8 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg113

b:33.1
occ:1.00
 O A:HOH257 1.9 36.1 1.0
O A:HOH204 2.0 36.7 1.0
O A:HOH258 2.2 30.4 1.0
O A:HOH203 2.2 37.1 1.0
O4 A:PEG115 3.2 19.6 1.0
OP2 A:G9 3.4 23.7 1.0
C4 A:PEG115 4.1 21.2 1.0
OP2 A:G25 4.3 15.9 1.0
O A:HOH209 4.6 29.5 1.0
P A:G9 4.8 28.7 1.0
O A:HOH233 4.9 27.8 1.0

Magnesium binding site 5 out of 8 in 8hzk

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Magnesium binding site 5 out of 8 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg114

b:25.9
occ:1.00
 N6 A:IRI105 1.8 36.9 1.0
O A:HOH246 1.9 24.3 1.0
N1 A:IRI105 3.0 62.1 1.0
IR A:IRI105 3.3 83.3 1.0
OP1 A:U16 3.9 27.8 1.0
N2 A:IRI105 4.0 37.6 1.0
N4 A:IRI105 4.1 61.6 1.0
O3' A:A15 4.8 24.4 1.0
P A:U16 4.8 22.5 1.0
N3 A:IRI105 4.9 32.8 1.0

Magnesium binding site 6 out of 8 in 8hzk

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Magnesium binding site 6 out of 8 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg106

b:19.8
occ:1.00
 O B:HOH205 1.8 26.9 1.0
O B:HOH227 1.9 35.2 1.0
O2' B:A3 3.9 25.3 1.0
N2 B:G2 4.0 14.5 1.0
C1' B:A3 4.2 22.2 1.0
N3 B:A3 4.2 18.6 1.0
O4' B:C36 4.3 23.0 1.0
C2' B:A3 4.6 21.6 1.0
C4' B:C36 4.8 23.8 1.0
C1' B:C36 4.8 26.1 1.0
O2 B:C35 4.9 25.4 1.0
C4 B:A3 4.9 15.9 1.0
N9 B:A3 5.0 21.9 1.0

Magnesium binding site 7 out of 8 in 8hzk

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Magnesium binding site 7 out of 8 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg107

b:13.8
occ:1.00
 O B:HOH236 1.9 37.8 1.0
O B:HOH223 1.9 33.4 1.0
O B:HOH222 3.9 20.1 1.0
O2' B:C18 4.2 21.1 1.0
O2 B:C18 4.3 20.8 1.0
O2' B:C26 4.8 30.7 1.0
O2' A:C19 4.9 22.1 1.0
N2 B:G25 4.9 21.3 1.0

Magnesium binding site 8 out of 8 in 8hzk

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Magnesium binding site 8 out of 8 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg108

b:23.4
occ:1.00
 O B:HOH204 3.1 33.0 1.0
OP2 B:G24 3.8 24.8 1.0
OP1 B:A23 3.9 21.6 1.0
N7 B:G24 4.3 21.5 1.0
C8 B:G24 4.6 20.1 1.0
P B:A23 4.9 26.9 1.0
N1 B:IRI103 4.9 16.8 1.0

Reference:

K.Huang, Q.Song, M.Fang, D.Yao, X.Shen, X.Xu, X.Chen, L.Zhu, Y.Yang, A.Ren. Structural Basis of A Small Monomeric Clivia Fluorogenic Rna with A Large Stokes Shift. Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
PubMed: 38816645
DOI: 10.1038/S41589-024-01633-1
Page generated: Fri Oct 4 08:57:19 2024

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