Atomistry » Magnesium » PDB 8hs0-8i24 » 8hzk
Atomistry »
  Magnesium »
    PDB 8hs0-8i24 »
      8hzk »

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

Go back to Magnesium Binding Sites List in 8hzk
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

Go back to Magnesium Binding Sites List in 8hzk
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

Go back to Magnesium Binding Sites List in 8hzk
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

Go back to Magnesium Binding Sites List in 8hzk
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

Go back to Magnesium Binding Sites List in 8hzk
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

Go back to Magnesium Binding Sites List in 8hzk
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

Go back to Magnesium Binding Sites List in 8hzk
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

Go back to Magnesium Binding Sites List in 8hzk
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy