Atomistry » Magnesium » PDB 7en3-7ev2 » 7eok
Atomistry »
  Magnesium »
    PDB 7en3-7ev2 »
      7eok »

Magnesium in PDB 7eok: Crystal Structure of the Pepper Aptamer in Complex with HBC485

Protein crystallography data

The structure of Crystal Structure of the Pepper Aptamer in Complex with HBC485, PDB code: 7eok 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) 45.22 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.982, 37.72, 56.74, 90, 127.08, 90
R / Rfree (%) 20.2 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Pepper Aptamer in Complex with HBC485 (pdb code 7eok). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the Pepper Aptamer in Complex with HBC485, PDB code: 7eok:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 7eok

Go back to Magnesium Binding Sites List in 7eok
Magnesium binding site 1 out of 9 in the Crystal Structure of the Pepper Aptamer in Complex with HBC485


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 Pepper Aptamer in Complex with HBC485 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:46.0
occ:1.00
 OP2 A:U8 2.2 56.8 1.0
OP2 A:C7 2.3 54.2 1.0
N7 A:G9 2.5 50.7 1.0
C8 A:G9 3.4 54.0 1.0
P A:C7 3.5 48.6 1.0
C5 A:G9 3.5 51.3 1.0
P A:U8 3.7 65.9 1.0
OP1 A:C7 3.8 42.8 1.0
O6 A:G9 3.8 49.5 1.0
C6 A:G9 4.0 48.3 1.0
OP1 A:U8 4.4 61.6 1.0
O3' A:C7 4.4 67.0 1.0
O5' A:C7 4.5 51.9 1.0
O3' A:A6 4.6 52.3 1.0
N9 A:G9 4.6 51.1 1.0
C5' A:C7 4.6 47.1 1.0
C4 A:G9 4.7 51.0 1.0
O5' A:U8 4.7 56.0 1.0
C3' A:C7 4.8 59.7 1.0
C5 A:U8 5.0 61.0 1.0

Magnesium binding site 2 out of 9 in 7eok

Go back to Magnesium Binding Sites List in 7eok
Magnesium binding site 2 out of 9 in the Crystal Structure of the Pepper Aptamer in Complex with HBC485


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 Pepper Aptamer in Complex with HBC485 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:30.9
occ:1.00
 O A:HOH214 2.0 45.2 1.0
O A:HOH203 2.3 57.9 1.0
O4 A:U35 2.3 53.0 1.0
OP2 A:C38 2.8 49.2 1.0
O6 A:G34 3.0 45.0 1.0
O2 A:U32 3.1 46.0 1.0
OP1 A:C38 3.3 55.5 1.0
C4 A:U35 3.3 52.2 1.0
P A:C38 3.4 56.5 1.0
N3 A:U35 3.6 46.8 1.0
C2 A:U32 4.0 46.5 1.0
N3 A:U32 4.0 46.2 1.0
C6 A:G34 4.0 45.0 1.0
O3' A:G37 4.5 49.1 1.0
C5 A:U35 4.6 52.0 1.0
O5' A:C38 4.7 62.6 1.0
N1 A:G34 4.7 46.0 1.0
N1 A:A31 4.8 44.2 1.0
C2 A:U35 4.9 45.7 1.0

Magnesium binding site 3 out of 9 in 7eok

Go back to Magnesium Binding Sites List in 7eok
Magnesium binding site 3 out of 9 in the Crystal Structure of the Pepper Aptamer in Complex with HBC485


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 Pepper Aptamer in Complex with HBC485 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:45.2
occ:1.00
 O A:HOH201 2.2 38.0 1.0
OP2 A:U32 2.3 42.2 1.0
O A:HOH210 2.3 36.1 1.0
O A:HOH215 2.4 35.4 1.0
O A:HOH208 2.7 51.8 1.0
P A:U32 3.4 44.4 1.0
O A:HOH217 3.5 38.8 1.0
OP1 A:U32 3.8 51.9 1.0
OP2 A:C33 4.2 45.7 1.0
O5' A:U32 4.3 37.3 1.0
OP2 A:G34 4.6 38.0 1.0
O3' A:A31 4.7 37.1 1.0
OP1 A:A31 4.8 44.5 1.0
OP1 A:G34 4.8 36.6 1.0

Magnesium binding site 4 out of 9 in 7eok

Go back to Magnesium Binding Sites List in 7eok
Magnesium binding site 4 out of 9 in the Crystal Structure of the Pepper Aptamer in Complex with HBC485


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 Pepper Aptamer in Complex with HBC485 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:65.0
occ:1.00
 OP2 A:G44 1.9 79.9 1.0
OP2 A:C43 1.9 74.1 1.0
P A:C43 3.2 79.4 1.0
P A:G44 3.2 77.8 1.0
O A:HOH216 3.3 54.4 1.0
O2' A:U42 3.3 61.7 1.0
O3' A:C43 3.5 74.8 1.0
C3' A:C43 3.5 79.2 1.0
O3' A:U42 3.6 82.8 1.0
O5' A:C43 3.7 67.4 1.0
C3' A:U42 3.9 75.0 1.0
C2' A:U42 4.1 66.9 1.0
C5' A:C43 4.2 77.3 1.0
O5' A:G44 4.2 62.3 1.0
OP1 A:G44 4.2 83.3 1.0
C5' A:G44 4.4 66.5 1.0
C4' A:C43 4.4 78.5 1.0
OP1 A:C43 4.5 77.3 1.0
C8 A:G44 4.5 72.5 1.0
C2' A:C43 4.7 78.1 1.0
N7 A:G44 4.8 70.6 1.0
C6 A:C43 4.8 77.0 1.0

Magnesium binding site 5 out of 9 in 7eok

Go back to Magnesium Binding Sites List in 7eok
Magnesium binding site 5 out of 9 in the Crystal Structure of the Pepper Aptamer in Complex with HBC485


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 Pepper Aptamer in Complex with HBC485 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:54.1
occ:1.00
 OP2 A:G37 2.4 60.0 1.0
OP2 A:A36 2.7 41.2 1.0
C5' A:A36 2.7 45.4 1.0
P A:G37 3.0 47.2 1.0
O A:HOH205 3.1 44.7 1.0
O3' A:A36 3.2 52.7 1.0
OP1 A:G37 3.3 54.3 1.0
O5' A:A36 3.5 45.3 1.0
C4' A:A36 3.5 51.5 1.0
C3' A:A36 3.6 52.6 1.0
P A:A36 3.7 44.1 1.0
C3' A:U35 3.9 44.0 1.0
O A:HOH219 4.2 19.9 1.0
C6 A:U35 4.2 46.0 1.0
O3' A:U35 4.3 48.5 1.0
C2' A:U35 4.4 46.2 1.0
O5' A:G37 4.6 49.1 1.0
OP2 A:C29 4.6 52.0 1.0
OP1 A:C29 4.6 53.1 1.0
C5 A:U35 4.6 52.0 1.0
N1 A:U35 4.6 43.4 1.0
O5' A:U35 4.7 42.8 1.0
O4' A:A36 4.9 52.2 1.0
OP2 A:U35 4.9 47.6 1.0
C1' A:U35 5.0 51.8 1.0
C4' A:U35 5.0 49.1 1.0

Magnesium binding site 6 out of 9 in 7eok

Go back to Magnesium Binding Sites List in 7eok
Magnesium binding site 6 out of 9 in the Crystal Structure of the Pepper Aptamer in Complex with HBC485


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 Pepper Aptamer in Complex with HBC485 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:69.9
occ:1.00
 O1A A:GTP101 2.5 61.2 1.0
O A:HOH211 2.6 54.1 1.0
O3A A:GTP101 2.8 69.8 1.0
PA A:GTP101 3.2 60.2 1.0
O3G A:GTP101 3.3 75.8 1.0
O2G A:GTP101 3.7 76.9 1.0
O5' A:GTP101 3.9 44.3 1.0
PG A:GTP101 4.0 106.3 1.0
PB A:GTP101 4.2 74.6 1.0
O A:HOH216 4.5 54.4 1.0
O3B A:GTP101 4.5 93.7 1.0
O1B A:GTP101 4.5 59.0 1.0
C5' A:GTP101 4.5 40.6 1.0
O2A A:GTP101 4.6 48.2 1.0

Magnesium binding site 7 out of 9 in 7eok

Go back to Magnesium Binding Sites List in 7eok
Magnesium binding site 7 out of 9 in the Crystal Structure of the Pepper Aptamer in Complex with HBC485


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 Pepper Aptamer in Complex with HBC485 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg109

b:28.6
occ:1.00
 OP1 A:A30 2.5 46.0 1.0
O A:HOH209 2.6 48.3 1.0
O3' A:C29 3.0 41.6 1.0
P A:A30 3.3 42.6 1.0
OP2 A:A30 4.1 34.4 1.0
C3' A:C29 4.2 38.9 1.0
C4' A:C29 4.4 45.2 1.0
O A:HOH219 4.4 19.9 1.0
C5' A:C29 4.5 42.9 1.0
O5' A:A30 4.5 40.3 1.0
OP1 A:C28 4.6 47.1 1.0
C5' A:A30 4.8 40.2 1.0
O2' A:C29 4.9 45.2 1.0

Magnesium binding site 8 out of 9 in 7eok

Go back to Magnesium Binding Sites List in 7eok
Magnesium binding site 8 out of 9 in the Crystal Structure of the Pepper Aptamer in Complex with HBC485


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 Pepper Aptamer in Complex with HBC485 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg110

b:42.0
occ:1.00
 O A:HOH205 2.3 44.7 1.0
OP2 A:A30 2.5 34.4 1.0
O5' A:A30 3.3 40.3 1.0
N7 A:A31 3.4 43.5 1.0
P A:A30 3.4 42.6 1.0
OP2 A:A31 3.7 43.7 1.0
C8 A:A30 3.8 42.8 1.0
N7 A:A30 3.8 43.9 1.0
O4 A:U32 3.8 52.0 1.0
C8 A:A31 4.2 42.8 1.0
OP1 A:A30 4.4 46.0 1.0
N6 A:A31 4.5 40.8 1.0
C5 A:A31 4.5 42.8 1.0
O A:HOH219 4.5 19.9 1.0
C3' A:A30 4.5 44.1 1.0
C4 A:U32 4.7 49.4 1.0
N9 A:A30 4.7 39.6 1.0
C5' A:A30 4.7 40.2 1.0
O3' A:C29 4.7 41.6 1.0
C5 A:A30 4.7 43.0 1.0
C6 A:A31 4.9 43.1 1.0
C5 A:U32 4.9 43.2 1.0
P A:A31 4.9 39.5 1.0
C3' A:C29 4.9 38.9 1.0

Magnesium binding site 9 out of 9 in 7eok

Go back to Magnesium Binding Sites List in 7eok
Magnesium binding site 9 out of 9 in the Crystal Structure of the Pepper Aptamer in Complex with HBC485


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 Pepper Aptamer in Complex with HBC485 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg111

b:34.0
occ:1.00
 O2' A:C49 1.9 41.8 1.0
O3' A:C49 2.0 44.0 1.0
C2' A:C49 2.8 39.3 1.0
C3' A:C49 2.8 35.7 1.0
C4' A:C49 3.6 41.5 1.0
C1' A:C49 4.0 39.1 1.0
O4' A:C49 4.3 43.2 1.0
C5' A:C49 4.8 45.9 1.0

Reference:

K.Huang, X.Chen, C.Li, Q.Song, H.Li, L.Zhu, Y.Yang, A.Ren. Structure-Based Investigation of Fluorogenic Pepper Aptamer. Nat.Chem.Biol. 2021.
ISSN: ESSN 1552-4469
PubMed: 34725509
DOI: 10.1038/S41589-021-00884-6
Page generated: Wed Oct 2 20:52:10 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