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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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