Atomistry » Magnesium » PDB 6c7y-6cfv » 6c8j
Atomistry »
  Magnesium »
    PDB 6c7y-6cfv »
      6c8j »

Magnesium in PDB 6c8j: Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking

Protein crystallography data

The structure of Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking, PDB code: 6c8j was solved by W.Zhang, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.50
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 49.091, 49.091, 81.097, 90.00, 90.00, 120.00
R / Rfree (%) 21.1 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking (pdb code 6c8j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking, PDB code: 6c8j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6c8j

Go back to Magnesium Binding Sites List in 6c8j
Magnesium binding site 1 out of 6 in the Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:22.2
occ:1.00
 O A:HOH220 2.0 26.9 1.0
O B:HOH209 2.0 27.4 1.0
O B:HOH208 2.0 25.4 1.0
O A:HOH209 2.1 25.6 1.0
O B:HOH247 2.1 27.4 1.0
O A:HOH257 2.1 26.8 1.0
O4 A:U7 4.2 22.5 1.0
O4 B:U7 4.2 22.2 1.0
O A:HOH251 4.3 29.4 1.0
O B:HOH243 4.4 29.7 1.0
O A:HOH238 4.4 30.7 1.0
O B:HOH239 4.4 27.4 1.0
O A:HOH243 4.4 27.1 1.0
O B:HOH230 4.4 30.9 1.0
O4 B:U8 4.4 25.0 1.0
O4 A:U8 4.5 25.2 1.0
C4 A:U7 5.0 22.9 1.0
C4 B:U7 5.0 22.6 1.0

Magnesium binding site 2 out of 6 in 6c8j

Go back to Magnesium Binding Sites List in 6c8j
Magnesium binding site 2 out of 6 in the Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:29.9
occ:1.00
 O A:HOH259 2.0 30.8 1.0
O A:HOH258 2.0 32.7 1.0
O A:HOH202 2.0 28.1 1.0
O A:HOH253 2.1 31.9 1.0
O A:HOH214 2.1 30.1 1.0
O A:HOH239 2.1 32.2 1.0
O A:HOH221 4.0 35.1 1.0
O A:HOH224 4.1 34.6 1.0
O B:HOH237 4.2 27.1 1.0
N7 A:A10 4.2 28.5 1.0
O A:HOH236 4.2 28.2 1.0
O A:HOH255 4.3 35.0 1.0
O6 A:G11 4.3 24.3 1.0
N6 A:A10 4.4 25.0 1.0
N7 A:G11 4.6 26.5 1.0
C5 A:A10 4.9 26.0 1.0

Magnesium binding site 3 out of 6 in 6c8j

Go back to Magnesium Binding Sites List in 6c8j
Magnesium binding site 3 out of 6 in the Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:23.5
occ:1.00
 O A:HOH206 4.1 21.3 1.0
O2' A:A5 4.3 20.3 1.0
C5' A:C6 4.6 20.4 1.0

Magnesium binding site 4 out of 6 in 6c8j

Go back to Magnesium Binding Sites List in 6c8j
Magnesium binding site 4 out of 6 in the Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking within 5.0Å range:

Magnesium binding site 5 out of 6 in 6c8j

Go back to Magnesium Binding Sites List in 6c8j
Magnesium binding site 5 out of 6 in the Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:48.1
occ:0.33
 O A:HOH254 2.5 37.6 1.0

Magnesium binding site 6 out of 6 in 6c8j

Go back to Magnesium Binding Sites List in 6c8j
Magnesium binding site 6 out of 6 in the Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Rna-Activated 2-Aipg Monomer Complex, 15 Min Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:23.6
occ:1.00
 O A:HOH252 2.0 22.2 1.0
O B:HOH226 2.0 27.0 1.0
O B:HOH203 2.0 28.9 1.0
O A:HOH230 2.1 27.4 1.0
O A:HOH242 2.2 26.4 1.0
O A:HOH206 4.1 21.3 1.0
OP2 B:A5 4.1 22.8 1.0
O A:HOH219 4.2 24.0 1.0
O A:HOH256 4.3 39.2 1.0
OP1 B:A5 4.3 24.1 1.0
OP2 A:U7 4.3 23.6 1.0
OP1 B:LCG4 4.4 20.8 1.0
O B:HOH207 4.4 34.6 1.0
OP1 A:C6 4.5 22.7 1.0
P B:A5 4.7 22.1 1.0
OP2 B:LCG4 4.9 24.7 1.0
OP1 A:U7 5.0 27.2 1.0
P B:LCG4 5.0 21.1 1.0

Reference:

W.Zhang, T.Walton, L.Li, J.W.Szostak. Crystallographic Observation of Nonenzymatic Rna Primer Extension. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29851379
DOI: 10.7554/ELIFE.36422
Page generated: Mon Sep 30 20:21:33 2024

Last articles

F in 8SHF
F in 8SHE
F in 8SHD
F in 8SHA
F in 8SGL
F in 8SH9
F in 8SHC
F in 8SGC
F in 8SG9
F in 8SGI
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy