Atomistry » Magnesium » PDB 7scw-7sq2 » 7sf0
Atomistry »
  Magnesium »
    PDB 7scw-7sq2 »
      7sf0 »

Magnesium in PDB 7sf0: Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate

Protein crystallography data

The structure of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate, PDB code: 7sf0 was solved by J.K.Peters, R.W.Tibble, M.Warminski, J.Jemielity, J.D.Gross, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.00 / 1.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 52.74, 139.99, 76.02, 90, 90, 90
R / Rfree (%) 20.1 / 24.7

Other elements in 7sf0:

The structure of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate (pdb code 7sf0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate, PDB code: 7sf0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7sf0

Go back to Magnesium Binding Sites List in 7sf0
Magnesium binding site 1 out of 2 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate


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 Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:55.1
occ:1.00
O3B A:8NK301 2.0 77.1 1.0
O1A A:8NK301 2.5 68.2 1.0
NE2 A:GLN57 2.9 40.3 1.0
PB A:8NK301 3.3 81.7 1.0
NH2 A:ARG50 3.6 27.3 1.0
PA A:8NK301 3.7 74.4 1.0
CD A:GLN57 3.7 36.0 1.0
OE1 A:GLN57 3.7 34.5 1.0
O3A A:8NK301 3.8 66.4 1.0
O1B A:8NK301 3.9 57.7 1.0
CM7 A:8NK301 3.9 32.1 1.0
O2B A:8NK301 4.4 82.1 1.0
O2A A:8NK301 4.5 73.1 1.0
C8 A:8NK301 4.7 36.4 1.0
N7 A:8NK301 4.8 35.3 1.0
CZ A:ARG50 4.9 28.8 1.0
O5' A:8NK301 4.9 58.5 1.0

Magnesium binding site 2 out of 2 in 7sf0

Go back to Magnesium Binding Sites List in 7sf0
Magnesium binding site 2 out of 2 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate


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 Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:40.5
occ:1.00
O A:HOH473 2.0 38.0 1.0
O A:HOH414 2.1 44.6 1.0
O A:HOH444 2.2 40.7 1.0
OE2 A:GLU183 2.2 42.4 1.0
OE1 A:GLU126 2.2 40.9 1.0
OE2 A:GLU130 2.2 44.5 1.0
CD A:GLU183 3.0 52.2 1.0
OE1 A:GLU183 3.1 61.9 1.0
CD A:GLU130 3.2 42.7 1.0
CD A:GLU126 3.4 38.6 1.0
O A:HOH540 3.5 47.8 1.0
CG A:GLU130 3.5 36.3 1.0
O A:GLY110 3.7 39.2 1.0
O A:HOH420 3.7 44.1 1.0
O A:HOH432 3.7 49.8 1.0
OE2 A:GLU126 3.9 37.4 1.0
CA A:GLY111 4.4 32.7 1.0
O A:HOH452 4.4 51.0 1.0
OE1 A:GLU130 4.4 41.7 1.0
C A:GLY110 4.4 31.0 1.0
CG A:GLU183 4.5 40.1 1.0
OE1 A:GLU129 4.5 40.9 1.0
CG A:GLU126 4.6 31.2 1.0
O A:HOH526 4.7 42.7 1.0
CB A:GLU126 4.7 29.2 1.0
N A:GLY111 4.8 27.0 1.0
CB A:GLU183 5.0 31.7 1.0
O A:GLU126 5.0 31.1 1.0

Reference:

J.K.Peters, R.W.Tibble, M.Warminski, J.Jemielity, J.D.Gross. Structure of the Poxvirus Decapping Enzyme D9 Reveals Its Mechanism of Cap Recognition and Catalysis. Structure V. 30 721 2022.
ISSN: ISSN 0969-2126
PubMed: 35290794
DOI: 10.1016/J.STR.2022.02.012
Page generated: Thu Oct 3 08:43:08 2024

Last articles

Na in 7Q78
Na in 7Q77
Na in 7Q76
Na in 7Q6Q
Na in 7Q75
Na in 7Q5F
Na in 7Q47
Na in 7Q3Z
Na in 7Q5E
Na in 7Q36
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy