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Magnesium in PDB 4izk: Crystal Structure of Yellowtail Ascites Virus VP4 Protease Active Site Mutant (K674A) Reveals Both An Acyl-Enzyme Complex and An Empty Active Site

Enzymatic activity of Crystal Structure of Yellowtail Ascites Virus VP4 Protease Active Site Mutant (K674A) Reveals Both An Acyl-Enzyme Complex and An Empty Active Site

All present enzymatic activity of Crystal Structure of Yellowtail Ascites Virus VP4 Protease Active Site Mutant (K674A) Reveals Both An Acyl-Enzyme Complex and An Empty Active Site:
3.4.21.115;

Protein crystallography data

The structure of Crystal Structure of Yellowtail Ascites Virus VP4 Protease Active Site Mutant (K674A) Reveals Both An Acyl-Enzyme Complex and An Empty Active Site, PDB code: 4izk was solved by M.Paetzel, I.Y.W.Chung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.80 / 2.30
Space group F 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 273.520, 273.520, 273.520, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Yellowtail Ascites Virus VP4 Protease Active Site Mutant (K674A) Reveals Both An Acyl-Enzyme Complex and An Empty Active Site (pdb code 4izk). 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 Yellowtail Ascites Virus VP4 Protease Active Site Mutant (K674A) Reveals Both An Acyl-Enzyme Complex and An Empty Active Site, PDB code: 4izk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4izk

Go back to Magnesium Binding Sites List in 4izk
Magnesium binding site 1 out of 2 in the Crystal Structure of Yellowtail Ascites Virus VP4 Protease Active Site Mutant (K674A) Reveals Both An Acyl-Enzyme Complex and An Empty Active Site


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 Yellowtail Ascites Virus VP4 Protease Active Site Mutant (K674A) Reveals Both An Acyl-Enzyme Complex and An Empty Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:31.9
occ:1.00
 O A:HOH939 3.2 28.6 1.0
O A:HOH1033 3.2 41.3 1.0
N A:CSO669 3.3 32.7 1.0
O A:HOH988 3.4 49.9 1.0
CB A:ILE668 3.7 27.4 1.0
CB A:CSO669 3.9 41.0 1.0
CD A:PRO632 4.0 27.0 1.0
CB A:SER633 4.1 23.3 1.0
SG A:CSO669 4.1 54.7 0.8
O A:CSO669 4.1 41.1 1.0
CG2 A:ILE668 4.1 25.4 1.0
CA A:ILE668 4.1 29.3 1.0
CA A:CSO669 4.1 37.0 1.0
C A:ILE668 4.2 34.2 1.0
N A:SER633 4.5 20.7 1.0
OG A:SER633 4.5 26.4 1.0
C A:CSO669 4.6 38.8 1.0
CG A:PRO632 4.7 28.9 1.0
N A:PRO632 4.7 29.0 1.0
O A:HOH940 4.8 38.4 1.0
CA A:SER633 4.8 23.1 1.0
CG1 A:ILE668 4.9 24.4 1.0

Magnesium binding site 2 out of 2 in 4izk

Go back to Magnesium Binding Sites List in 4izk
Magnesium binding site 2 out of 2 in the Crystal Structure of Yellowtail Ascites Virus VP4 Protease Active Site Mutant (K674A) Reveals Both An Acyl-Enzyme Complex and An Empty Active Site


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 Yellowtail Ascites Virus VP4 Protease Active Site Mutant (K674A) Reveals Both An Acyl-Enzyme Complex and An Empty Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:54.8
occ:1.00
 O B:HOH1073 2.0 43.4 1.0
O B:HOH1038 2.1 48.3 1.0
O B:HOH1040 2.2 32.3 1.0
O B:HOH1037 2.2 33.8 1.0
O B:HOH1039 2.2 42.3 1.0
O B:HOH1074 2.7 51.8 1.0
O B:HOH973 3.8 26.3 1.0
O A:HOH993 4.0 58.5 1.0
O B:HOH972 4.1 48.0 1.0
O B:HOH1075 4.3 59.0 1.0
OE2 B:GLU530 4.4 33.1 1.0
OE1 B:GLU530 4.6 32.6 1.0
O A:HOH994 4.9 48.6 1.0
CD B:GLU530 5.0 30.0 1.0

Reference:

I.Y.Chung, M.Paetzel. Crystal Structures of Yellowtail Ascites Virus VP4 Protease: Trapping An Internal Cleavage Site Trans Acyl-Enzyme Complex in A Native Ser/Lys Dyad Active Site. J.Biol.Chem. V. 288 13068 2013.
ISSN: ISSN 0021-9258
PubMed: 23511637
DOI: 10.1074/JBC.M112.386953
Page generated: Mon Dec 14 18:55:21 2020

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