Atomistry » Magnesium » PDB 3hx0-3i5x » 3hxy
Atomistry »
  Magnesium »
    PDB 3hx0-3i5x »
      3hxy »

Magnesium in PDB 3hxy: Crystal Structure of Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp

Enzymatic activity of Crystal Structure of Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp

All present enzymatic activity of Crystal Structure of Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp:
6.1.1.7;

Protein crystallography data

The structure of Crystal Structure of Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp, PDB code: 3hxy was solved by M.Guo, X.-L.Yang, P.Schimmel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.56 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.355, 108.745, 118.985, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp (pdb code 3hxy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp, PDB code: 3hxy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3hxy

Go back to Magnesium Binding Sites List in 3hxy
Magnesium binding site 1 out of 4 in the Crystal Structure of Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp


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 Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg445

b:17.0
occ:1.00
 O2B A:ACP444 1.8 12.0 0.5
OE2 A:GLU183 2.4 28.0 1.0
O2A A:ACP444 2.5 12.3 0.5
O A:HOH804 2.5 42.1 1.0
MG A:MG447 2.6 12.1 0.5
OE1 A:GLU209 2.6 18.6 1.0
O2A A:5AL442 2.6 9.1 0.5
O3 A:MDN443 3.0 18.1 0.5
O A:HOH570 3.0 21.2 1.0
PB A:ACP444 3.2 6.9 0.5
CD A:GLU183 3.3 22.7 1.0
CD A:GLU209 3.3 15.0 1.0
OE2 A:GLU209 3.3 18.9 1.0
MG A:MG448 3.4 28.2 0.5
ND2 A:ASN212 3.5 13.7 1.0
PA A:ACP444 3.5 15.3 0.5
OE1 A:GLU183 3.6 23.4 1.0
O3A A:ACP444 3.7 10.3 0.5
P A:5AL442 3.9 7.0 0.5
CG A:ASN212 4.0 14.6 1.0
O1A A:ACP444 4.2 14.7 0.5
O1B A:ACP444 4.2 5.2 0.5
C3B A:ACP444 4.3 10.5 0.5
O A:HOH581 4.3 27.2 1.0
CB A:ASN212 4.3 9.6 1.0
P1 A:MDN443 4.4 18.8 0.5
O3A A:5AL442 4.5 7.1 0.5
O1A A:5AL442 4.5 8.6 0.5
O A:ASP167 4.5 16.9 1.0
O3G A:ACP444 4.5 13.9 0.5
CG A:GLU183 4.5 17.1 1.0
C4 A:MDN443 4.6 17.6 0.5
O3' A:5AL442 4.8 8.6 0.5
CG A:GLU209 4.8 13.1 1.0
O A:HOH692 4.8 39.5 1.0
OD1 A:ASN212 4.8 14.6 1.0
O5' A:ACP444 4.9 13.2 0.5
O A:HOH563 5.0 22.2 1.0

Magnesium binding site 2 out of 4 in 3hxy

Go back to Magnesium Binding Sites List in 3hxy
Magnesium binding site 2 out of 4 in the Crystal Structure of Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp


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 Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg446

b:18.0
occ:0.50
 O2G A:ACP444 1.9 19.5 0.5
O A:HOH778 1.9 17.0 1.0
O A:HOH823 2.0 30.5 1.0
O1B A:ACP444 2.1 5.2 0.5
O7 A:MDN443 2.4 22.7 0.5
O2 A:MDN443 2.4 14.2 0.5
O A:HOH491 2.5 60.9 1.0
O A:HOH595 2.7 22.6 1.0
PG A:ACP444 3.1 13.7 0.5
O A:HOH824 3.2 47.3 1.0
PB A:ACP444 3.4 6.9 0.5
O3G A:ACP444 3.5 13.9 0.5
P5 A:MDN443 3.6 18.2 0.5
P1 A:MDN443 3.6 18.8 0.5
C3B A:ACP444 3.7 10.5 0.5
C4 A:MDN443 3.8 17.6 0.5
O8 A:MDN443 4.2 19.4 0.5
O3 A:MDN443 4.3 18.1 0.5
O1G A:ACP444 4.4 16.1 0.5
OD1 A:ASP76 4.4 26.0 1.0
O2B A:ACP444 4.4 12.0 0.5
O3A A:ACP444 4.5 10.3 0.5
NE2 A:HIS86 4.6 10.1 1.0
NH1 A:ARG69 4.6 11.6 1.0
CD2 A:HIS74 4.6 42.7 1.0
OD2 A:ASP76 4.6 21.5 1.0
O A:HOH806 4.7 39.2 1.0
O6 A:MDN443 4.8 14.4 0.5
O1 A:MDN443 4.9 20.5 0.5
CG A:ASP76 4.9 26.2 1.0
MG A:MG448 4.9 28.2 0.5
O A:HOH841 5.0 29.3 1.0
N7 A:ACP444 5.0 11.8 0.5

Magnesium binding site 3 out of 4 in 3hxy

Go back to Magnesium Binding Sites List in 3hxy
Magnesium binding site 3 out of 4 in the Crystal Structure of Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp


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 Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg447

b:12.1
occ:0.50
 MG A:MG448 1.8 28.2 0.5
O3 A:MDN443 1.9 18.1 0.5
O A:HOH563 2.5 22.2 1.0
MG A:MG445 2.6 17.0 1.0
OE1 A:GLU183 2.6 23.4 1.0
OE2 A:GLU209 2.6 18.9 1.0
OE2 A:GLU183 2.9 28.0 1.0
O2B A:ACP444 3.0 12.0 0.5
CD A:GLU183 3.1 22.7 1.0
P1 A:MDN443 3.2 18.8 0.5
O A:HOH804 3.4 42.1 1.0
CD A:GLU209 3.4 15.0 1.0
O1 A:MDN443 3.5 20.5 0.5
O3G A:ACP444 3.6 13.9 0.5
OE1 A:GLU209 3.6 18.6 1.0
O A:ASP167 3.6 16.9 1.0
OD1 A:ASP167 3.7 30.4 1.0
C4 A:MDN443 4.0 17.6 0.5
O A:HOH570 4.0 21.2 1.0
CB A:ASP167 4.1 20.6 1.0
O A:HOH482 4.1 14.7 1.0
CG A:ASP167 4.2 25.9 1.0
O A:HOH692 4.2 39.5 1.0
O A:HOH492 4.4 22.5 1.0
PB A:ACP444 4.4 6.9 0.5
O2 A:MDN443 4.4 14.2 0.5
CA A:ASP167 4.4 19.1 1.0
C A:ASP167 4.4 16.9 1.0
O A:HOH494 4.6 21.2 1.0
CG A:GLU183 4.6 17.1 1.0
C3B A:ACP444 4.8 10.5 0.5
CG A:GLU209 4.8 13.1 1.0
PG A:ACP444 4.9 13.7 0.5
O2A A:ACP444 5.0 12.3 0.5

Magnesium binding site 4 out of 4 in 3hxy

Go back to Magnesium Binding Sites List in 3hxy
Magnesium binding site 4 out of 4 in the Crystal Structure of Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp


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 Catalytic Fragment of E. Coli Alars in Complex with Amppcp, Ala-Amp and Pcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg448

b:28.2
occ:0.50
 O3 A:MDN443 1.1 18.1 0.5
P1 A:MDN443 1.6 18.8 0.5
MG A:MG447 1.8 12.1 0.5
O3G A:ACP444 1.9 13.9 0.5
O1 A:MDN443 2.0 20.5 0.5
O A:HOH563 2.2 22.2 1.0
OE2 A:GLU209 2.3 18.9 1.0
C4 A:MDN443 2.4 17.6 0.5
O2B A:ACP444 2.9 12.0 0.5
O2 A:MDN443 3.0 14.2 0.5
PG A:ACP444 3.2 13.7 0.5
O A:HOH494 3.3 21.2 1.0
CD A:GLU209 3.4 15.0 1.0
MG A:MG445 3.4 17.0 1.0
C3B A:ACP444 3.6 10.5 0.5
PB A:ACP444 3.7 6.9 0.5
OE1 A:GLU209 3.9 18.6 1.0
OE1 A:GLU183 3.9 23.4 1.0
O A:HOH804 3.9 42.1 1.0
OD1 A:ASP167 4.0 30.4 1.0
P5 A:MDN443 4.0 18.2 0.5
O1G A:ACP444 4.0 16.1 0.5
O A:HOH839 4.1 30.7 1.0
O A:HOH838 4.2 29.5 1.0
O8 A:MDN443 4.2 19.4 0.5
O1B A:ACP444 4.3 5.2 0.5
O2G A:ACP444 4.3 19.5 0.5
OE2 A:GLU183 4.5 28.0 1.0
O A:HOH841 4.6 29.3 1.0
CD A:GLU183 4.6 22.7 1.0
CG A:ASP167 4.6 25.9 1.0
CG A:GLU209 4.6 13.1 1.0
O A:HOH692 4.6 39.5 1.0
O7 A:MDN443 4.7 22.7 0.5
O A:HOH492 4.7 22.5 1.0
CB A:GLU209 4.7 9.2 1.0
O A:HOH824 4.8 47.3 1.0
O6 A:MDN443 4.9 14.4 0.5
MG A:MG446 4.9 18.0 0.5

Reference:

M.Guo, Y.E.Chong, R.Shapiro, K.Beebe, X.L.Yang, P.Schimmel. Paradox of Mistranslation of Serine For Alanine Caused By Alars Recognition Dilemma. Nature V. 462 808 2009.
ISSN: ISSN 0028-0836
PubMed: 20010690
DOI: 10.1038/NATURE08612
Page generated: Wed Aug 14 15:28:12 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