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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: Mon Dec 14 08:15:05 2020

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