Magnesium in PDB 4yzd: Crystal Structure of Human Phosphorylated IRE1ALPHA in Complex with Adp-Mg

All present enzymatic activity of Crystal Structure of Human Phosphorylated IRE1ALPHA in Complex with Adp-Mg:
2.7.11.1;

The structure of Crystal Structure of Human Phosphorylated IRE1ALPHA in Complex with Adp-Mg, PDB code: 4yzd was solved by N.O.Concha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.64 / 3.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	191.751, 122.492, 77.876, 90.00, 107.07, 90.00
R / Rfree (%)	23.2 / 27.3

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphorylated IRE1ALPHA in Complex with Adp-Mg (pdb code 4yzd). 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 Human Phosphorylated IRE1ALPHA in Complex with Adp-Mg, PDB code: 4yzd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Phosphorylated IRE1ALPHA in Complex with Adp-Mg


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 Human Phosphorylated IRE1ALPHA in Complex with Adp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:0.1 occ:1.00 OD1 A:ASN693 2.0 80.3 1.0 O2A A:ADP1002 2.1 81.8 1.0 OD2 A:ASP711 2.1 92.9 1.0 O2B A:ADP1002 2.4 0.4 1.0 CG A:ASP711 2.8 93.3 1.0 HZ3 A:LYS599 3.1 89.8 1.0 HA A:ASN693 3.2 75.4 1.0 OD1 A:ASP711 3.2 92.2 1.0 CG A:ASN693 3.3 84.4 1.0 PA A:ADP1002 3.3 81.7 1.0 PB A:ADP1002 3.5 78.2 1.0 O3B A:ADP1002 3.6 93.1 1.0 H8 A:ADP1002 3.7 92.8 1.0 O5' A:ADP1002 3.7 80.5 1.0 O A:HIS692 3.8 68.2 1.0 O3A A:ADP1002 3.8 92.7 1.0 NZ A:LYS599 3.9 74.8 1.0 CA A:ASN693 3.9 62.8 1.0 HB2 A:ASP711 4.0 99.9 1.0 CB A:ASP711 4.0 83.3 1.0 HB3 A:HIS692 4.0 89.1 1.0 HZ1 A:LYS599 4.1 89.8 1.0 HZ2 A:LYS599 4.1 89.8 1.0 HD22 A:ASN693 4.2 0.8 1.0 C A:HIS692 4.2 61.0 1.0 CB A:ASN693 4.2 72.4 1.0 ND2 A:ASN693 4.2 84.0 1.0 N A:ASN693 4.2 60.5 1.0 HB3 A:ASP711 4.3 99.9 1.0 HE3 A:LYS690 4.5 90.9 1.0 H3' A:ADP1002 4.5 98.2 1.0 C8 A:ADP1002 4.5 77.3 1.0 HB3 A:ASN693 4.6 86.9 1.0 O1A A:ADP1002 4.7 75.8 1.0 HD22 A:LEU695 4.7 70.6 1.0 H A:ASN693 4.8 72.6 1.0 CB A:HIS692 4.8 74.3 1.0 O1B A:ADP1002 4.9 77.9 1.0 H5'2 A:ADP1002 4.9 0.4 1.0 HB2 A:HIS692 4.9 89.1 1.0 HE2 A:LYS690 4.9 90.9 1.0 C5' A:ADP1002 4.9 85.4 1.0 HB2 A:ASN693 4.9 86.9 1.0 N7 A:ADP1002 5.0 69.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Phosphorylated IRE1ALPHA in Complex with Adp-Mg


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 Human Phosphorylated IRE1ALPHA in Complex with Adp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:65.9 occ:1.00 O2B B:ADP1002 2.6 78.6 1.0 OD2 B:ASP711 2.7 73.0 1.0 OD1 B:ASN693 2.8 65.8 1.0 HA B:ASN693 2.8 79.2 1.0 O2A B:ADP1002 3.1 63.0 1.0 O B:HIS692 3.1 64.0 1.0 CG B:ASP711 3.1 69.8 1.0 OD1 B:ASP711 3.1 59.1 1.0 H8 B:ADP1002 3.3 95.1 1.0 CA B:ASN693 3.7 66.0 1.0 C B:HIS692 3.8 67.5 1.0 HD23 B:LEU695 3.8 79.1 1.0 CG B:ASN693 3.9 70.5 1.0 C8 B:ADP1002 3.9 79.2 1.0 HZ1 B:LYS599 3.9 81.9 1.0 H3' B:ADP1002 3.9 90.3 1.0 O5' B:ADP1002 4.0 62.5 1.0 N B:ASN693 4.0 66.2 1.0 HB3 B:HIS692 4.0 91.0 1.0 PB B:ADP1002 4.0 72.2 1.0 PA B:ADP1002 4.1 76.8 1.0 HB2 B:ASP711 4.2 82.1 1.0 N7 B:ADP1002 4.2 67.4 1.0 HB3 B:SER710 4.3 62.9 1.0 CB B:ASP711 4.3 68.4 1.0 CB B:ASN693 4.4 70.8 1.0 HD11 B:LEU695 4.4 71.1 1.0 O3A B:ADP1002 4.5 75.2 1.0 HG B:SER710 4.5 71.3 1.0 O1B B:ADP1002 4.7 53.6 1.0 H5'1 B:ADP1002 4.7 86.7 1.0 H B:ASN693 4.7 79.4 1.0 CD2 B:LEU695 4.7 65.9 1.0 C B:ASN693 4.7 70.2 1.0 HB3 B:ASN693 4.7 85.0 1.0 OG B:SER710 4.7 59.4 1.0 NZ B:LYS599 4.8 68.3 1.0 HG B:LEU695 4.8 68.9 1.0 HB3 B:ASP711 4.8 82.1 1.0 CB B:HIS692 4.8 75.8 1.0 H2' B:ADP1002 4.8 88.8 1.0 HZ2 B:LYS599 4.8 81.9 1.0 C5' B:ADP1002 4.9 72.2 1.0 CA B:HIS692 4.9 72.5 1.0 C3' B:ADP1002 5.0 75.3 1.0 CB B:SER710 5.0 52.4 1.0 O B:ASN693 5.0 77.7 1.0

N.O.Concha, A.Smallwood, W.Bonnette, R.Totoritis, G.Zhang, K.Federowicz, J.Yang, H.Qi, S.Chen, N.Campobasso, A.E.Choudhry, L.E.Shuster, K.A.Evans, J.Ralph, S.Sweitzer, D.A.Heerding, C.A.Buser, D.S.Su, M.P.Deyoung. Long-Range Inhibitor-Induced Conformational Regulation of Human IRE1 Alpha Endoribonuclease Activity. Mol.Pharmacol. V. 88 1011 2015.
ISSN: ESSN 1521-0111
PubMed: 26438213
DOI: 10.1124/MOL.115.100917