Magnesium in PDB 4gvj: TYK2 (JH1) in Complex with Adenosine Di-Phosphate

All present enzymatic activity of TYK2 (JH1) in Complex with Adenosine Di-Phosphate:
2.7.10.2;

The structure of TYK2 (JH1) in Complex with Adenosine Di-Phosphate, PDB code: 4gvj was solved by J.Liang, A.V.Abbema, L.Bao, K.Barrett, M.Beresini, L.Berezhkovskiy, W.Blair, C.Chang, J.Driscoll, C.Eigenbrot, N.Ghilardi, P.Gibbons, J.Halladay, A.Johnson, P.B.Kohli, Y.Lai, M.Liimatta, P.Mantik, K.Menghrajani, J.Murray, A.Sambrone, Y.Shao, S.Shia, Y.Shin, J.Smith, S.Sohn, M.Stanley, V.Tsui, M.Ultsch, L.Wu, B.Zhang, S.Magnuson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.93 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.326, 74.051, 105.321, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.1

The binding sites of Magnesium atom in the TYK2 (JH1) in Complex with Adenosine Di-Phosphate (pdb code 4gvj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the TYK2 (JH1) in Complex with Adenosine Di-Phosphate, PDB code: 4gvj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the TYK2 (JH1) in Complex with Adenosine Di-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of TYK2 (JH1) in Complex with Adenosine Di-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1202 b:34.8 occ:1.00 O A:HOH1344 1.9 41.0 1.0 O A:HOH1325 1.9 36.0 1.0 OD2 A:ASP1041 2.1 30.5 1.0 OD1 A:ASP1041 2.1 31.4 1.0 O1B A:ADP1201 2.2 32.3 1.0 O A:HOH1343 2.2 30.0 1.0 CG A:ASP1041 2.4 30.7 1.0 PB A:ADP1201 3.3 32.2 1.0 O3B A:ADP1201 3.3 28.1 1.0 OD2 A:ASP1023 3.6 34.8 1.0 MG A:MG1203 3.6 29.8 1.0 O A:HOH1342 3.7 31.2 1.0 CB A:ASP1041 3.9 29.9 1.0 O A:HOH1332 4.2 36.7 1.0 NZ A:LYS930 4.2 33.9 1.0 O3A A:ADP1201 4.3 35.0 1.0 O2B A:ADP1201 4.4 35.4 1.0 CA A:GLY1043 4.5 30.8 1.0 O2A A:ADP1201 4.5 30.8 1.0 N A:GLY1043 4.6 29.2 1.0 O A:HOH1350 4.7 42.9 1.0 CG A:ASP1023 4.8 35.3 1.0 CA A:ASP1041 4.8 29.4 1.0 PA A:ADP1201 4.9 33.1 1.0 O A:ASP1041 4.9 32.7 1.0 C A:ASP1041 4.9 32.8 1.0 OD1 A:ASN1028 4.9 26.0 1.0 ND2 A:ASN1028 5.0 25.4 1.0

Magnesium binding site 2 out of 2 in the TYK2 (JH1) in Complex with Adenosine Di-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of TYK2 (JH1) in Complex with Adenosine Di-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1203 b:29.8 occ:1.00 O A:HOH1301 2.0 30.5 1.0 O2A A:ADP1201 2.0 30.8 1.0 OD2 A:ASP1041 2.0 30.5 1.0 O3B A:ADP1201 2.1 28.1 1.0 OD1 A:ASN1028 2.1 26.0 1.0 O A:HOH1342 2.2 31.2 1.0 CG A:ASP1041 3.0 30.7 1.0 CG A:ASN1028 3.1 31.8 1.0 PB A:ADP1201 3.2 32.2 1.0 PA A:ADP1201 3.3 33.1 1.0 ND2 A:ASN1028 3.5 25.4 1.0 O3A A:ADP1201 3.5 35.0 1.0 CB A:ASP1041 3.6 29.9 1.0 MG A:MG1202 3.6 34.8 1.0 O1B A:ADP1201 3.7 32.3 1.0 O A:HOH1350 4.0 42.9 1.0 O A:HOH1344 4.0 41.0 1.0 OD1 A:ASP1041 4.0 31.4 1.0 O1A A:ADP1201 4.2 31.6 1.0 O A:HOH1359 4.3 41.8 1.0 O5' A:ADP1201 4.3 33.8 1.0 O A:HOH1330 4.3 32.5 1.0 C5' A:ADP1201 4.4 34.4 1.0 OD2 A:ASP1023 4.4 34.8 1.0 CB A:ASN1028 4.5 28.9 1.0 O2B A:ADP1201 4.5 35.4 1.0 CG A:ARG1027 4.5 25.3 1.0 O3' A:ADP1201 4.6 35.8 1.0 CD A:ARG1027 4.6 29.3 1.0 O A:ARG1027 4.7 30.0 1.0 CA A:ASN1028 4.9 28.6 1.0 O A:HOH1343 4.9 30.0 1.0 C A:ARG1027 5.0 29.4 1.0

J.Liang, V.Tsui, A.Van Abbema, L.Bao, K.Barrett, M.Beresini, L.Berezhkovskiy, W.S.Blair, C.Chang, J.Driscoll, C.Eigenbrot, N.Ghilardi, P.Gibbons, J.Halladay, A.Johnson, P.B.Kohli, Y.Lai, M.Liimatta, P.Mantik, K.Menghrajani, J.Murray, A.Sambrone, Y.Xiao, S.Shia, Y.Shin, J.Smith, S.Sohn, M.Stanley, M.Ultsch, B.Zhang, L.C.Wu, S.Magnuson. Lead Identification of Novel and Selective TYK2 Inhibitors. Eur.J.Med.Chem. V. 67 175 2013.
ISSN: ISSN 0223-5234
PubMed: 23867602
DOI: 10.1016/J.EJMECH.2013.03.070