Magnesium in PDB 4dn5: Crystal Structure of Nf-Kb-Inducing Kinase (Nik)

All present enzymatic activity of Crystal Structure of Nf-Kb-Inducing Kinase (Nik):
2.7.11.25;

The structure of Crystal Structure of Nf-Kb-Inducing Kinase (Nik), PDB code: 4dn5 was solved by X.Min, J.Liu, A.Sudom, N.P.Walker, Z.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	85.060, 85.060, 115.400, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.2

The binding sites of Magnesium atom in the Crystal Structure of Nf-Kb-Inducing Kinase (Nik) (pdb code 4dn5). 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 Nf-Kb-Inducing Kinase (Nik), PDB code: 4dn5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Nf-Kb-Inducing Kinase (Nik)


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 Nf-Kb-Inducing Kinase (Nik) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:38.3 occ:1.00 O1A A:AGS1008 1.8 35.3 1.0 O2B A:AGS1008 2.0 39.9 1.0 OD2 A:ASP534 2.1 39.2 1.0 OD1 A:ASN520 2.2 36.2 1.0 O A:HOH1118 2.2 40.1 1.0 O A:HOH1119 2.2 39.0 1.0 PB A:AGS1008 3.1 38.1 1.0 PA A:AGS1008 3.1 36.2 1.0 CG A:ASP534 3.1 38.6 1.0 CG A:ASN520 3.2 36.4 1.0 O3B A:AGS1008 3.5 43.4 1.0 O3A A:AGS1008 3.5 37.6 1.0 ND2 A:ASN520 3.5 35.3 1.0 CB A:ASP534 3.7 37.9 1.0 O3' A:AGS1008 4.1 33.5 1.0 OD1 A:ASP534 4.1 37.9 1.0 O5' A:AGS1008 4.2 35.7 1.0 O2G A:AGS1008 4.2 46.0 1.0 O2A A:AGS1008 4.2 35.0 1.0 PG A:AGS1008 4.2 49.5 1.0 C5' A:AGS1008 4.3 34.9 1.0 S1G A:AGS1008 4.4 50.3 1.0 OD2 A:ASP515 4.5 33.4 1.0 O1B A:AGS1008 4.5 39.0 1.0 CB A:ASN520 4.5 35.6 1.0 C3' A:AGS1008 4.5 33.8 1.0 CA A:GLY409 4.8 38.3 1.0 O A:ASP519 4.8 34.5 1.0 CA A:ASN520 4.9 35.5 1.0 C4' A:AGS1008 5.0 34.0 1.0 C A:ASP519 5.0 35.0 1.0 CB A:ASP519 5.0 35.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Nf-Kb-Inducing Kinase (Nik)


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 Nf-Kb-Inducing Kinase (Nik) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:35.1 occ:1.00 O2A B:AGS1003 1.9 36.5 1.0 O2B B:AGS1003 1.9 40.5 1.0 O B:HOH1108 2.1 39.5 1.0 OD1 B:ASP534 2.2 40.4 1.0 OD1 B:ASN520 2.3 38.1 1.0 O B:HOH1109 2.5 46.5 1.0 PB B:AGS1003 3.1 39.0 1.0 PA B:AGS1003 3.1 36.9 1.0 CG B:ASP534 3.2 41.2 1.0 CG B:ASN520 3.3 38.9 1.0 O3A B:AGS1003 3.5 38.5 1.0 O3B B:AGS1003 3.5 42.4 1.0 ND2 B:ASN520 3.7 38.6 1.0 CB B:ASP534 3.9 40.6 1.0 O2G B:AGS1003 4.0 44.2 1.0 O1A B:AGS1003 4.2 36.7 1.0 PG B:AGS1003 4.2 46.8 1.0 OD2 B:ASP534 4.2 40.2 1.0 O5' B:AGS1003 4.2 36.5 1.0 O3' B:AGS1003 4.3 38.8 1.0 C5' B:AGS1003 4.3 37.7 1.0 O1B B:AGS1003 4.4 39.8 1.0 S1G B:AGS1003 4.4 47.6 1.0 CB B:ASN520 4.7 39.0 1.0 O B:ASP519 4.7 39.9 1.0 CA B:GLY409 4.7 40.5 1.0 C3' B:AGS1003 4.7 37.9 1.0 C B:ASP519 4.9 41.0 1.0 OD2 B:ASP515 4.9 43.6 1.0 CA B:ASN520 5.0 39.7 1.0

J.Liu, A.Sudom, X.Min, Z.Cao, X.Gao, M.Ayres, F.Lee, P.Cao, S.Johnstone, O.Plotnikova, N.Walker, G.Chen, Z.Wang. Structure of Nuclear Factor Kappa B-Inducing Kinase Domain Reveals A Constitutively Active Conformation J.Biol.Chem. V. 287 27326 2012.
ISSN: ISSN 0021-9258
PubMed: 22718757
DOI: 10.1074/JBC.M112.366658