Magnesium in PDB 4g3d: Crystal Structure of Human Nf-Kappab Inducing Kinase (Nik)

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

The structure of Crystal Structure of Human Nf-Kappab Inducing Kinase (Nik), PDB code: 4g3d was solved by S.G.Hymowitz, G.De Leon-Boenig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.57 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.746, 145.851, 230.818, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 26.6

The binding sites of Magnesium atom in the Crystal Structure of Human Nf-Kappab Inducing Kinase (Nik) (pdb code 4g3d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Nf-Kappab Inducing Kinase (Nik), PDB code: 4g3d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Nf-Kappab 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 Human Nf-Kappab Inducing Kinase (Nik) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:76.5 occ:1.00 OD1 A:ASN520 2.5 48.5 1.0 OD2 A:ASP534 3.0 76.9 1.0 O A:HOH805 3.1 63.2 1.0 O A:HOH804 3.4 62.2 1.0 CG A:ASN520 3.7 46.4 1.0 CB A:ASP534 3.7 52.4 1.0 CG A:ASP534 3.8 57.6 1.0 OE2 A:GLU413 4.1 80.0 1.0 ND2 A:ASN520 4.3 49.7 1.0 N A:SER410 4.4 61.3 1.0 O A:ASP519 4.4 47.8 1.0 CB A:SER410 4.7 78.5 1.0 C A:ASP519 4.8 46.3 1.0 CA A:GLY409 4.9 58.7 1.0 CB A:ASN520 4.9 38.1 1.0 CA A:ASN520 4.9 40.4 1.0 OD1 A:ASP534 4.9 48.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Nf-Kappab 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 Human Nf-Kappab Inducing Kinase (Nik) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:90.3 occ:1.00 OD2 D:ASP534 2.5 96.1 1.0 OD1 D:ASN520 2.7 67.4 1.0 CB D:SER410 3.4 72.0 1.0 CG D:ASN520 3.7 66.3 1.0 CG D:ASP534 3.7 91.1 1.0 ND2 D:ASN520 3.9 67.4 1.0 CE D:LYS517 4.1 58.4 1.0 OG D:SER410 4.1 75.8 1.0 OE2 D:GLU413 4.2 87.9 1.0 N D:SER410 4.2 66.4 1.0 NZ D:LYS517 4.3 61.1 1.0 CB D:ASP534 4.4 83.0 1.0 CA D:SER410 4.5 65.9 1.0 OD1 D:ASP534 4.7 76.0 1.0 OD1 D:ASP515 4.8 71.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Nf-Kappab Inducing Kinase (Nik)


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 Human Nf-Kappab Inducing Kinase (Nik) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg701 b:82.0 occ:1.00 OD2 E:ASP534 3.0 0.7 1.0 OD1 E:ASN520 3.5 87.5 1.0 NZ E:LYS517 3.7 0.4 1.0 CB E:SER410 3.8 0.6 1.0 CE E:LYS517 4.0 0.1 1.0 CG E:ASP534 4.2 0.8 1.0 N E:SER410 4.2 0.3 1.0 OG E:SER410 4.4 0.1 1.0 CA E:SER410 4.5 0.9 1.0 CG E:ASN520 4.5 88.9 1.0 ND2 E:ASN520 4.8 88.4 1.0 CB E:ASP534 4.9 92.2 1.0 CB E:ASP519 5.0 0.7 1.0 C E:GLY409 5.0 0.7 1.0

G.De Leon-Boenig, K.K.Bowman, J.A.Feng, T.Crawford, C.Everett, Y.Franke, A.Oh, M.Stanley, S.T.Staben, M.A.Starovasnik, H.J.Wallweber, J.Wu, L.C.Wu, A.R.Johnson, S.G.Hymowitz. The Crystal Structure of the Catalytic Domain of the Nf-Kappab Inducing Kinase Reveals A Narrow But Flexible Active Site. Structure V. 20 1704 2012.
ISSN: ISSN 0969-2126
PubMed: 22921830
DOI: 10.1016/J.STR.2012.07.013