Magnesium in PDB 8yhw: The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus

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

The structure of The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus, PDB code: 8yhw was solved by F.Wang, W.Cheng, Z.Lv, Q.Meng, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.56 / 2.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	119.652, 119.652, 115.586, 90, 90, 90
R / Rfree (%)	19.4 / 24.1

The binding sites of Magnesium atom in the The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus (pdb code 8yhw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus, PDB code: 8yhw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:41.6 occ:1.00 OD2 A:ASP534 2.0 45.2 1.0 O A:HOH803 2.0 40.8 1.0 O A:HOH801 2.0 37.6 1.0 OD1 A:ASN520 2.0 39.9 1.0 O2A A:AGS701 2.0 36.8 1.0 O2B A:AGS701 2.0 40.2 1.0 CG A:ASP534 3.0 48.0 1.0 CG A:ASN520 3.0 38.9 1.0 PB A:AGS701 3.2 35.1 1.0 PA A:AGS701 3.3 36.6 1.0 ND2 A:ASN520 3.5 39.9 1.0 O3A A:AGS701 3.5 36.7 1.0 O3B A:AGS701 3.6 45.2 1.0 CB A:ASP534 3.7 48.3 1.0 OD1 A:ASP534 4.0 50.6 1.0 O2G A:AGS701 4.0 55.8 1.0 C5' A:AGS701 4.2 34.6 1.0 PG A:AGS701 4.2 62.1 1.0 O5' A:AGS701 4.2 32.8 1.0 O3' A:AGS701 4.3 32.3 1.0 CB A:ASN520 4.4 36.6 1.0 O1A A:AGS701 4.4 36.6 1.0 S1G A:AGS701 4.4 64.9 1.0 O A:ASP519 4.5 39.3 1.0 O1B A:AGS701 4.5 32.0 1.0 C3' A:AGS701 4.7 34.2 1.0 CA A:GLY409 4.7 38.7 1.0 CA A:ASN520 4.7 36.4 1.0 C A:ASP519 4.8 37.5 1.0 OD2 A:ASP515 4.8 31.5 1.0 CB A:ASP519 4.9 42.0 1.0 N A:ASN520 4.9 35.5 1.0 C4' A:AGS701 4.9 35.5 1.0

Magnesium binding site 2 out of 4 in the The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:34.5 occ:1.00 OD2 B:ASP534 2.0 39.2 1.0 O B:HOH804 2.0 32.4 1.0 O B:HOH807 2.0 28.3 1.0 O2B B:AGS701 2.0 36.9 1.0 O2A B:AGS701 2.0 32.1 1.0 OD1 B:ASN520 2.0 42.1 1.0 CG B:ASN520 3.0 42.7 1.0 CG B:ASP534 3.1 41.8 1.0 PB B:AGS701 3.2 36.6 1.0 PA B:AGS701 3.3 30.4 1.0 ND2 B:ASN520 3.4 43.6 1.0 O3A B:AGS701 3.5 34.3 1.0 O3B B:AGS701 3.6 48.4 1.0 O B:HOH814 3.7 27.8 1.0 CB B:ASP534 3.8 41.9 1.0 O2G B:AGS701 4.0 64.6 1.0 OD1 B:ASP534 4.0 42.6 1.0 PG B:AGS701 4.2 68.2 1.0 O3' B:AGS701 4.2 29.2 1.0 O5' B:AGS701 4.3 28.9 1.0 O1A B:AGS701 4.3 33.3 1.0 C5' B:AGS701 4.4 28.6 1.0 CB B:ASN520 4.4 38.6 1.0 S1G B:AGS701 4.4 67.5 1.0 O B:ASP519 4.5 32.7 1.0 O1B B:AGS701 4.5 33.0 1.0 C3' B:AGS701 4.6 29.1 1.0 OD2 B:ASP515 4.7 28.8 1.0 CA B:GLY409 4.7 42.0 1.0 CA B:ASN520 4.8 36.1 1.0 C B:ASP519 4.8 34.1 1.0 CB B:ASP519 4.9 32.3 1.0 N B:ASN520 4.9 34.4 1.0

Magnesium binding site 3 out of 4 in the The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:35.0 occ:1.00 OD2 C:ASP534 2.0 36.1 1.0 O C:HOH807 2.0 32.8 1.0 O C:HOH804 2.0 34.7 1.0 O2B C:AGS701 2.0 35.3 1.0 O2A C:AGS701 2.0 35.9 1.0 OD1 C:ASN520 2.0 33.2 1.0 CG C:ASN520 3.0 33.5 1.0 CG C:ASP534 3.0 38.0 1.0 PB C:AGS701 3.2 35.7 1.0 PA C:AGS701 3.3 33.6 1.0 ND2 C:ASN520 3.4 35.1 1.0 O3A C:AGS701 3.6 35.1 1.0 O3B C:AGS701 3.7 48.1 1.0 CB C:ASP534 3.7 39.4 1.0 OD1 C:ASP534 4.0 39.4 1.0 C5' C:AGS701 4.2 32.2 1.0 PG C:AGS701 4.3 66.7 1.0 S1G C:AGS701 4.3 68.0 1.0 O2G C:AGS701 4.3 73.3 1.0 O5' C:AGS701 4.3 32.4 1.0 O3' C:AGS701 4.3 26.7 1.0 CB C:ASN520 4.4 31.7 1.0 O1A C:AGS701 4.4 33.0 1.0 O C:ASP519 4.5 36.5 1.0 O1B C:AGS701 4.5 31.1 1.0 C3' C:AGS701 4.7 29.2 1.0 CA C:GLY409 4.8 37.8 1.0 CA C:ASN520 4.8 32.0 1.0 OD2 C:ASP515 4.8 32.7 1.0 C C:ASP519 4.8 32.9 1.0 N C:ASN520 4.9 32.9 1.0

Magnesium binding site 4 out of 4 in the The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:35.8 occ:1.00 OD2 D:ASP534 2.0 35.7 1.0 O D:HOH804 2.0 37.7 1.0 O D:HOH812 2.0 30.5 1.0 O2A D:AGS701 2.0 32.6 1.0 O2B D:AGS701 2.0 36.4 1.0 OD1 D:ASN520 2.0 40.6 1.0 CG D:ASN520 3.0 37.4 1.0 CG D:ASP534 3.1 36.0 1.0 PB D:AGS701 3.2 36.6 1.0 PA D:AGS701 3.3 31.4 1.0 ND2 D:ASN520 3.4 38.7 1.0 O3A D:AGS701 3.5 35.3 1.0 O3B D:AGS701 3.6 48.3 1.0 CB D:ASP534 3.8 37.3 1.0 OD1 D:ASP534 4.0 36.6 1.0 O2G D:AGS701 4.1 72.0 1.0 PG D:AGS701 4.2 70.8 1.0 O3' D:AGS701 4.3 31.9 1.0 O1A D:AGS701 4.3 32.5 1.0 O5' D:AGS701 4.4 30.9 1.0 CB D:ASN520 4.4 35.3 1.0 C5' D:AGS701 4.4 31.6 1.0 O2 D:EDO704 4.4 58.6 1.0 S1G D:AGS701 4.5 71.8 1.0 O1B D:AGS701 4.5 34.4 1.0 O D:ASP519 4.5 30.0 1.0 OD2 D:ASP515 4.7 29.9 1.0 CA D:GLY409 4.7 38.4 1.0 C3' D:AGS701 4.8 32.1 1.0 CA D:ASN520 4.8 34.3 1.0 C D:ASP519 4.8 34.1 1.0 CB D:ASP519 4.9 34.9 1.0 N D:ASN520 4.9 33.8 1.0

F.Wang, W.Cheng, Z.Lv, Q.Meng, Y.Xu. The Crystal Structure of Nf-Kb-Inducing Kinase (Nik) From Biortus To Be Published.