Magnesium in PDB 6bxi: X-Ray Crystal Structure of NDR1 Kinase Domain

All present enzymatic activity of X-Ray Crystal Structure of NDR1 Kinase Domain:
2.7.11.1;

The structure of X-Ray Crystal Structure of NDR1 Kinase Domain, PDB code: 6bxi was solved by S.Xiong, F.Sicheri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.07 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.191, 117.967, 95.044, 90.00, 124.88, 90.00
R / Rfree (%)	17.1 / 21.2

The binding sites of Magnesium atom in the X-Ray Crystal Structure of NDR1 Kinase Domain (pdb code 6bxi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Crystal Structure of NDR1 Kinase Domain, PDB code: 6bxi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Crystal Structure of NDR1 Kinase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of NDR1 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:30.6 occ:1.00 O1A A:ANP501 1.9 19.3 1.0 O1B A:ANP501 2.1 22.7 1.0 O1G A:ANP501 2.2 21.3 1.0 OD1 A:ASN217 2.3 18.4 1.0 O A:HOH700 2.4 21.9 1.0 PB A:ANP501 3.1 24.5 1.0 PA A:ANP501 3.2 24.3 1.0 PG A:ANP501 3.2 23.5 1.0 CG A:ASN217 3.4 20.1 1.0 O3A A:ANP501 3.5 28.4 1.0 O2G A:ANP501 3.7 23.9 1.0 N3B A:ANP501 3.7 26.5 1.0 ND2 A:ASN217 3.9 20.3 1.0 O A:HOH608 3.9 27.4 1.0 O A:HOH739 4.1 28.6 1.0 O A:HOH742 4.1 23.6 1.0 O A:HOH683 4.1 40.4 1.0 O A:HOH651 4.1 43.8 1.0 O2A A:ANP501 4.2 22.7 1.0 C5' A:ANP501 4.3 24.3 1.0 O5' A:ANP501 4.3 28.4 1.0 O2B A:ANP501 4.5 28.8 1.0 O A:ASP216 4.5 18.0 1.0 OD2 A:ASP216 4.5 25.6 1.0 O3G A:ANP501 4.5 22.1 1.0 CG A:ASP216 4.5 23.7 1.0 OD1 A:ASP216 4.6 24.2 1.0 CB A:ASN217 4.7 14.3 1.0 CA A:ASN217 4.9 28.0 1.0 C A:ASP216 4.9 21.2 1.0 O A:HOH705 4.9 25.8 1.0 O A:HOH776 4.9 24.6 1.0

Magnesium binding site 2 out of 2 in the X-Ray Crystal Structure of NDR1 Kinase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of NDR1 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:31.6 occ:1.00 O2A B:ANP501 1.8 26.2 1.0 O2B B:ANP501 2.1 20.0 1.0 O3G B:ANP501 2.1 21.3 1.0 OD1 B:ASN217 2.2 18.1 1.0 O B:HOH620 2.2 20.5 1.0 O B:HOH659 2.3 17.2 1.0 PB B:ANP501 3.1 22.2 1.0 PA B:ANP501 3.1 24.7 1.0 PG B:ANP501 3.2 23.9 1.0 CG B:ASN217 3.3 23.3 1.0 O3A B:ANP501 3.5 26.3 1.0 O2G B:ANP501 3.7 23.6 1.0 N3B B:ANP501 3.7 25.6 1.0 ND2 B:ASN217 3.8 19.3 1.0 O B:HOH619 3.9 26.6 1.0 O B:HOH628 4.0 44.6 1.0 O1A B:ANP501 4.0 21.9 1.0 O B:HOH708 4.2 26.3 1.0 OD2 B:ASP216 4.2 24.5 1.0 O B:HOH733 4.2 27.1 1.0 C5' B:ANP501 4.2 24.9 1.0 O5' B:ANP501 4.2 25.2 1.0 O1B B:ANP501 4.5 27.2 1.0 O1G B:ANP501 4.5 24.3 1.0 CB B:ASN217 4.6 20.2 1.0 O B:ASP216 4.6 18.7 1.0 CA B:ASN217 4.7 21.7 1.0 C B:ASP216 4.9 22.2 1.0 OG B:SER229 4.9 26.6 1.0 N B:ASN217 5.0 15.8 1.0

S.Xiong, K.Lorenzen, A.L.Couzens, C.M.Templeton, D.Rajendran, D.Y.L.Mao, Y.C.Juang, D.Chiovitti, I.Kurinov, S.Guettler, A.C.Gingras, F.Sicheri. Structural Basis For Auto-Inhibition of the NDR1 Kinase Domain By An Atypically Long Activation Segment. Structure V. 26 1101 2018.
ISSN: ISSN 1878-4186
PubMed: 29983373
DOI: 10.1016/J.STR.2018.05.014