Magnesium in PDB 5d9h: Crystal Structure of Spak (STK39) Dimer in the Basal Activity State

All present enzymatic activity of Crystal Structure of Spak (STK39) Dimer in the Basal Activity State:
2.7.11.1;

The structure of Crystal Structure of Spak (STK39) Dimer in the Basal Activity State, PDB code: 5d9h was solved by C.A.Taylor, Y.C.Juang, E.J.Goldsmith, M.H.Cobb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.87 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.386, 56.105, 99.958, 90.00, 108.28, 90.00
R / Rfree (%)	23.6 / 26.9

The binding sites of Magnesium atom in the Crystal Structure of Spak (STK39) Dimer in the Basal Activity State (pdb code 5d9h). 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 Spak (STK39) Dimer in the Basal Activity State, PDB code: 5d9h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Spak (STK39) Dimer in the Basal Activity State


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 Spak (STK39) Dimer in the Basal Activity State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:41.0 occ:1.00 OD1 A:ASN209 1.9 68.5 1.0 O2B A:ATP501 1.9 60.2 1.0 O2A A:ATP501 2.0 75.8 1.0 O1G A:ATP501 2.0 0.5 1.0 OD1 A:ASP222 2.6 93.1 1.0 CG A:ASP222 2.7 69.0 1.0 CG A:ASN209 3.0 63.8 1.0 PB A:ATP501 3.0 47.5 1.0 PA A:ATP501 3.1 86.7 1.0 OD2 A:ASP222 3.2 63.0 1.0 O3A A:ATP501 3.2 47.2 1.0 NZ A:LYS104 3.2 66.4 1.0 PG A:ATP501 3.3 0.2 1.0 CB A:ASP222 3.4 66.0 1.0 O3B A:ATP501 3.5 55.0 1.0 ND2 A:ASN209 3.5 68.4 1.0 O5' A:ATP501 3.8 50.0 1.0 O3G A:ATP501 3.8 91.6 1.0 O A:GLY208 4.1 72.8 1.0 CB A:ASN209 4.2 69.0 1.0 H8 A:ATP501 4.3 87.6 1.0 O1B A:ATP501 4.3 50.9 1.0 O1A A:ATP501 4.4 78.2 1.0 CA A:ASN209 4.5 63.3 1.0 O2G A:ATP501 4.5 88.9 1.0 C A:GLY208 4.6 68.5 1.0 H2' A:ATP501 4.6 84.1 1.0 CE A:LYS104 4.7 54.0 1.0 OG A:SER226 4.7 61.8 1.0 N A:ASN209 4.8 69.7 1.0 CA A:ASP222 4.8 40.5 1.0 OD2 A:ASP204 4.8 91.0 1.0 H5'1 A:ATP501 4.8 66.0 1.0 C5' A:ATP501 5.0 55.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Spak (STK39) Dimer in the Basal Activity State


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 Spak (STK39) Dimer in the Basal Activity State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:19.0 occ:1.00 O1A B:ATP501 1.8 91.1 1.0 OD1 B:ASN209 1.9 56.6 1.0 O1B B:ATP501 2.3 60.7 1.0 O3G B:ATP501 2.4 58.8 1.0 OD1 B:ASP222 2.8 73.1 1.0 CG B:ASP222 2.9 65.6 1.0 PA B:ATP501 3.0 0.6 1.0 CG B:ASN209 3.0 49.6 1.0 OD2 B:ASP222 3.3 67.0 1.0 O5' B:ATP501 3.4 44.2 1.0 PB B:ATP501 3.4 55.3 1.0 CB B:ASP222 3.5 50.9 1.0 ND2 B:ASN209 3.6 50.9 1.0 PG B:ATP501 3.6 41.2 1.0 O3A B:ATP501 3.6 74.0 1.0 O3B B:ATP501 3.9 70.0 1.0 H8 B:ATP501 3.9 69.5 1.0 O B:GLY208 4.0 87.5 1.0 O2G B:ATP501 4.1 33.9 1.0 CB B:ASN209 4.2 37.6 1.0 O2A B:ATP501 4.3 71.1 1.0 CA B:ASN209 4.4 67.8 1.0 NZ B:LYS104 4.4 71.9 1.0 H2' B:ATP501 4.5 49.8 1.0 C B:GLY208 4.5 65.2 1.0 C5' B:ATP501 4.6 45.9 1.0 H5'1 B:ATP501 4.6 55.0 1.0 H3' B:ATP501 4.7 49.2 1.0 N B:ASN209 4.7 40.0 1.0 O2B B:ATP501 4.8 49.9 1.0 O1G B:ATP501 4.9 56.4 1.0 C8 B:ATP501 4.9 57.9 1.0 CA B:ASP222 4.9 34.3 1.0

C.A.Taylor, Y.C.Juang, S.Earnest, S.Sengupta, E.J.Goldsmith, M.H.Cobb. Domain-Swapping Switch Point in STE20 Protein Kinase Spak. Biochemistry V. 54 5063 2015.
ISSN: ISSN 0006-2960
PubMed: 26208601
DOI: 10.1021/ACS.BIOCHEM.5B00593