Magnesium in PDB 3dak: Crystal Structure of Domain-Swapped OSR1 Kinase Domain

All present enzymatic activity of Crystal Structure of Domain-Swapped OSR1 Kinase Domain:
2.7.11.1;

The structure of Crystal Structure of Domain-Swapped OSR1 Kinase Domain, PDB code: 3dak was solved by S.Lee, M.H.Cobb, E.J.Goldsmith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.208, 104.484, 162.903, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 26.7

The binding sites of Magnesium atom in the Crystal Structure of Domain-Swapped OSR1 Kinase Domain (pdb code 3dak). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Domain-Swapped OSR1 Kinase Domain, PDB code: 3dak:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Domain-Swapped OSR1 Kinase Domain


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 Domain-Swapped OSR1 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg296 b:54.5 occ:1.00 O A:GLY150 3.1 17.9 1.0 O2B A:ANP1 3.2 82.1 1.0 OD1 A:ASN151 3.4 20.4 1.0 O2' A:ANP1 3.6 58.2 1.0 C2' A:ANP1 3.6 61.0 1.0 OD2 A:ASP164 3.9 26.9 1.0 CB A:ALA163 4.0 14.3 1.0 N3B A:ANP1 4.0 84.8 1.0 C8 A:ANP1 4.0 59.4 1.0 CD2 A:LEU153 4.0 23.8 1.0 C A:GLY150 4.2 17.5 1.0 PB A:ANP1 4.2 83.4 1.0 O1A A:ANP1 4.3 73.3 1.0 CA A:ASN151 4.3 17.5 1.0 CG A:ASP164 4.4 21.5 1.0 N9 A:ANP1 4.5 59.8 1.0 OD1 A:ASP164 4.5 24.2 1.0 CG A:ASN151 4.6 19.1 1.0 C3' A:ANP1 4.6 62.4 1.0 N A:ASN151 4.7 16.7 1.0 CG A:LEU153 4.7 23.2 1.0 C1' A:ANP1 4.7 59.9 1.0 N7 A:ANP1 4.7 58.9 1.0 CD1 A:LEU153 4.7 26.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Domain-Swapped OSR1 Kinase Domain


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 Domain-Swapped OSR1 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg296 b:52.1 occ:1.00 O B:GLY150 2.9 19.6 1.0 OD1 B:ASN151 3.2 19.8 1.0 O2B B:ANP1 3.5 88.9 1.0 O3G B:ANP1 3.5 94.9 1.0 C2' B:ANP1 3.6 60.7 1.0 O2' B:ANP1 3.9 59.7 1.0 CD2 B:LEU153 3.9 22.3 1.0 C8 B:ANP1 4.0 54.6 1.0 C B:GLY150 4.0 18.8 1.0 CB B:ALA163 4.1 16.9 1.0 CA B:ASN151 4.1 19.2 1.0 OD2 B:ASP164 4.3 26.6 1.0 CG B:ASN151 4.3 20.6 1.0 N9 B:ANP1 4.4 55.7 1.0 O1A B:ANP1 4.4 79.4 1.0 N B:ASN151 4.5 19.1 1.0 C1' B:ANP1 4.6 58.0 1.0 N7 B:ANP1 4.6 54.3 1.0 CG B:LEU153 4.6 23.1 1.0 CG B:ASP164 4.6 23.7 1.0 C3' B:ANP1 4.7 62.6 1.0 OD1 B:ASP164 4.7 26.1 1.0 CD1 B:LEU153 4.7 22.1 1.0 CB B:ASN151 4.8 19.4 1.0 C5' B:ANP1 4.9 68.6 1.0 PB B:ANP1 4.9 89.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Domain-Swapped OSR1 Kinase Domain


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 Domain-Swapped OSR1 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg296 b:52.2 occ:1.00 O C:GLY150 3.0 19.2 1.0 O1A C:ANP1 3.2 54.5 1.0 OD1 C:ASN151 3.4 18.7 1.0 C8 C:ANP1 3.4 31.0 1.0 CD2 C:LEU153 3.8 20.9 1.0 O2B C:ANP1 3.8 68.2 1.0 CB C:ALA163 3.8 18.7 1.0 C2' C:ANP1 3.8 34.9 1.0 N7 C:ANP1 4.0 32.4 1.0 C C:GLY150 4.1 19.5 1.0 CA C:ASN151 4.1 19.4 1.0 N9 C:ANP1 4.2 33.2 1.0 O5' C:ANP1 4.2 51.1 1.0 CG C:LEU153 4.2 22.1 1.0 O2' C:ANP1 4.3 33.4 1.0 O C:HOH348 4.3 44.8 1.0 OD2 C:ASP164 4.3 28.7 1.0 CD1 C:LEU153 4.3 19.3 1.0 PA C:ANP1 4.4 56.3 1.0 O C:HOH537 4.5 51.2 1.0 O2G C:ANP1 4.5 73.1 1.0 CG C:ASN151 4.5 19.5 1.0 N C:ASN151 4.5 19.7 1.0 C1' C:ANP1 4.6 32.1 1.0 CG C:ASP164 4.7 24.6 1.0 OD1 C:ASP164 4.7 23.2 1.0 C3' C:ANP1 4.8 34.7 1.0 CB C:ASN151 4.9 19.4 1.0 C C:ASN151 4.9 19.4 1.0 C5 C:ANP1 4.9 33.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Domain-Swapped OSR1 Kinase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Domain-Swapped OSR1 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg296 b:67.9 occ:1.00 O1A D:ANP1 2.9 50.5 1.0 OD1 D:ASN151 2.9 23.2 1.0 OD2 D:ASP164 3.0 28.0 1.0 O3A D:ANP1 3.1 58.7 1.0 CG D:ASP164 3.5 26.2 1.0 OD1 D:ASP164 3.6 23.0 1.0 PA D:ANP1 3.6 52.6 1.0 C8 D:ANP1 3.8 35.3 1.0 O D:GLY150 3.9 24.8 1.0 O5' D:ANP1 4.0 47.0 1.0 CG D:ASN151 4.1 24.3 1.0 CB D:ALA163 4.2 23.1 1.0 O2B D:ANP1 4.2 66.6 1.0 C2' D:ANP1 4.3 34.4 1.0 NZ D:LYS46 4.4 36.1 1.0 N7 D:ANP1 4.4 36.6 1.0 PB D:ANP1 4.4 65.8 1.0 CA D:ASN151 4.6 25.1 1.0 CB D:ASP164 4.7 25.6 1.0 N9 D:ANP1 4.7 36.3 1.0 C D:GLY150 4.7 24.9 1.0 O3G D:ANP1 4.9 75.7 1.0 CB D:ASN151 4.9 25.2 1.0 O2' D:ANP1 4.9 32.6 1.0 C3' D:ANP1 5.0 35.1 1.0

S.J.Lee, M.H.Cobb, E.J.Goldsmith. Crystal Structure of Domain-Swapped STE20 OSR1 Kinase Domain. Protein Sci. V. 18 304 2008.
ISSN: ISSN 0961-8368
PubMed: 19177573
DOI: 10.1002/PRO.27