Magnesium in PDB 4dh8: Room Temperature X-Ray Structure of Camp Dependent Protein Kinase A Catalytic Subunit with High MG2+, Amp-Pnp and IP20

All present enzymatic activity of Room Temperature X-Ray Structure of Camp Dependent Protein Kinase A Catalytic Subunit with High MG2+, Amp-Pnp and IP20:
2.7.11.11;

The structure of Room Temperature X-Ray Structure of Camp Dependent Protein Kinase A Catalytic Subunit with High MG2+, Amp-Pnp and IP20, PDB code: 4dh8 was solved by A.Y.Kovalevsky, P.Langan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.211, 80.031, 99.202, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18.8

The binding sites of Magnesium atom in the Room Temperature X-Ray Structure of Camp Dependent Protein Kinase A Catalytic Subunit with High MG2+, Amp-Pnp and IP20 (pdb code 4dh8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Room Temperature X-Ray Structure of Camp Dependent Protein Kinase A Catalytic Subunit with High MG2+, Amp-Pnp and IP20, PDB code: 4dh8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Room Temperature X-Ray Structure of Camp Dependent Protein Kinase A Catalytic Subunit with High MG2+, Amp-Pnp and IP20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Room Temperature X-Ray Structure of Camp Dependent Protein Kinase A Catalytic Subunit with High MG2+, Amp-Pnp and IP20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:22.8 occ:1.00 O A:HOH1003 2.1 20.5 1.0 O A:HOH1001 2.1 21.9 1.0 O1B A:ANP403 2.1 20.8 1.0 O3G A:ANP403 2.2 21.0 1.0 OD2 A:ASP184 2.3 17.3 1.0 OD1 A:ASP184 2.4 19.3 1.0 CG A:ASP184 2.7 19.1 1.0 PG A:ANP403 3.2 21.5 1.0 PB A:ANP403 3.3 18.9 1.0 N3B A:ANP403 3.6 21.2 1.0 CD2 A:PHE54 3.7 32.7 1.0 O2G A:ANP403 3.7 20.1 1.0 CE2 A:PHE54 3.9 32.5 1.0 MG A:MG402 4.0 18.8 1.0 O A:HOH1020 4.0 21.6 1.0 O2B A:ANP403 4.0 23.3 1.0 OD2 A:ASP166 4.1 20.9 1.0 CB A:ASP184 4.2 15.9 1.0 CA A:GLY186 4.2 17.4 1.0 NZ A:LYS72 4.3 17.1 1.0 O2A A:ANP403 4.4 15.5 1.0 N A:GLY186 4.5 19.4 1.0 O1G A:ANP403 4.5 26.4 1.0 O3A A:ANP403 4.6 22.6 1.0 O1A A:ANP403 4.8 18.3 1.0 PA A:ANP403 4.8 18.9 1.0 CB I:ALA21 4.9 31.8 1.0 O A:HOH1038 4.9 29.4 1.0 CG A:PHE54 5.0 34.5 1.0

Magnesium binding site 2 out of 2 in the Room Temperature X-Ray Structure of Camp Dependent Protein Kinase A Catalytic Subunit with High MG2+, Amp-Pnp and IP20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Room Temperature X-Ray Structure of Camp Dependent Protein Kinase A Catalytic Subunit with High MG2+, Amp-Pnp and IP20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:18.8 occ:1.00 O A:HOH1002 2.0 17.2 1.0 O2A A:ANP403 2.1 15.5 1.0 OD1 A:ASN171 2.2 15.4 1.0 OD2 A:ASP184 2.3 17.3 1.0 O2G A:ANP403 2.4 20.1 1.0 N3B A:ANP403 2.5 21.2 1.0 PG A:ANP403 3.0 21.5 1.0 CG A:ASP184 3.2 19.1 1.0 CG A:ASN171 3.2 17.8 1.0 PA A:ANP403 3.5 18.9 1.0 CB A:ASP184 3.6 15.9 1.0 PB A:ANP403 3.6 18.9 1.0 ND2 A:ASN171 3.6 14.0 1.0 O3G A:ANP403 3.8 21.0 1.0 O1B A:ANP403 3.8 20.8 1.0 MG A:MG401 4.0 22.8 1.0 O I:HOH103 4.0 29.7 1.0 O3A A:ANP403 4.0 22.6 1.0 CE A:LYS168 4.2 13.6 1.0 O1G A:ANP403 4.2 26.4 1.0 O1A A:ANP403 4.2 18.3 1.0 OD1 A:ASP184 4.3 19.3 1.0 O3' A:ANP403 4.3 19.9 1.0 O5' A:ANP403 4.4 21.4 1.0 OD2 A:ASP166 4.5 20.9 1.0 C5' A:ANP403 4.5 18.9 1.0 NZ A:LYS168 4.5 13.7 1.0 CB A:ASN171 4.5 15.1 1.0 O A:GLU170 4.8 16.2 1.0 O A:HOH1003 4.8 20.5 1.0 CA A:ASN171 4.8 15.9 1.0 C3' A:ANP403 4.8 19.0 1.0 O2B A:ANP403 4.9 23.3 1.0

A.Y.Kovalevsky, H.Johnson, B.L.Hanson, M.J.Waltman, S.Z.Fisher, S.Taylor, P.Langan. Low- and Room-Temperature X-Ray Structures of Protein Kinase A Ternary Complexes Shed New Light on Its Activity. Acta Crystallogr.,Sect.D V. 68 854 2012.
ISSN: ISSN 0907-4449
PubMed: 22751671
DOI: 10.1107/S0907444912014886