Magnesium in PDB 6no7: Crystal Structure of the Full-Length Wild-Type Pka Ria Holoenzyme

All present enzymatic activity of Crystal Structure of the Full-Length Wild-Type Pka Ria Holoenzyme:
2.7.11.11;

The structure of Crystal Structure of the Full-Length Wild-Type Pka Ria Holoenzyme, PDB code: 6no7 was solved by T.Lu, J.Wu, S.S.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.63 / 3.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	139.778, 184.811, 183.406, 90.00, 90.00, 90.00
R / Rfree (%)	25.6 / 26.9

The binding sites of Magnesium atom in the Crystal Structure of the Full-Length Wild-Type Pka Ria Holoenzyme (pdb code 6no7). 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 the Full-Length Wild-Type Pka Ria Holoenzyme, PDB code: 6no7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Full-Length Wild-Type Pka Ria Holoenzyme


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 the Full-Length Wild-Type Pka Ria Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg401 b:0.1 occ:1.00 O3G E:ATP403 2.2 0.3 1.0 NZ E:LYS168 2.8 0.0 1.0 PG E:ATP403 2.8 0.2 1.0 CE E:LYS168 2.9 0.5 1.0 O2A E:ATP403 2.9 0.3 1.0 O2G E:ATP403 3.0 0.0 1.0 O3B E:ATP403 3.0 0.1 1.0 C5' E:ATP403 3.5 0.1 1.0 ND2 E:ASN171 3.8 0.1 1.0 OD2 E:ASP184 3.9 0.8 1.0 PA E:ATP403 4.1 0.8 1.0 CG E:ASN171 4.2 0.2 1.0 CD E:LYS168 4.3 0.2 1.0 CB E:GLU170 4.3 0.3 1.0 O5' E:ATP403 4.3 0.5 1.0 O1G E:ATP403 4.3 0.9 1.0 O E:GLU170 4.3 0.3 1.0 C3' E:ATP403 4.4 0.2 1.0 PB E:ATP403 4.4 0.1 1.0 C E:GLU170 4.5 0.1 1.0 MG E:MG402 4.5 0.2 1.0 OD2 E:ASP166 4.5 0.3 1.0 C4' E:ATP403 4.6 0.3 1.0 O2B E:ATP403 4.7 0.5 1.0 OD1 E:ASN171 4.7 0.4 1.0 N E:ASN171 4.7 0.5 1.0 CB E:ASN171 4.7 0.4 1.0 O3A E:ATP403 4.8 0.8 1.0 CA E:ASN171 4.9 0.1 1.0 CG E:ASP184 4.9 0.1 1.0 O3' E:ATP403 5.0 98.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Full-Length Wild-Type Pka Ria Holoenzyme


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 the Full-Length Wild-Type Pka Ria Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:0.2 occ:1.00 OD2 E:ASP184 1.9 0.8 1.0 O2B E:ATP403 2.0 0.5 1.0 O2G E:ATP403 2.0 0.0 1.0 CG E:ASP184 2.7 0.1 1.0 OD1 E:ASP184 2.9 0.3 1.0 OD2 E:ASP166 3.0 0.3 1.0 PB E:ATP403 3.2 0.1 1.0 PG E:ATP403 3.2 0.2 1.0 O3B E:ATP403 3.4 0.1 1.0 O1G E:ATP403 3.7 0.9 1.0 O2A E:ATP403 3.9 0.3 1.0 CB F:ALA97 4.1 0.8 1.0 CG E:ASP166 4.1 0.0 1.0 CB E:ASP184 4.1 0.9 1.0 O1B E:ATP403 4.1 0.6 1.0 NZ E:LYS168 4.2 0.0 1.0 O3A E:ATP403 4.3 0.8 1.0 O3G E:ATP403 4.5 0.3 1.0 MG E:MG401 4.5 0.1 1.0 ND2 E:ASN171 4.5 0.1 1.0 CE2 E:PHE187 4.6 0.9 1.0 CZ E:PHE187 4.6 0.7 1.0 PA E:ATP403 4.8 0.8 1.0 CE1 E:PHE54 4.9 0.2 1.0 CB E:ASP166 4.9 0.5 1.0 OD1 E:ASP166 4.9 0.1 1.0 CD1 E:PHE54 5.0 0.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Full-Length Wild-Type Pka Ria Holoenzyme


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 the Full-Length Wild-Type Pka Ria Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg401 b:0.9 occ:1.00 O3G G:ATP403 2.1 0.2 1.0 PG G:ATP403 2.6 0.9 1.0 O2G G:ATP403 2.6 0.2 1.0 O G:GLU170 2.7 0.4 1.0 C5' G:ATP403 2.7 0.0 1.0 O3B G:ATP403 2.8 0.3 1.0 O2A G:ATP403 2.9 0.2 1.0 C G:GLU170 3.4 0.1 1.0 CA G:ASN171 3.5 0.6 1.0 CG G:ASN171 3.6 0.1 1.0 O5' G:ATP403 3.7 1.0 1.0 N G:ASN171 3.7 0.0 1.0 OD1 G:ASN171 3.8 0.4 1.0 ND2 G:ASN171 3.8 0.5 1.0 PA G:ATP403 3.9 0.6 1.0 C4' G:ATP403 3.9 0.6 1.0 CB G:ASN171 4.0 0.3 1.0 O1G G:ATP403 4.1 0.0 1.0 C3' G:ATP403 4.1 0.8 1.0 PB G:ATP403 4.2 0.4 1.0 CE G:LYS168 4.3 0.0 1.0 O3A G:ATP403 4.4 0.8 1.0 CB G:GLU170 4.4 1.0 1.0 CA G:GLU170 4.5 0.4 1.0 MG G:MG402 4.5 0.9 1.0 CG2 G:THR183 4.5 0.2 1.0 O2B G:ATP403 4.6 1.0 1.0 O3' G:ATP403 4.6 0.1 1.0 NZ G:LYS168 4.7 0.7 1.0 C G:ASN171 4.8 0.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Full-Length Wild-Type Pka Ria Holoenzyme


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 the Full-Length Wild-Type Pka Ria Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:0.9 occ:1.00 OD2 G:ASP184 2.0 0.0 1.0 O2G G:ATP403 2.0 0.2 1.0 O2B G:ATP403 2.0 1.0 1.0 OD2 G:ASP166 2.8 0.5 1.0 PG G:ATP403 3.0 0.9 1.0 CG G:ASP184 3.1 0.8 1.0 O1G G:ATP403 3.1 0.0 1.0 PB G:ATP403 3.2 0.4 1.0 ND2 G:ASN171 3.3 0.5 1.0 O2A G:ATP403 3.4 0.2 1.0 NZ G:LYS168 3.4 0.7 1.0 O3B G:ATP403 3.5 0.3 1.0 CB G:ASP184 3.9 0.3 1.0 OD1 G:ASP184 4.0 0.3 1.0 CG G:ASP166 4.0 0.2 1.0 CE G:LYS168 4.1 0.0 1.0 CB H:ALA97 4.2 0.8 1.0 O3A G:ATP403 4.3 0.8 1.0 O3G G:ATP403 4.3 0.2 1.0 O1B G:ATP403 4.3 0.7 1.0 PA G:ATP403 4.4 0.6 1.0 CG G:ASN171 4.4 0.1 1.0 MG G:MG401 4.5 0.9 1.0 OD1 G:ASP166 4.7 0.4 1.0 OD1 G:ASN171 4.9 0.4 1.0

T.W.Lu, J.Wu, P.C.Aoto, J.H.Weng, L.G.Ahuja, N.Sun, C.Y.Cheng, P.Zhang, S.S.Taylor. Two Pka Ri Alpha Holoenzyme States Define Atp As An Isoform-Specific Orthosteric Inhibitor That Competes with the Allosteric Activator, Camp. Proc.Natl.Acad.Sci.Usa V. 116 16347 2019.
ISSN: ESSN 1091-6490
PubMed: 31363049
DOI: 10.1073/PNAS.1906036116