Magnesium in PDB 6yp4: Putative Adenylyl Cyclase HPAC1 From Hippeastrum Reveals A Dominant Triphophatase Activity

The structure of Putative Adenylyl Cyclase HPAC1 From Hippeastrum Reveals A Dominant Triphophatase Activity, PDB code: 6yp4 was solved by S.Kleinboelting, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.39 / 1.95
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.808, 59.808, 146.982, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 25.2

The structure of Putative Adenylyl Cyclase HPAC1 From Hippeastrum Reveals A Dominant Triphophatase Activity also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Putative Adenylyl Cyclase HPAC1 From Hippeastrum Reveals A Dominant Triphophatase Activity (pdb code 6yp4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Putative Adenylyl Cyclase HPAC1 From Hippeastrum Reveals A Dominant Triphophatase Activity, PDB code: 6yp4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Putative Adenylyl Cyclase HPAC1 From Hippeastrum Reveals A Dominant Triphophatase Activity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Putative Adenylyl Cyclase HPAC1 From Hippeastrum Reveals A Dominant Triphophatase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:84.3 occ:1.00 OE1 A:GLU81 2.2 56.0 0.5 O1A A:GCP301 2.7 95.5 1.0 OE2 A:GLU81 2.9 44.0 0.5 CD A:GLU81 2.9 49.5 0.5 OE2 A:GLU4 3.0 26.1 0.5 O3A A:GCP301 3.1 66.1 1.0 CG A:GLU2 3.2 26.6 0.5 OE2 A:GLU2 3.3 47.2 0.5 CD A:GLU2 3.5 39.5 0.5 PA A:GCP301 3.6 85.8 1.0 MG A:MG303 3.7 92.9 1.0 CD A:GLU4 3.9 38.2 0.5 NZ A:LYS67 3.9 54.2 1.0 CE A:LYS67 4.0 52.2 1.0 CB A:GLU2 4.1 35.7 0.5 CB A:GLU2 4.2 36.4 0.5 CG A:GLU81 4.3 46.4 0.5 PB A:GCP301 4.3 51.6 1.0 O1B A:GCP301 4.4 43.2 1.0 CG A:GLU81 4.4 45.0 0.5 OE1 A:GLU4 4.4 43.9 0.5 C4' A:GCP301 4.5 68.3 1.0 O4' A:GCP301 4.5 61.9 1.0 OE1 A:GLU4 4.5 42.5 0.5 O2A A:GCP301 4.6 94.5 1.0 CG1 A:VAL79 4.6 39.1 1.0 CG A:GLU2 4.6 37.0 0.5 OE1 A:GLU2 4.6 32.7 0.5 O5' A:GCP301 4.8 69.1 1.0 C3B A:GCP301 4.8 51.6 1.0 O A:HOH438 4.8 46.9 1.0 CG A:GLU4 4.8 41.2 0.5 CB A:GLU81 4.9 42.2 0.5 CB A:GLU81 5.0 42.1 0.5

Magnesium binding site 2 out of 2 in the Putative Adenylyl Cyclase HPAC1 From Hippeastrum Reveals A Dominant Triphophatase Activity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Putative Adenylyl Cyclase HPAC1 From Hippeastrum Reveals A Dominant Triphophatase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:92.9 occ:1.00 OE1 A:GLU81 2.5 56.0 0.5 CD A:GLU81 2.6 49.5 0.5 O1A A:GCP301 2.7 95.5 1.0 OE2 A:GLU83 3.0 41.5 1.0 OE2 A:GLU81 3.1 44.0 0.5 CE A:LYS67 3.2 52.2 1.0 CG A:GLU81 3.2 45.0 0.5 CD A:GLU83 3.3 53.8 1.0 CB A:GLU81 3.6 42.1 0.5 CB A:GLU81 3.6 42.2 0.5 O2A A:GCP301 3.7 94.5 1.0 MG A:MG302 3.7 84.3 1.0 OE1 A:GLU81 3.7 46.9 0.5 PA A:GCP301 3.8 85.8 1.0 OE1 A:GLU83 3.9 53.6 1.0 CG A:GLU83 3.9 46.9 1.0 CG A:GLU81 3.9 46.4 0.5 CG A:LYS67 4.0 41.4 1.0 CD A:LYS67 4.1 45.6 1.0 NH2 A:ARG52 4.2 31.3 1.0 CB A:SER65 4.2 31.0 1.0 CB A:GLU83 4.2 31.6 1.0 CD A:GLU81 4.3 48.9 0.5 NZ A:LYS67 4.4 54.2 1.0 O3A A:GCP301 4.5 66.1 1.0 OG A:SER65 4.7 39.2 1.0 O1B A:GCP301 4.8 43.2 1.0 CA A:GLU81 5.0 40.9 0.5 CA A:GLU81 5.0 40.8 0.5

S.Kleinboelting, J.Miehling, C.Steegborn. Crystal Structure and Enzymatic Characterization of the Putative Adenylyl Cyclase HPAC1 From Hippeastrum Reveal Dominant Triphosphatase Activity. J.Struct.Biol. V. 212 07649 2020.
ISSN: ESSN 1095-8657
PubMed: 33075486
DOI: 10.1016/J.JSB.2020.107649