Magnesium in PDB 6aqe: Crystal Structure of PPK2 in Complex with Mg Atp

The structure of Crystal Structure of PPK2 in Complex with Mg Atp, PDB code: 6aqe was solved by B.Nocek, A.Joachimiak, A.Yakunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.52 / 1.81
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	88.376, 88.376, 190.016, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.6

The structure of Crystal Structure of PPK2 in Complex with Mg Atp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of PPK2 in Complex with Mg Atp (pdb code 6aqe). 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 PPK2 in Complex with Mg Atp, PDB code: 6aqe:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of PPK2 in Complex with Mg Atp


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 PPK2 in Complex with Mg Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:31.0 occ:0.93 O1B A:ATP501 2.0 24.6 1.0 OD2 A:ASP196 2.0 49.1 1.0 O A:HOH656 2.1 31.0 1.0 O A:HOH655 2.1 29.0 1.0 O A:HOH615 2.1 32.8 1.0 O A:HOH695 2.2 30.4 1.0 CG A:ASP196 3.0 53.4 1.0 PB A:ATP501 3.3 26.7 1.0 OD1 A:ASP196 3.5 57.2 1.0 O2B A:ATP501 3.9 25.5 1.0 OD2 A:ASP66 4.1 27.0 1.0 O2A A:ATP501 4.1 34.0 1.0 CB A:ASP196 4.2 44.6 1.0 O2G A:ATP501 4.2 23.6 1.0 O3B A:ATP501 4.2 24.7 1.0 O A:HOH708 4.3 28.3 1.0 O3' A:ATP501 4.3 27.9 1.0 O3A A:ATP501 4.4 26.9 1.0 O A:HOH776 4.4 40.7 1.0 O5' A:ATP501 4.4 27.3 1.0 O A:HOH644 4.5 31.1 1.0 CG A:ASP66 4.5 25.1 1.0 O A:HOH621 4.6 52.8 1.0 PA A:ATP501 4.7 28.7 1.0 O A:HOH646 4.8 31.9 1.0 O A:HOH613 4.9 41.9 1.0 PG A:ATP501 4.9 25.1 1.0 OD1 A:ASP66 4.9 25.0 1.0 CB A:ASN193 5.0 47.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of PPK2 in Complex with Mg Atp


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 PPK2 in Complex with Mg Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:21.9 occ:1.00 O3G A:ATP503 2.0 18.0 1.0 O1B A:ATP503 2.0 22.0 1.0 O3G A:ATP501 2.0 23.7 1.0 O2B A:ATP501 2.1 25.5 1.0 O1A A:ATP503 2.1 21.2 1.0 OD1 A:ASP66 2.1 25.0 1.0 PB A:ATP503 3.1 23.6 1.0 CG A:ASP66 3.2 25.1 1.0 PB A:ATP501 3.3 26.7 1.0 PA A:ATP503 3.3 22.9 1.0 PG A:ATP503 3.3 25.8 1.0 PG A:ATP501 3.3 25.1 1.0 O3B A:ATP501 3.4 24.7 1.0 O3A A:ATP503 3.5 24.5 1.0 O3B A:ATP503 3.6 20.2 1.0 CA A:ASP66 3.8 23.7 1.0 CB A:ASP66 4.0 25.8 1.0 N A:ALA67 4.0 20.2 1.0 NH2 A:ARG182 4.0 29.2 1.0 NZ A:LYS70 4.0 23.6 1.0 O A:HOH708 4.1 28.3 1.0 OD2 A:ASP66 4.1 27.0 1.0 O3A A:ATP501 4.2 26.9 1.0 O2G A:ATP501 4.2 23.6 1.0 C5' A:ATP503 4.2 27.4 1.0 O1G A:ATP503 4.2 38.8 1.0 O5' A:ATP503 4.3 25.9 1.0 O2G A:ATP503 4.4 41.5 1.0 O1B A:ATP501 4.4 24.6 1.0 O1G A:ATP501 4.5 23.5 1.0 C A:ASP66 4.5 28.1 1.0 O2B A:ATP503 4.5 20.5 1.0 O2A A:ATP503 4.5 24.7 1.0 NH2 A:ARG122 4.5 28.9 1.0 CE A:LYS70 4.7 20.0 1.0 O A:HOH615 4.7 32.8 1.0 CZ A:ARG182 4.9 29.9 1.0 N A:ASP66 4.9 25.1 1.0 NH1 A:ARG182 4.9 27.5 1.0 O A:HOH673 5.0 37.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of PPK2 in Complex with Mg Atp


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 PPK2 in Complex with Mg Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:33.9 occ:1.00 OD2 B:ASP196 1.9 49.5 1.0 O1B B:ATP501 1.9 25.3 1.0 O B:HOH665 2.1 30.3 1.0 O B:HOH628 2.1 36.8 1.0 O B:HOH650 2.1 31.2 1.0 O B:HOH721 2.2 31.6 1.0 CG B:ASP196 3.0 52.8 1.0 PB B:ATP501 3.3 22.7 1.0 OD1 B:ASP196 3.7 57.2 1.0 O2B B:ATP501 3.9 23.5 1.0 OD1 B:ASN193 3.9 37.2 0.4 O2A B:ATP501 4.1 32.8 1.0 CB B:ASP196 4.1 41.5 1.0 ND2 B:ASN193 4.2 41.7 0.4 O3G B:ATP501 4.2 25.7 1.0 O B:HOH715 4.2 33.0 1.0 O3B B:ATP501 4.2 25.1 1.0 OD2 B:ASP66 4.3 27.2 1.0 O3' B:ATP501 4.3 33.0 1.0 O B:HOH777 4.4 47.7 1.0 O3A B:ATP501 4.4 26.6 1.0 O B:HOH695 4.5 25.4 1.0 CG B:ASN193 4.5 36.2 0.4 O5' B:ATP501 4.5 29.6 1.0 CG B:ASP66 4.6 27.9 1.0 PA B:ATP501 4.7 29.2 1.0 O B:HOH691 4.8 44.8 1.0 PG B:ATP501 4.9 24.6 1.0 O B:HOH677 5.0 33.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of PPK2 in Complex with Mg Atp


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 PPK2 in Complex with Mg Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:23.6 occ:1.00 O1G B:ATP503 2.0 23.9 1.0 O2B B:ATP501 2.0 23.5 1.0 O2B B:ATP503 2.1 23.9 1.0 O2G B:ATP501 2.1 21.9 1.0 OD1 B:ASP66 2.1 25.1 1.0 O1A B:ATP503 2.1 22.1 1.0 PB B:ATP503 3.2 25.2 1.0 CG B:ASP66 3.2 27.9 1.0 PB B:ATP501 3.3 22.7 1.0 PG B:ATP501 3.3 24.6 1.0 PA B:ATP503 3.3 24.1 1.0 PG B:ATP503 3.4 24.3 1.0 O3B B:ATP501 3.5 25.1 1.0 O3B B:ATP503 3.6 37.4 1.0 O3A B:ATP503 3.6 27.2 1.0 CA B:ASP66 3.9 24.9 1.0 CB B:ASP66 4.0 27.4 1.0 O B:HOH715 4.0 33.0 1.0 NH2 B:ARG182 4.0 27.8 1.0 NZ B:LYS70 4.1 20.7 1.0 N B:ALA67 4.1 24.1 1.0 OD2 B:ASP66 4.1 27.2 1.0 O3G B:ATP501 4.1 25.7 1.0 O3A B:ATP501 4.2 26.6 1.0 O3G B:ATP503 4.2 23.6 1.0 C5' B:ATP503 4.2 29.1 1.0 O5' B:ATP503 4.3 26.3 1.0 O1B B:ATP501 4.4 25.3 1.0 O1G B:ATP501 4.4 26.5 1.0 O2G B:ATP503 4.4 24.4 1.0 O2A B:ATP503 4.5 25.3 1.0 NH2 B:ARG122 4.5 28.9 1.0 C B:ASP66 4.6 27.5 1.0 O1B B:ATP503 4.6 22.0 1.0 O B:HOH665 4.7 30.3 1.0 CE B:LYS70 4.7 20.5 1.0 O B:HOH634 4.9 36.7 1.0 CZ B:ARG182 4.9 31.3 1.0 NH1 B:ARG182 4.9 34.0 1.0 N B:ASP66 4.9 25.3 1.0

B.Nocek, B.Nocek, A.Joachimiak, A.Yakunin. N/A N/A.