Magnesium in PDB 6cqd: Crystal Structure of HPK1 in Complex with Atp Analogue (Amppnp)

All present enzymatic activity of Crystal Structure of HPK1 in Complex with Atp Analogue (Amppnp):
2.7.11.1;

The structure of Crystal Structure of HPK1 in Complex with Atp Analogue (Amppnp), PDB code: 6cqd was solved by P.Wu, I.Lehoux, Y.Franke, K.Mortara, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.99 / 2.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	146.886, 51.882, 107.500, 90.00, 131.03, 90.00
R / Rfree (%)	20.3 / 25

The binding sites of Magnesium atom in the Crystal Structure of HPK1 in Complex with Atp Analogue (Amppnp) (pdb code 6cqd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of HPK1 in Complex with Atp Analogue (Amppnp), PDB code: 6cqd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of HPK1 in Complex with Atp Analogue (Amppnp)


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 HPK1 in Complex with Atp Analogue (Amppnp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:39.6 occ:1.00 OD2 A:ASP155 2.1 27.2 1.0 O2A A:ANP301 2.1 46.9 1.0 O A:HOH402 2.2 38.8 1.0 O1G A:ANP301 2.2 0.2 1.0 O A:HOH445 2.2 33.7 1.0 OD1 A:ASN142 2.2 22.4 1.0 PG A:ANP301 3.1 87.0 1.0 O3G A:ANP301 3.1 0.1 1.0 CG A:ASN142 3.2 27.6 1.0 CG A:ASP155 3.2 28.2 1.0 PA A:ANP301 3.5 37.4 1.0 ND2 A:ASN142 3.6 29.7 1.0 O5' A:ANP301 3.6 41.9 1.0 O A:HOH498 3.7 38.1 1.0 MG A:MG303 3.7 49.9 1.0 CB A:ASP155 3.8 24.3 1.0 N3B A:ANP301 3.8 47.3 1.0 O2B A:ANP301 3.9 51.0 1.0 O A:HOH405 4.0 42.5 1.0 PB A:ANP301 4.2 48.5 1.0 OD1 A:ASP155 4.3 31.4 1.0 O3A A:ANP301 4.3 51.2 1.0 O2G A:ANP301 4.4 88.6 1.0 O A:ALA141 4.4 28.0 1.0 O3' A:ANP301 4.4 32.9 1.0 CB A:ASN142 4.5 24.5 1.0 O1A A:ANP301 4.6 39.9 1.0 C A:ALA141 4.7 23.3 1.0 CB A:ALA141 4.8 32.6 1.0 CA A:ASN142 4.8 22.4 1.0 OD2 A:ASP137 4.9 35.0 1.0 N A:ASN142 5.0 21.1 1.0 C5' A:ANP301 5.0 36.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of HPK1 in Complex with Atp Analogue (Amppnp)


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 HPK1 in Complex with Atp Analogue (Amppnp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:49.9 occ:1.00 OD2 A:ASP155 2.1 27.2 1.0 O A:HOH405 2.1 42.5 1.0 OD1 A:ASP155 2.2 31.4 1.0 O3G A:ANP301 2.2 0.1 1.0 O2B A:ANP301 2.3 51.0 1.0 CG A:ASP155 2.4 28.2 1.0 O A:HOH445 3.6 33.7 1.0 O2A A:ANP301 3.7 46.9 1.0 PG A:ANP301 3.7 87.0 1.0 PB A:ANP301 3.7 48.5 1.0 MG A:MG302 3.7 39.6 1.0 OD2 A:ASP137 3.8 35.0 1.0 CB A:ASP155 3.9 24.3 1.0 N3B A:ANP301 4.4 47.3 1.0 O1G A:ANP301 4.4 0.2 1.0 O A:HOH455 4.4 39.8 1.0 O3A A:ANP301 4.5 51.2 1.0 O1B A:ANP301 4.7 67.1 1.0 NZ A:LYS46 4.7 35.4 1.0 PA A:ANP301 4.7 37.4 1.0 O2G A:ANP301 4.7 88.6 1.0 CA A:ASP155 4.8 24.5 1.0 CD1 A:ILE158 4.8 42.7 1.0 N A:GLY157 4.9 26.4 1.0 O A:ASP155 4.9 29.0 1.0 C A:ASP155 5.0 26.9 1.0 CA A:GLY157 5.0 31.0 1.0 OD1 A:ASN142 5.0 22.4 1.0 ND2 A:ASN142 5.0 29.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of HPK1 in Complex with Atp Analogue (Amppnp)


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 HPK1 in Complex with Atp Analogue (Amppnp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:65.0 occ:1.00 OD2 B:ASP155 2.2 41.5 1.0 O2G B:ANP302 2.2 0.5 1.0 OD1 B:ASN142 2.2 29.1 1.0 O2A B:ANP302 2.2 84.0 1.0 O3A B:ANP302 2.7 0.7 1.0 PA B:ANP302 3.0 81.7 1.0 CG B:ASN142 3.2 30.6 1.0 CG B:ASP155 3.2 41.0 1.0 PG B:ANP302 3.5 0.9 1.0 ND2 B:ASN142 3.6 32.7 1.0 CB B:ASP155 3.7 36.0 1.0 O5' B:ANP302 3.8 57.2 1.0 O1G B:ANP302 3.9 0.1 1.0 PB B:ANP302 3.9 82.3 1.0 N3B B:ANP302 4.3 0.9 1.0 OD1 B:ASP155 4.3 40.8 1.0 O1A B:ANP302 4.3 79.2 1.0 O2B B:ANP302 4.3 83.0 1.0 O B:ALA141 4.4 27.8 1.0 CB B:ASN142 4.6 29.9 1.0 O3G B:ANP302 4.6 0.7 1.0 O3' B:ANP302 4.7 45.8 1.0 C B:ALA141 4.7 24.6 1.0 CA B:ASN142 4.8 25.7 1.0 CB B:ALA141 4.9 27.4 1.0 N B:ASN142 4.9 23.6 1.0 OD2 B:ASP137 5.0 32.1 1.0

P.Wu, C.J.Sneeringer, K.E.Pitts, E.S.Day, B.K.Chan, B.Wei, I.Lehoux, K.Mortara, H.Li, J.Wu, Y.Franke, J.G.Moffat, J.L.Grogan, T.P.Heffron, W.Wang. Hematopoietic Progenitor Kinase-1 Structure in A Domain-Swapped Dimer. Structure V. 27 125 2019.
ISSN: ISSN 1878-4186
PubMed: 30503777
DOI: 10.1016/J.STR.2018.10.025