Magnesium in PDB 6b4k: Crystal Structure of Human DDX19B(Amppnp)

All present enzymatic activity of Crystal Structure of Human DDX19B(Amppnp):
3.6.4.13;

The structure of Crystal Structure of Human DDX19B(Amppnp), PDB code: 6b4k was solved by D.H.Lin, A.R.Correia, S.W.Cai, F.M.Huber, C.A.Jette, A.Hoelz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.14 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.233, 45.364, 127.391, 90.00, 97.03, 90.00
R / Rfree (%)	20.7 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Human DDX19B(Amppnp) (pdb code 6b4k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human DDX19B(Amppnp), PDB code: 6b4k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human DDX19B(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 Human DDX19B(Amppnp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:54.9 occ:1.00 HOG2 A:ANP502 1.7 76.5 1.0 O2G A:ANP502 2.0 63.8 1.0 HOB2 A:ANP502 2.1 46.5 1.0 HG1 A:THR145 2.4 54.7 1.0 O2B A:ANP502 2.6 38.8 1.0 O A:HOH604 2.8 69.4 1.0 HE2 A:LYS144 2.9 40.0 1.0 OG1 A:THR145 3.0 45.6 1.0 PG A:ANP502 3.1 60.5 1.0 O A:HOH653 3.2 0.8 1.0 O1G A:ANP502 3.2 53.1 1.0 HB2 A:LYS144 3.2 39.8 1.0 OD1 A:ASP242 3.3 48.1 1.0 HG2 A:GLU243 3.4 80.2 1.0 PB A:ANP502 3.6 37.7 1.0 N3B A:ANP502 3.7 61.6 1.0 O A:HOH619 3.8 91.6 1.0 CE A:LYS144 3.8 33.3 1.0 HZ3 A:LYS144 3.8 46.9 1.0 H A:THR145 3.9 42.7 1.0 OD2 A:ASP242 3.9 72.1 1.0 HE3 A:LYS64 4.0 98.7 1.0 O1B A:ANP502 4.0 43.1 1.0 CG A:ASP242 4.0 54.2 1.0 HZ2 A:LYS144 4.1 46.9 1.0 NZ A:LYS144 4.1 39.1 1.0 CB A:LYS144 4.2 33.2 1.0 OE2 A:GLU243 4.2 88.8 1.0 HE3 A:LYS144 4.2 40.0 1.0 CG A:GLU243 4.2 66.8 1.0 N A:THR145 4.2 35.6 1.0 CB A:THR145 4.2 31.1 1.0 HZ1 A:LYS64 4.3 0.8 1.0 HG3 A:GLU243 4.3 80.2 1.0 HB3 A:LYS144 4.3 39.8 1.0 O3G A:ANP502 4.4 93.1 1.0 HE2 A:PHE148 4.5 30.1 1.0 HB A:THR145 4.5 37.4 1.0 H A:GLU243 4.6 43.0 1.0 HA A:THR145 4.6 39.2 1.0 HNB1 A:ANP502 4.7 73.9 1.0 CA A:THR145 4.7 32.7 1.0 CD A:GLU243 4.7 85.9 1.0 CE A:LYS64 4.8 82.2 1.0 HB3 A:PHE273 4.8 34.4 1.0 NZ A:LYS64 4.8 0.5 1.0 HZ2 A:LYS64 4.8 0.8 1.0 CD A:LYS144 4.9 35.3 1.0 C A:LYS144 4.9 32.8 1.0 HB2 A:PHE273 4.9 34.4 1.0 H A:LYS144 5.0 40.6 1.0 O3A A:ANP502 5.0 42.4 1.0 HOG3 A:ANP502 5.0 0.8 1.0 CG A:LYS144 5.0 39.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human DDX19B(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 Human DDX19B(Amppnp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:69.3 occ:1.00 HOG2 B:ANP502 1.8 0.1 1.0 O2G B:ANP502 2.0 83.4 1.0 HOB2 B:ANP502 2.0 48.7 1.0 O B:HOH601 2.6 70.6 1.0 HG1 B:THR145 2.9 44.4 1.0 HE2 B:LYS144 2.9 48.3 1.0 OG1 B:THR145 2.9 37.0 1.0 O2B B:ANP502 3.0 40.5 1.0 PG B:ANP502 3.1 79.0 1.0 OD1 B:ASP242 3.1 46.5 1.0 HG2 B:GLU243 3.1 72.0 1.0 O1G B:ANP502 3.2 71.6 1.0 HB2 B:LYS144 3.4 44.3 1.0 OD2 B:ASP242 3.7 62.6 1.0 O B:HOH617 3.7 44.7 1.0 CG B:ASP242 3.8 56.4 1.0 N3B B:ANP502 3.8 74.1 1.0 CE B:LYS144 3.8 40.3 1.0 PB B:ANP502 3.9 44.3 1.0 CG B:GLU243 3.9 60.0 1.0 OE2 B:GLU243 3.9 96.5 1.0 HZ1 B:LYS144 4.0 56.0 1.0 HG3 B:GLU243 4.0 72.0 1.0 H B:THR145 4.1 38.9 1.0 HE3 B:LYS144 4.1 48.3 1.0 HZ1 B:LYS64 4.2 0.2 1.0 O1B B:ANP502 4.2 45.7 1.0 HE2 B:LYS64 4.2 0.3 1.0 CB B:THR145 4.3 30.6 1.0 NZ B:LYS144 4.3 46.6 1.0 HE3 B:LYS64 4.3 0.3 1.0 CB B:LYS144 4.3 36.9 1.0 H B:GLU243 4.3 46.4 1.0 HZ3 B:LYS144 4.4 56.0 1.0 O3G B:ANP502 4.4 1.0 1.0 CD B:GLU243 4.4 84.6 1.0 N B:THR145 4.4 32.4 1.0 HB3 B:LYS144 4.4 44.3 1.0 HE2 B:PHE148 4.4 35.3 1.0 HB B:THR145 4.6 36.7 1.0 CE B:LYS64 4.7 94.4 1.0 HA B:THR145 4.7 38.9 1.0 HNB1 B:ANP502 4.7 88.9 1.0 CA B:THR145 4.8 32.4 1.0 HB3 B:PHE273 4.8 41.8 1.0 O B:HOH620 4.9 41.8 0.4 HB2 B:PHE273 4.9 41.8 1.0 HA B:GLU243 4.9 48.5 1.0 NZ B:LYS64 4.9 0.9 1.0 N B:GLU243 4.9 38.7 1.0 HOG3 B:ANP502 4.9 0.2 1.0 CD B:LYS144 4.9 40.3 1.0 HD2 B:LYS144 5.0 48.3 1.0

D.H.Lin, A.R.Correia, S.W.Cai, F.M.Huber, C.A.Jette, A.Hoelz. Structural and Functional Analysis of Mrna Export Regulation By the Nuclear Pore Complex. Nat Commun V. 9 2319 2018.
ISSN: ESSN 2041-1723
PubMed: 29899397
DOI: 10.1038/S41467-018-04459-3