Magnesium in PDB 6wqx: Human Prpk-Tprkb Complex

All present enzymatic activity of Human Prpk-Tprkb Complex:
2.7.11.1;

The structure of Human Prpk-Tprkb Complex, PDB code: 6wqx was solved by J.Li, X.L.Ma, S.Banerjee, Z.G.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.36 / 2.53
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.856, 77.54, 100.413, 90, 106.81, 90
R / Rfree (%)	21.1 / 26.5

The binding sites of Magnesium atom in the Human Prpk-Tprkb Complex (pdb code 6wqx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Prpk-Tprkb Complex, PDB code: 6wqx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Prpk-Tprkb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Prpk-Tprkb Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:57.1 occ:1.00 O2B C:ANP301 2.2 63.5 1.0 O2A C:ANP301 2.3 60.6 1.0 OD2 C:ASP183 2.4 59.4 1.0 OD1 C:ASN167 2.4 47.8 1.0 O3G C:ANP301 2.4 77.6 1.0 HD21 C:ASN167 2.9 58.5 1.0 CG C:ASN167 3.3 44.5 1.0 HB2 C:ASP183 3.4 56.8 1.0 CG C:ASP183 3.4 51.4 1.0 ND2 C:ASN167 3.4 48.7 1.0 O C:HOH423 3.6 51.0 1.0 PB C:ANP301 3.6 60.5 1.0 PG C:ANP301 3.6 95.2 1.0 PA C:ANP301 3.7 56.2 1.0 CB C:ASP183 3.8 47.3 1.0 O1G C:ANP301 3.9 79.1 1.0 HB3 C:ASP183 3.9 56.8 1.0 O3A C:ANP301 4.1 58.4 1.0 O C:HOH404 4.2 69.7 1.0 N3B C:ANP301 4.2 71.5 1.0 HD22 C:ASN167 4.3 58.5 1.0 HB2 C:SER166 4.4 63.2 1.0 HNB1 C:ANP301 4.5 85.8 1.0 OD1 C:ASP183 4.5 53.5 1.0 O1A C:ANP301 4.6 49.9 1.0 O1B C:ANP301 4.7 63.7 1.0 HG1 C:THR164 4.7 52.4 1.0 CB C:ASN167 4.7 42.6 1.0 OD2 C:ASP162 4.7 59.0 1.0 O5' C:ANP301 4.7 57.4 1.0 H5'2 C:ANP301 4.7 69.7 1.0 HA C:ASN167 4.8 54.7 1.0 HD12 C:ILE182 4.9 62.0 1.0 MG C:MG303 4.9 67.6 1.0 HO3' C:ANP301 5.0 77.2 1.0 O2G C:ANP301 5.0 82.4 1.0

Magnesium binding site 2 out of 3 in the Human Prpk-Tprkb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Prpk-Tprkb Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:67.6 occ:1.00 O1B C:ANP301 2.2 63.7 1.0 OD1 C:ASP183 2.8 53.5 1.0 HH21 C:ARG62 3.1 57.7 1.0 O2B C:ANP301 3.1 63.5 1.0 PB C:ANP301 3.1 60.5 1.0 HZ1 C:LYS60 3.2 65.7 1.0 OD2 C:ASP183 3.3 59.4 1.0 CG C:ASP183 3.4 51.4 1.0 NH2 C:ARG62 3.7 48.1 1.0 HD3 C:LYS60 3.8 61.8 1.0 O C:HOH408 3.9 61.6 1.0 O3A C:ANP301 3.9 58.4 1.0 NZ C:LYS60 4.0 54.8 1.0 HZ3 C:LYS60 4.0 65.7 1.0 HH22 C:ARG62 4.0 57.7 1.0 O C:HOH412 4.1 62.3 1.0 HB3 C:ALA45 4.2 67.5 1.0 HE C:ARG62 4.3 57.5 1.0 HZ2 C:LYS60 4.5 65.7 1.0 HB2 C:GLU44 4.5 84.4 1.0 N3B C:ANP301 4.5 71.5 1.0 CZ C:ARG62 4.6 46.6 1.0 O1G C:ANP301 4.7 79.1 1.0 HB2 C:ALA45 4.7 67.5 1.0 NE C:ARG62 4.7 47.9 1.0 CD C:LYS60 4.7 51.5 1.0 PA C:ANP301 4.8 56.2 1.0 HA C:ASP183 4.8 59.0 1.0 CB C:ASP183 4.8 47.3 1.0 O2A C:ANP301 4.9 60.6 1.0 MG C:MG302 4.9 57.1 1.0 O1A C:ANP301 4.9 49.9 1.0 CE C:LYS60 4.9 50.8 1.0 CB C:ALA45 4.9 56.2 1.0 HA3 C:GLY185 5.0 53.3 1.0

Magnesium binding site 3 out of 3 in the Human Prpk-Tprkb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Prpk-Tprkb Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:63.8 occ:1.00 O2A D:ANP301 1.9 65.1 1.0 O2B D:ANP301 2.0 66.0 1.0 OD1 D:ASN167 2.4 59.8 1.0 OD2 D:ASP183 2.5 64.0 1.0 O2G D:ANP301 2.8 79.0 1.0 PB D:ANP301 3.3 72.6 1.0 PA D:ANP301 3.3 67.9 1.0 O3G D:ANP301 3.4 82.3 1.0 CG D:ASN167 3.4 49.4 1.0 HD21 D:ASN167 3.4 58.5 1.0 PG D:ANP301 3.5 85.0 1.0 CG D:ASP183 3.6 56.7 1.0 O3A D:ANP301 3.7 68.6 1.0 HG D:SER166 3.8 84.9 1.0 ND2 D:ASN167 3.8 48.7 1.0 HB2 D:ASP183 3.9 64.3 1.0 N3B D:ANP301 3.9 74.4 1.0 O5' D:ANP301 4.2 64.7 1.0 CB D:ASP183 4.3 53.6 1.0 O1A D:ANP301 4.4 60.7 1.0 O1B D:ANP301 4.4 63.5 1.0 HA D:ASN167 4.4 64.5 1.0 OG D:SER166 4.5 70.7 1.0 HB3 D:ASP183 4.5 64.3 1.0 HNB1 D:ANP301 4.6 89.3 1.0 H5'2 D:ANP301 4.6 81.7 1.0 OD1 D:ASP183 4.6 59.9 1.0 HD12 D:ILE182 4.6 65.4 1.0 O3' D:ANP301 4.6 70.2 1.0 HB3 D:SER166 4.6 68.2 1.0 O D:SER166 4.6 57.5 1.0 HD22 D:ASN167 4.7 58.5 1.0 CB D:ASN167 4.7 50.7 1.0 HO3' D:ANP301 4.8 84.2 1.0 C D:SER166 4.9 61.7 1.0 O1G D:ANP301 4.9 74.9 1.0 C5' D:ANP301 4.9 68.1 1.0 CA D:ASN167 5.0 53.7 1.0 H3' D:ANP301 5.0 80.3 1.0

J.Li, X.Ma, S.Banerjee, H.Chen, W.Ma, A.M.Bode, Z.Dong. Crystal Structure of the Human Prpk-Tprkb Complex. Commun Biol V. 4 167 2021.
ISSN: ESSN 2399-3642
PubMed: 33547416
DOI: 10.1038/S42003-021-01683-4