Magnesium in PDB 6d3k: Crystal Structure of Unphosphorylated Human Pkr Kinase Domain in Complex with Adp

All present enzymatic activity of Crystal Structure of Unphosphorylated Human Pkr Kinase Domain in Complex with Adp:
2.7.10.2; 2.7.11.1;

The structure of Crystal Structure of Unphosphorylated Human Pkr Kinase Domain in Complex with Adp, PDB code: 6d3k was solved by H.Erlandsen, C.B.Mayo, V.L.Robinson, J.L.Cole, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	172.99 / 2.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	106.480, 159.600, 172.990, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 26.6

The binding sites of Magnesium atom in the Crystal Structure of Unphosphorylated Human Pkr Kinase Domain in Complex with Adp (pdb code 6d3k). 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 Unphosphorylated Human Pkr Kinase Domain in Complex with Adp, PDB code: 6d3k:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Unphosphorylated Human Pkr Kinase Domain in Complex with Adp


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 Unphosphorylated Human Pkr Kinase Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:66.8 occ:1.00 OD1 B:ASN419 2.2 74.1 1.0 O3B B:ADP601 2.2 82.8 1.0 O2A B:ADP601 2.2 63.1 1.0 OD2 B:ASP432 2.7 89.2 1.0 O1 B:PO4602 3.1 0.7 1.0 CG B:ASN419 3.2 72.7 1.0 PB B:ADP601 3.2 92.2 1.0 CG B:ASP432 3.3 85.9 1.0 O1B B:ADP601 3.4 81.8 1.0 PA B:ADP601 3.5 80.4 1.0 ND2 B:ASN419 3.6 64.8 1.0 O3A B:ADP601 3.7 0.0 1.0 OD1 B:ASP432 3.9 89.7 1.0 CB B:ASP432 3.9 81.3 1.0 C5' B:ADP601 4.0 79.9 1.0 O5' B:ADP601 4.3 64.3 1.0 P B:PO4602 4.3 0.0 1.0 O2 B:PO4602 4.3 0.6 1.0 OG B:SER418 4.5 78.1 1.0 CB B:ASN419 4.5 74.9 1.0 OD2 B:ASP414 4.6 68.1 1.0 O2B B:ADP601 4.6 78.6 1.0 O1A B:ADP601 4.8 81.3 1.0 O B:SER418 4.8 62.7 1.0 CA B:ASN419 5.0 65.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Unphosphorylated Human Pkr Kinase Domain in Complex with Adp


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 Unphosphorylated Human Pkr Kinase Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:72.7 occ:1.00 OD1 A:ASN419 2.3 61.4 1.0 O3A A:ADP601 2.4 84.1 1.0 OD2 A:ASP432 2.5 73.5 1.0 O1A A:ADP601 3.0 83.9 1.0 O3 A:PO4602 3.3 0.1 1.0 O2B A:ADP601 3.3 72.8 1.0 CG A:ASN419 3.3 60.7 1.0 PB A:ADP601 3.3 82.7 1.0 O1B A:ADP601 3.4 65.5 1.0 PA A:ADP601 3.5 71.4 1.0 ND2 A:ASN419 3.6 58.6 1.0 CG A:ASP432 3.7 76.3 1.0 C5' A:ADP601 4.2 70.9 1.0 OG A:SER418 4.3 66.7 1.0 O5' A:ADP601 4.4 62.4 1.0 CB A:ASP432 4.4 71.2 1.0 OD1 A:ASP432 4.6 80.5 1.0 P A:PO4602 4.6 0.3 1.0 O2A A:ADP601 4.7 59.9 1.0 O4 A:PO4602 4.7 0.3 1.0 O3B A:ADP601 4.7 92.7 1.0 CB A:ASN419 4.7 58.3 1.0 O3' A:ADP601 4.8 65.3 1.0 O A:SER418 4.8 57.6 1.0 CE A:LYS416 4.9 79.6 1.0 OD2 A:ASP414 4.9 68.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Unphosphorylated Human Pkr Kinase Domain in Complex with Adp


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 Unphosphorylated Human Pkr Kinase Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:65.6 occ:1.00 OD2 C:ASP432 1.9 69.3 1.0 O2B C:ADP601 2.0 73.5 1.0 O1A C:ADP601 2.3 83.5 1.0 OD1 C:ASN419 2.3 66.8 1.0 CG C:ASN419 3.1 58.4 1.0 CG C:ASP432 3.1 69.8 1.0 ND2 C:ASN419 3.2 56.0 1.0 PB C:ADP601 3.4 83.0 1.0 PA C:ADP601 3.7 76.7 1.0 O4 C:PO4602 3.8 0.1 1.0 CB C:ASP432 3.9 66.3 1.0 O3B C:ADP601 4.0 73.3 1.0 O3A C:ADP601 4.0 80.3 1.0 OD1 C:ASP432 4.1 55.6 1.0 OD2 C:ASP414 4.2 0.3 1.0 OG C:SER418 4.4 66.4 1.0 O5' C:ADP601 4.5 70.7 1.0 CB C:ASN419 4.6 56.6 1.0 C5' C:ADP601 4.6 72.6 1.0 O1B C:ADP601 4.6 90.8 1.0 O2A C:ADP601 4.8 74.7 1.0

C.B.Mayo, H.Erlandsen, D.J.Mouser, A.G.Feinstein, V.L.Robinson, E.R.May, J.L.Cole. Structural Basis of Protein Kinase R Autophosphorylation. Biochemistry V. 58 2967 2019.
ISSN: ISSN 0006-2960
PubMed: 31246429
DOI: 10.1021/ACS.BIOCHEM.9B00161