Nickel in PDB 5lhs: The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator

All present enzymatic activity of The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator:
3.4.21.73;

The structure of The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator, PDB code: 5lhs was solved by T.Kromann-Hansen, E.L.Lange, H.P.Sorensen, G.H.Ghassabeh, M.Huang, J.K.Jensen, S.Muyldermans, P.J.Declerck, P.A.Andreasen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.68 / 3.05
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	194.700, 194.700, 37.000, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 26

The binding sites of Nickel atom in the The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator (pdb code 5lhs). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator, PDB code: 5lhs:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni303 b:0.5 occ:1.00 OE1 A:GLU185B 2.7 73.9 1.0 NE2 B:HIS233 2.7 79.6 1.0 OD2 A:ASP185 2.8 62.7 1.0 CE1 B:HIS233 3.6 72.2 1.0 CG A:ASP185 3.6 63.6 1.0 OD1 A:ASP185 3.7 64.3 1.0 CD2 B:HIS233 3.7 68.8 1.0 NE1 A:TRP186 3.8 54.4 1.0 CD A:GLU185B 3.8 67.9 1.0 CB A:GLU185B 4.2 51.0 1.0 CD1 A:TRP186 4.2 51.6 1.0 CG A:GLU185B 4.4 62.7 1.0 NH1 B:ARG230 4.4 60.0 1.0 ND1 B:HIS233 4.7 48.4 1.0 OE2 A:GLU185B 4.8 63.8 1.0 CD B:ARG230 4.8 39.4 1.0 CE2 A:TRP186 4.8 65.9 1.0 CG B:HIS233 4.8 54.9 1.0 CZ B:ARG230 5.0 45.8 1.0

Nickel binding site 2 out of 4 in the The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:0.5 occ:1.00 NE2 A:HIS233 2.4 69.4 1.0 OE1 B:GLU185B 2.9 75.9 1.0 OD2 B:ASP185 3.0 68.8 1.0 CE1 A:HIS233 3.2 61.0 1.0 CD2 A:HIS233 3.5 58.8 1.0 CG B:ASP185 3.8 59.7 1.0 OD1 B:ASP185 3.9 56.2 1.0 CD B:GLU185B 4.0 66.6 1.0 NE1 B:TRP186 4.0 52.7 1.0 NH1 A:ARG230 4.3 52.9 1.0 ND1 A:HIS233 4.4 46.9 1.0 CD1 B:TRP186 4.5 51.8 1.0 CB B:GLU185B 4.5 61.3 1.0 CD A:ARG230 4.5 40.1 1.0 CG A:HIS233 4.5 51.3 1.0 CG B:GLU185B 4.7 67.6 1.0 CZ A:ARG230 4.8 48.5 1.0 OE2 B:GLU185B 4.9 69.6 1.0 NE A:ARG230 4.9 45.4 1.0 CE2 B:TRP186 5.0 57.4 1.0

Nickel binding site 3 out of 4 in the The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni303 b:0.3 occ:1.00 NE2 D:HIS233 2.5 74.3 1.0 OD2 C:ASP185 2.6 74.4 1.0 OE1 C:GLU185B 2.9 61.8 1.0 CG C:ASP185 3.4 66.1 1.0 OD1 C:ASP185 3.4 65.6 1.0 CD2 D:HIS233 3.5 61.6 1.0 CE1 D:HIS233 3.5 71.0 1.0 NE1 C:TRP186 3.9 54.3 1.0 CD C:GLU185B 3.9 60.3 1.0 CB C:GLU185B 4.2 51.3 1.0 CD1 C:TRP186 4.2 52.1 1.0 CG C:GLU185B 4.5 61.3 1.0 ND1 D:HIS233 4.6 55.0 1.0 CG D:HIS233 4.6 52.9 1.0 NH1 D:ARG230 4.7 60.1 1.0 CB C:ASP185 4.8 54.0 1.0 CD D:ARG230 4.9 47.9 1.0 OE2 C:GLU185B 4.9 67.1 1.0

Nickel binding site 4 out of 4 in the The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Ligand Free Catalytic Domain of Murine Urokinase-Type Plasminogen Activator within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni304 b:0.3 occ:1.00 NE2 C:HIS233 2.5 79.6 1.0 OE1 D:GLU185B 2.5 92.2 1.0 OD2 D:ASP185 2.6 69.0 1.0 CD D:GLU185B 3.2 76.5 1.0 CG D:ASP185 3.3 70.0 1.0 OD1 D:ASP185 3.4 70.9 1.0 CE1 C:HIS233 3.4 69.3 1.0 CD2 C:HIS233 3.5 65.2 1.0 NE1 D:TRP186 3.9 53.9 1.0 CG D:GLU185B 3.9 71.9 1.0 OE2 D:GLU185B 3.9 68.0 1.0 CD1 D:TRP186 4.2 47.9 1.0 CB D:GLU185B 4.2 60.2 1.0 ND1 C:HIS233 4.5 52.6 1.0 CG C:HIS233 4.6 54.6 1.0 NH1 C:ARG230 4.7 62.1 1.0 CB D:ASP185 4.8 60.9 1.0 CD C:ARG230 4.9 39.6 1.0 CE2 D:TRP186 5.0 64.8 1.0

T.Kromann-Hansen, E.Louise Lange, H.Peter Srensen, G.Hassanzadeh-Ghassabeh, M.Huang, J.K.Jensen, S.Muyldermans, P.J.Declerck, E.A.Komives, P.A.Andreasen. Discovery of A Novel Conformational Equilibrium in Urokinase-Type Plasminogen Activator. Sci Rep V. 7 3385 2017.
ISSN: ESSN 2045-2322
PubMed: 28611361
DOI: 10.1038/S41598-017-03457-7