Chlorine in PDB 5hdo: Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator

The structure of Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator, PDB code: 5hdo was solved by T.Kromann-Hansen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.28 / 2.16
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.830, 99.830, 127.330, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.8

The binding sites of Chlorine atom in the Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator (pdb code 5hdo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator, PDB code: 5hdo:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:68.3 occ:1.00 O B:HOH409 3.3 57.4 1.0 C B:SER49 3.7 36.3 1.0 CA B:SER49 3.7 33.6 1.0 N B:SER49 3.7 33.7 1.0 O B:HOH418 3.8 51.0 1.0 N B:CYS50 4.0 26.6 1.0 O B:SER49 4.0 34.1 1.0 C B:VAL48 4.1 39.5 1.0 SG B:CYS50 4.2 40.0 1.0 O B:ASN59 4.3 33.5 1.0 N B:VAL48 4.4 32.7 1.0 O B:VAL48 4.4 33.0 1.0 CB B:CYS50 4.4 36.6 1.0 CB B:ASN59 4.4 43.0 1.0 C B:GLY47 4.4 30.5 1.0 C B:ASN59 4.6 36.8 1.0 CA B:GLY47 4.8 28.4 1.0 O B:GLY47 4.8 35.0 1.0 N B:TYR60 4.8 39.6 1.0 CA B:CYS50 4.8 34.8 1.0 CA B:VAL48 4.9 32.5 1.0 CD1 B:LEU103 4.9 43.4 1.0 N B:ALA61 4.9 34.4 1.0 C B:TYR60 4.9 37.1 1.0 CA B:TYR60 5.0 36.8 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl202 b:66.7 occ:1.00 N C:SER49 3.9 26.1 1.0 CA C:SER49 3.9 27.6 1.0 C C:SER49 4.0 30.4 1.0 C C:VAL48 4.1 33.7 1.0 O C:VAL48 4.2 27.4 1.0 N C:CYS50 4.3 28.3 1.0 O C:SER49 4.4 26.0 1.0 N C:ALA61 4.4 36.3 1.0 N C:VAL48 4.4 23.8 1.0 O C:ASN59 4.5 33.1 1.0 C C:GLY47 4.5 31.6 1.0 CB C:ASN59 4.5 38.5 1.0 C C:TYR60 4.5 35.8 1.0 C C:ASN59 4.5 43.6 1.0 SG C:CYS50 4.6 32.4 1.0 N C:TYR60 4.6 36.3 1.0 CA C:TYR60 4.6 35.6 1.0 CA C:GLY47 4.7 27.6 1.0 CB C:CYS50 4.8 29.0 1.0 O C:GLY47 4.8 36.4 1.0 CA C:VAL48 4.9 25.1 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl202 b:73.5 occ:1.00 O D:HOH362 3.4 42.3 1.0 N D:SER49 4.1 33.6 1.0 C D:SER49 4.1 34.0 1.0 CA D:SER49 4.1 29.6 1.0 SG D:CYS50 4.2 34.5 1.0 N D:CYS50 4.3 26.1 1.0 C D:VAL48 4.4 33.9 1.0 O D:ASN59 4.4 33.1 1.0 CB D:ASN59 4.5 36.9 1.0 O D:SER49 4.5 33.8 1.0 C D:ASN59 4.6 36.6 1.0 O D:VAL48 4.6 27.7 1.0 CB D:CYS50 4.6 31.6 1.0 N D:VAL48 4.7 29.0 1.0 N D:ALA61 4.7 33.3 1.0 C D:GLY47 4.8 29.4 1.0 CD1 D:LEU103 4.8 35.0 1.0 N D:TYR60 4.8 34.2 1.0 C D:TYR60 4.9 39.2 1.0 CA D:GLY47 5.0 30.1 1.0 CA D:TYR60 5.0 26.4 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of A Nanobody Raised Against Urokinase-Type Plasminogen Activator within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl203 b:55.5 occ:1.00 O1 D:SO4201 2.7 75.0 1.0 O D:HOH389 3.0 44.0 1.0 OG D:SER54 3.6 32.1 1.0 N D:SER54 3.6 33.1 1.0 O D:HOH371 3.6 39.0 1.0 CB D:SER52 3.7 32.3 1.0 OG D:SER52 3.8 29.8 1.0 S D:SO4201 3.8 74.0 1.0 N D:ALA53 3.8 28.1 1.0 O2 D:SO4201 3.8 54.5 1.0 O D:HOH381 3.9 51.2 1.0 CB D:SER54 3.9 36.0 1.0 CB D:ALA53 4.1 36.5 1.0 CA D:ALA53 4.3 31.5 1.0 CA D:SER54 4.4 30.9 1.0 C D:ALA53 4.4 37.7 1.0 O3 D:SO4201 4.4 98.1 1.0 C D:SER52 4.4 27.9 1.0 CA D:SER52 4.6 28.3 1.0 O4 D:SO4201 4.9 55.1 1.0

T.Kromann-Hansen, E.Oldenburg, K.W.Yung, G.H.Ghassabeh, S.Muyldermans, P.J.Declerck, M.Huang, P.A.Andreasen, J.C.Ngo. A Camelid-Derived Antibody Fragment Targeting the Active Site of A Serine Protease Balances Between Inhibitor and Substrate Behavior. J.Biol.Chem. V. 291 15156 2016.
ISSN: ESSN 1083-351X
PubMed: 27226628
DOI: 10.1074/JBC.M116.732503