Atomistry » Chlorine » PDB 5h3g-5hi2 » 5hdo
Atomistry »
  Chlorine »
    PDB 5h3g-5hi2 »
      5hdo »

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

Protein crystallography data

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

Chlorine Binding Sites:

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 5hdo

Go back to Chlorine Binding Sites List in 5hdo
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 5hdo

Go back to Chlorine Binding Sites List in 5hdo
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 5hdo

Go back to Chlorine Binding Sites List in 5hdo
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 5hdo

Go back to Chlorine Binding Sites List in 5hdo
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

Reference:

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
Page generated: Sat Dec 12 11:48:22 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy