Chlorine in PDB 4gly: Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504

Enzymatic activity of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504

All present enzymatic activity of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504:
3.4.21.73;

Protein crystallography data

The structure of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504, PDB code: 4gly was solved by S.A.Buth, P.G.Leiman, S.Chen, C.Heinis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.13 / 1.52
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 120.800, 120.800, 43.080, 90.00, 90.00, 120.00
R / Rfree (%) 12.8 / 20.4

Other elements in 4gly:

The structure of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504 (pdb code 4gly). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504, PDB code: 4gly:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4gly

Go back to Chlorine Binding Sites List in 4gly
Chlorine binding site 1 out of 3 in the Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:40.8
occ:1.00
 NH1 A:ARG217 2.5 90.9 1.0
N A:GLY218 3.3 8.7 1.0
CZ A:ARG217 3.5 59.8 1.0
CA B:GLY4 3.6 13.9 1.0
N B:GLY4 3.8 15.9 1.0
CA A:GLY218 3.9 8.5 1.0
NH2 A:ARG217 4.1 62.0 1.0
C A:ARG217 4.3 9.1 1.0
NE A:ARG217 4.4 46.1 1.0
CA A:ARG217 4.5 10.4 1.0
O A:HOH542 4.5 35.2 1.0
C B:GLY4 4.6 14.4 1.0
CD A:ARG217 4.7 30.2 1.0
CB A:ARG217 4.8 13.4 1.0
C B:LEU3 5.0 17.0 1.0

Chlorine binding site 2 out of 3 in 4gly

Go back to Chlorine Binding Sites List in 4gly
Chlorine binding site 2 out of 3 in the Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:51.0
occ:1.00
 O A:ILE163 2.6 15.3 1.0
N A:CYS182 2.8 8.8 1.0
O A:HOH601 3.3 40.2 1.0
ND1 A:HIS165 3.3 38.8 1.0
CE1 A:HIS165 3.5 25.5 1.0
CA A:LEU181 3.5 9.8 1.0
C A:LEU181 3.6 7.4 1.0
CA A:CYS182 3.8 9.6 1.0
C A:ILE163 3.8 13.5 1.0
O A:CYS182 3.8 10.3 1.0
CB A:CYS182 3.8 9.4 1.0
O1 A:SO4309 3.9 45.8 1.0
N A:HIS165 3.9 15.7 1.0
C A:SER164 4.0 14.4 1.0
CG A:HIS165 4.1 31.6 1.0
O A:SER164 4.2 17.9 1.0
CA A:HIS165 4.3 17.9 1.0
C A:CYS182 4.3 9.6 1.0
CD2 A:LEU181 4.3 22.6 1.0
CB A:LEU181 4.3 10.8 1.0
NE2 A:HIS165 4.3 27.5 1.0
SG A:CYS182 4.3 14.5 1.0
O A:MET180 4.5 11.6 1.0
CA A:SER164 4.5 16.8 1.0
N A:SER164 4.6 12.8 1.0
CD2 A:HIS165 4.7 32.2 1.0
N A:ILE163 4.7 11.0 1.0
CA A:ILE163 4.7 13.6 1.0
N A:LEU181 4.7 8.6 1.0
CB A:HIS165 4.8 20.2 1.0
CB A:CYS168 4.8 18.4 1.0
O A:LEU181 4.9 9.6 1.0
CG A:LEU181 4.9 17.1 1.0
CB A:ILE163 5.0 17.4 1.0

Chlorine binding site 3 out of 3 in 4gly

Go back to Chlorine Binding Sites List in 4gly
Chlorine binding site 3 out of 3 in the Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Urokinase-Type Plasminogen Activator Upa in Complex with the Two-Disulfide Bridge Peptide UK504 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:67.4
occ:1.00
 O A:HOH498 2.7 49.0 1.0
O A:HOH600 2.8 46.3 1.0
O A:HOH648 2.9 80.0 1.0
O A:HOH684 3.3 38.7 1.0
ND2 A:ASN101 3.4 9.7 1.0
O A:HOH539 3.7 19.0 1.0
O A:HOH559 3.7 53.5 1.0
ND1 A:HIS100 4.1 15.4 1.0
CG A:ASN101 4.4 10.0 1.0
NZ A:LYS179 4.5 40.0 1.0
OD1 A:ASN101 4.5 12.6 1.0
CB A:HIS100 4.7 11.5 1.0
CG A:HIS100 4.9 12.8 1.0
O A:HOH466 4.9 33.3 1.0
O A:HOH454 4.9 28.0 1.0

Reference:

S.Chen, I.Rentero Rebollo, S.A.Buth, J.Morales-Sanfrutos, J.Touati, P.G.Leiman, C.Heinis. Bicyclic Peptide Ligands Pulled Out of Cysteine-Rich Peptide Libraries. J.Am.Chem.Soc. V. 135 6562 2013.
ISSN: ISSN 0002-7863
PubMed: 23560397
DOI: 10.1021/JA400461H
Page generated: Sun Jul 21 14:47:34 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy