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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

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