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Chlorine in PDB 5y5e: Crystal Structure of Phospholipase A2 with Inhibitor

Enzymatic activity of Crystal Structure of Phospholipase A2 with Inhibitor

All present enzymatic activity of Crystal Structure of Phospholipase A2 with Inhibitor:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of Phospholipase A2 with Inhibitor, PDB code: 5y5e was solved by S.Hou, J.Xu, T.Xu, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.78 / 1.80
Space group P 21 2 2
Cell size a, b, c (Å), α, β, γ (°) 48.726, 61.063, 63.356, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.5

Other elements in 5y5e:

The structure of Crystal Structure of Phospholipase A2 with Inhibitor also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Calcium (Ca) 1 atom
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Phospholipase A2 with Inhibitor (pdb code 5y5e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Phospholipase A2 with Inhibitor, PDB code: 5y5e:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5y5e

Go back to Chlorine Binding Sites List in 5y5e
Chlorine binding site 1 out of 5 in the Crystal Structure of Phospholipase A2 with Inhibitor


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 Phospholipase A2 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:34.6
occ:1.00
 O A:HOH320 3.1 24.4 1.0
NE2 A:GLN38 3.2 24.8 1.0
CA A:ASP37 3.6 14.1 1.0
C A:ASP37 3.6 14.1 1.0
N A:GLN38 3.7 15.5 1.0
CD1 A:TRP41 3.8 16.6 1.0
NE1 A:TRP41 4.0 17.0 1.0
CD A:GLN38 4.1 23.5 1.0
CG A:GLN38 4.1 20.9 1.0
O A:ASP37 4.2 13.7 1.0
O A:HOH372 4.3 19.9 1.0
N A:ASP37 4.4 15.0 1.0
CA A:GLN38 4.4 16.4 1.0
O A:HOH432 4.7 34.4 1.0
O A:HOH381 4.7 33.8 1.0
CB A:ASP37 4.7 13.9 1.0
O A:HOH385 4.7 34.5 1.0
O A:VAL36 4.7 15.7 1.0
C A:VAL36 4.8 15.3 1.0
CB A:GLN38 4.9 18.4 1.0

Chlorine binding site 2 out of 5 in 5y5e

Go back to Chlorine Binding Sites List in 5y5e
Chlorine binding site 2 out of 5 in the Crystal Structure of Phospholipase A2 with Inhibitor


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 Phospholipase A2 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:33.3
occ:1.00
 O A:HOH403 2.9 25.4 1.0
O A:HOH417 3.0 42.5 1.0
N A:ARG106 3.1 18.8 1.0
O A:HOH404 3.3 34.5 1.0
CZ A:ARG106 3.7 27.2 1.0
CB A:ARG106 3.8 20.7 1.0
NH1 A:ARG106 3.8 27.8 1.0
CA A:ASN105 3.8 17.6 1.0
OD1 A:ASN105 3.8 18.7 1.0
CG A:ARG106 3.8 21.5 1.0
NH2 A:ARG106 4.0 27.0 1.0
O A:TYR104 4.0 16.9 1.0
C A:ASN105 4.0 17.6 1.0
CA A:ARG106 4.1 19.4 1.0
NE A:ARG106 4.1 24.4 1.0
O A:HOH315 4.2 25.5 1.0
CG A:ASN105 4.4 19.5 1.0
CD A:ARG106 4.6 23.0 1.0
CB A:ASN105 4.7 17.8 1.0
N A:ASN105 4.7 17.2 1.0
C A:TYR104 4.7 17.8 1.0
O A:HOH384 4.9 38.7 1.0
O A:HOH422 4.9 42.6 1.0

Chlorine binding site 3 out of 5 in 5y5e

Go back to Chlorine Binding Sites List in 5y5e
Chlorine binding site 3 out of 5 in the Crystal Structure of Phospholipase A2 with Inhibitor


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 Phospholipase A2 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:42.0
occ:1.00
 N A:VAL69 3.5 25.2 1.0
CA A:SER68 3.6 19.0 1.0
C11 A:B3P209 3.8 30.1 0.5
CB A:SER68 3.9 18.8 1.0
C A:SER68 4.1 22.4 1.0
O3 A:B3P209 4.1 28.4 0.5
CE A:LYS11 4.2 38.1 1.0
O A:PHE67 4.3 14.6 1.0
O A:VAL69 4.3 38.9 1.0
CA A:VAL69 4.6 30.7 1.0
C10 A:B3P209 4.6 30.4 0.5
N A:SER68 4.8 16.2 1.0
NZ A:LYS11 4.8 39.3 1.0
CD A:LYS11 4.8 36.0 1.0
CB A:VAL69 4.9 32.5 1.0
C A:VAL69 4.9 34.9 1.0
C8 A:B3P209 4.9 28.9 0.5
C A:PHE67 5.0 14.8 1.0

Chlorine binding site 4 out of 5 in 5y5e

Go back to Chlorine Binding Sites List in 5y5e
Chlorine binding site 4 out of 5 in the Crystal Structure of Phospholipase A2 with Inhibitor


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 Phospholipase A2 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:21.1
occ:1.00
 O A:HOH436 3.1 21.4 1.0
O A:HOH365 3.1 19.8 1.0
NH2 A:ARG92 3.1 27.1 1.0
O A:HOH375 3.2 11.3 1.0
NH2 A:ARG52 3.3 17.2 1.0
CD A:ARG92 3.6 23.1 1.0
CB A:CYS49 3.6 12.2 1.0
O A:ALA45 3.7 13.3 1.0
SG A:CYS49 3.7 12.5 1.0
O A:HOH416 4.0 39.3 1.0
CZ A:ARG92 4.1 26.2 1.0
C A:ALA45 4.2 13.9 1.0
CB A:ALA45 4.2 13.8 1.0
NE A:ARG92 4.3 24.2 1.0
CZ A:ARG52 4.4 16.9 1.0
CG A:ARG92 4.5 19.7 1.0
CA A:CYS49 4.5 12.0 1.0
O A:HOH360 4.6 14.2 1.0
NH1 A:ARG52 4.7 17.4 1.0
CA A:ALA45 4.7 13.7 1.0
N A:CYS49 4.7 12.2 1.0
CB A:ARG92 4.8 16.8 1.0
O A:HOH433 4.8 17.2 1.0
N A:HIS46 4.8 13.4 1.0
O2 A:GOL201 4.9 23.2 1.0

Chlorine binding site 5 out of 5 in 5y5e

Go back to Chlorine Binding Sites List in 5y5e
Chlorine binding site 5 out of 5 in the Crystal Structure of Phospholipase A2 with Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Phospholipase A2 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:36.9
occ:1.00
 N A:ILE74 3.1 22.9 1.0
CA A:GLY73 3.4 31.8 1.0
CE A:LYS91 3.5 15.9 1.0
C A:GLY73 3.8 27.3 1.0
NZ A:LYS91 3.8 16.4 1.0
CD1 A:LEU95 3.9 15.9 1.0
O A:HOH352 3.9 36.6 1.0
O A:HOH383 4.0 38.3 1.0
CA A:ILE74 4.1 20.3 1.0
CB A:ILE74 4.1 19.9 1.0
O A:ILE74 4.1 17.2 1.0
CG1 A:ILE74 4.3 20.8 1.0
CD2 A:LEU95 4.3 16.7 1.0
O A:ARG72 4.4 39.1 1.0
C A:ILE74 4.6 18.0 1.0
CD A:LYS91 4.6 15.2 1.0
CG A:LEU95 4.6 15.6 1.0
N A:GLY73 4.7 35.6 1.0
CD1 A:ILE74 4.9 20.9 1.0
CG A:LYS91 5.0 14.8 1.0
C A:ARG72 5.0 39.9 1.0
O A:GLY73 5.0 26.7 1.0

Reference:

S.Hou, T.Xu, J.Xu, L.Qu, Y.Xu, L.Chen, J.Liu. Structural Basis For Functional Selectivity and Ligand Recognition Revealed By Crystal Structures of Human Secreted Phospholipase A2GROUP Iie Sci Rep V. 7 10815 2017.
ISSN: ESSN 2045-2322
PubMed: 28883454
DOI: 10.1038/S41598-017-11219-8
Page generated: Fri Jul 26 21:17:55 2024

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