Chlorine in PDB 5wzo: Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium

Enzymatic activity of Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium

All present enzymatic activity of Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium, PDB code: 5wzo 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) 18.76 / 1.90
Space group P 21 2 2
Cell size a, b, c (Å), α, β, γ (°) 49.060, 60.908, 63.199, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.5

Other elements in 5wzo:

The structure of Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium (pdb code 5wzo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium, PDB code: 5wzo:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 5wzo

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Chlorine binding site 1 out of 9 in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium


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 Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:24.2
occ:1.00
 O3 A:GOL212 2.9 16.3 1.0
O A:HOH334 3.2 13.0 1.0
CD1 A:LEU56 3.7 11.6 1.0
C3 A:GOL212 3.8 16.1 1.0
CB A:ARG52 4.0 10.7 1.0
CD A:ARG52 4.1 11.4 1.0
CG A:LEU56 4.2 12.9 1.0
CG A:ARG52 4.4 10.7 1.0
NE A:ARG52 4.6 11.1 1.0
O A:ARG52 4.6 9.8 1.0
CD2 A:LEU56 4.6 12.8 1.0
O A:HOH469 4.7 16.3 1.0
C A:ARG52 4.8 10.8 1.0
CA A:ARG52 4.8 10.8 1.0

Chlorine binding site 2 out of 9 in 5wzo

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Chlorine binding site 2 out of 9 in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium


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 Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:33.1
occ:1.00
 CA A:SER68 3.6 15.6 1.0
N A:VAL69 3.7 19.6 1.0
CB A:SER68 3.9 16.0 1.0
C A:SER68 4.2 18.9 1.0
O A:PHE67 4.2 11.6 1.0
CE A:LYS11 4.4 29.1 1.0
C7 A:B3P214 4.4 14.2 0.5
O A:VAL69 4.5 34.9 1.0
N A:SER68 4.7 14.0 1.0
O6 A:B3P214 4.8 14.3 0.5
CA A:VAL69 4.8 25.6 1.0
NZ A:LYS11 4.8 34.0 1.0
C A:PHE67 4.9 11.9 1.0
C5 A:B3P214 4.9 14.3 0.5
CD A:LYS11 5.0 28.6 1.0

Chlorine binding site 3 out of 9 in 5wzo

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Chlorine binding site 3 out of 9 in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium


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 Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:55.6
occ:1.00
 NH1 A:ARG98 3.3 19.1 1.0
NH2 A:ARG98 3.5 18.1 1.0
CA A:GLY73 3.6 25.4 1.0
CZ A:ARG98 3.8 19.5 1.0
N A:GLY73 4.1 32.9 1.0
O A:SER70 4.4 36.1 1.0
O A:GLU71 4.5 41.6 1.0
CE A:MET12 4.5 19.7 1.0
C A:GLY73 4.6 22.5 1.0
C A:ARG72 4.8 35.8 1.0
C A:GLU71 4.9 41.9 1.0
CL A:CL206 5.0 31.4 1.0

Chlorine binding site 4 out of 9 in 5wzo

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Chlorine binding site 4 out of 9 in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium


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 Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:16.6
occ:1.00
 NH2 A:ARG92 3.0 22.5 1.0
O A:HOH479 3.1 14.8 1.0
O A:HOH398 3.2 9.1 1.0
O A:HOH373 3.3 15.9 1.0
NH2 A:ARG52 3.3 11.7 1.0
O A:ALA45 3.6 11.2 1.0
CB A:CYS49 3.6 10.1 1.0
CD A:ARG92 3.6 16.7 1.0
SG A:CYS49 3.8 10.1 1.0
CZ A:ARG92 4.0 18.4 1.0
C A:ALA45 4.1 10.8 1.0
O A:HOH438 4.1 34.3 1.0
CB A:ALA45 4.2 11.0 1.0
NE A:ARG92 4.2 18.1 1.0
CZ A:ARG52 4.4 11.7 1.0
CA A:CYS49 4.5 9.4 1.0
CG A:ARG92 4.5 14.6 1.0
O A:HOH346 4.6 6.1 1.0
NH1 A:ARG52 4.7 11.1 1.0
N A:HIS46 4.7 10.2 1.0
CA A:ALA45 4.7 11.0 1.0
N A:CYS49 4.7 9.6 1.0
CB A:ARG92 4.7 11.7 1.0
O A:HOH480 4.8 13.2 1.0
CA A:HIS46 4.9 10.5 1.0

Chlorine binding site 5 out of 9 in 5wzo

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Chlorine binding site 5 out of 9 in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium


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 Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:24.8
occ:1.00
 O A:HOH430 3.1 19.7 1.0
NZ A:LYS15 3.2 19.9 1.0
NH1 A:ARG106 3.3 17.8 1.0
NE2 A:GLN19 3.7 21.1 1.0
CG A:ARG106 3.9 15.7 1.0
CD A:ARG106 3.9 16.2 1.0
CE A:LYS15 4.0 18.8 1.0
CE1 A:TYR104 4.2 11.6 1.0
CD A:LYS15 4.2 19.0 1.0
CD1 A:TYR104 4.3 11.9 1.0
CZ A:ARG106 4.4 17.8 1.0
O A:HOH464 4.6 29.8 1.0
NE A:ARG106 4.6 17.0 1.0
CD A:GLN19 4.8 22.1 1.0
O A:HOH309 4.8 26.4 1.0
CG A:LYS15 4.9 19.2 1.0
O A:HOH445 4.9 41.0 1.0
O A:HOH366 4.9 20.1 1.0

Chlorine binding site 6 out of 9 in 5wzo

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Chlorine binding site 6 out of 9 in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:31.4
occ:1.00
 O A:HOH463 2.7 30.1 1.0
N A:ILE74 3.0 19.9 1.0
CA A:GLY73 3.4 25.4 1.0
CE A:LYS91 3.4 9.2 1.0
NZ A:LYS91 3.7 8.6 1.0
C A:GLY73 3.7 22.5 1.0
CD1 A:LEU95 3.8 11.2 1.0
CA A:ILE74 4.0 17.4 1.0
O A:HOH312 4.0 31.1 1.0
CB A:ILE74 4.1 16.4 1.0
CD2 A:LEU95 4.2 10.8 1.0
O A:HOH394 4.2 28.5 1.0
O A:ILE74 4.2 16.7 1.0
O A:HOH444 4.3 35.9 1.0
CG1 A:ILE74 4.3 16.4 1.0
O A:HOH431 4.3 42.1 1.0
O A:ARG72 4.3 36.2 1.0
CD A:LYS91 4.5 9.6 1.0
CG A:LEU95 4.5 10.8 1.0
CD1 A:ILE74 4.6 15.2 1.0
C A:ILE74 4.6 16.4 1.0
O A:HOH450 4.6 32.0 1.0
N A:GLY73 4.6 32.9 1.0
CG A:LYS91 4.9 9.1 1.0
C A:ARG72 4.9 35.8 1.0
CL A:CL203 5.0 55.6 1.0
O A:GLY73 5.0 20.7 1.0

Chlorine binding site 7 out of 9 in 5wzo

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Chlorine binding site 7 out of 9 in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:22.4
occ:1.00
 O A:HOH425 3.0 14.2 1.0
O A:HOH441 3.0 29.1 1.0
O A:HOH460 3.0 33.6 1.0
O A:HOH430 3.1 19.7 1.0
N A:ARG106 3.2 13.8 1.0
CZ A:ARG106 3.7 17.8 1.0
NH1 A:ARG106 3.7 17.8 1.0
CB A:ARG106 3.8 14.4 1.0
CA A:ASN105 3.8 13.9 1.0
CG A:ARG106 3.9 15.7 1.0
OD1 A:ASN105 4.0 16.4 1.0
NH2 A:ARG106 4.0 17.2 1.0
O A:TYR104 4.0 13.3 1.0
C A:ASN105 4.0 13.0 1.0
CA A:ARG106 4.1 13.7 1.0
NE A:ARG106 4.1 17.0 1.0
O A:HOH331 4.3 16.8 1.0
CG A:ASN105 4.5 16.7 1.0
CD A:ARG106 4.6 16.2 1.0
O A:HOH464 4.6 29.8 1.0
N A:ASN105 4.7 13.1 1.0
O A:HOH355 4.7 26.2 1.0
C A:TYR104 4.7 13.3 1.0
CB A:ASN105 4.8 15.2 1.0
O A:HOH310 4.8 20.1 1.0
O A:HOH489 4.8 46.4 1.0
O A:HOH453 5.0 30.8 1.0

Chlorine binding site 8 out of 9 in 5wzo

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Chlorine binding site 8 out of 9 in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:42.1
occ:1.00
 NE2 A:GLN83 3.6 19.2 1.0
O A:HOH307 3.6 6.0 1.0
NE A:ARG79 3.7 11.1 0.4
NE A:ARG79 3.9 11.6 0.6
CD A:ARG79 4.1 12.1 0.6
OE1 A:GLN83 4.2 14.1 1.0
CB A:ARG79 4.2 11.9 0.6
CB A:ARG79 4.3 11.5 0.4
CD A:GLN83 4.3 13.8 1.0
CD A:ARG79 4.3 11.5 0.4
O1 A:GOL213 4.4 38.3 1.0
NH2 A:ARG79 4.6 10.2 0.4
CZ A:ARG79 4.7 10.9 0.4
CG A:ARG79 4.8 12.4 0.6
CG A:ARG79 4.9 11.6 0.4

Chlorine binding site 9 out of 9 in 5wzo

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Chlorine binding site 9 out of 9 in the Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Human Secreted Phospholipase A2 Group Iie, Crystallized with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:20.2
occ:1.00
 O A:HOH465 2.9 16.9 1.0
N A:CYS82 3.1 9.1 1.0
O A:HOH409 3.3 12.9 1.0
SG A:CYS82 3.5 11.4 1.0
N A:THR81 3.6 10.0 1.0
CB A:CYS82 3.6 9.7 1.0
CB A:THR80 3.6 10.8 1.0
CB A:THR81 3.8 9.6 1.0
O A:HOH475 3.9 37.2 1.0
CA A:CYS82 4.0 9.3 1.0
CA A:THR81 4.0 9.8 1.0
C A:THR81 4.0 9.3 1.0
OG1 A:THR80 4.0 10.3 1.0
C A:THR80 4.2 10.8 1.0
OG1 A:THR81 4.4 10.3 1.0
O A:HOH427 4.4 37.4 1.0
O A:HOH478 4.4 39.1 1.0
CA A:THR80 4.4 10.6 1.0
CG2 A:THR80 4.5 11.1 1.0
O A:HOH327 4.7 15.1 1.0
O A:HOH322 5.0 18.1 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 A2 Group Iie Sci Rep V. 7 10815 2017.
ISSN: ESSN 2045-2322
PubMed: 28883454
DOI: 10.1038/S41598-017-11219-8
Page generated: Sat Dec 12 12:37:57 2020

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