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Chlorine in PDB 6kqu: Crystal Structure of Phospholipase A2

Enzymatic activity of Crystal Structure of Phospholipase A2

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

Protein crystallography data

The structure of Crystal Structure of Phospholipase A2, PDB code: 6kqu was solved by S.Hou, T.Xu, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.80 / 2.00
Space group P 21 2 2
Cell size a, b, c (Å), α, β, γ (°) 48.839, 61.117, 63.404, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.9

Other elements in 6kqu:

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

Calcium (Ca) 1 atom
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Phospholipase A2 (pdb code 6kqu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Phospholipase A2, PDB code: 6kqu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6kqu

Go back to Chlorine Binding Sites List in 6kqu
Chlorine binding site 1 out of 6 in the Crystal Structure of Phospholipase A2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:17.2
occ:1.00
 NH2 A:ARG92 2.9 26.4 1.0
O A:HOH442 3.0 16.7 1.0
O A:HOH363 3.0 14.9 1.0
O A:HOH378 3.2 9.5 1.0
NH2 A:ARG52 3.3 14.8 1.0
CB A:CYS49 3.6 9.7 1.0
O A:ALA45 3.7 9.7 1.0
CD A:ARG92 3.7 20.6 1.0
SG A:CYS49 3.8 10.0 1.0
CZ A:ARG92 4.0 23.8 1.0
O A:HOH414 4.0 33.7 1.0
C A:ALA45 4.2 10.3 1.0
NE A:ARG92 4.2 22.4 1.0
CB A:ALA45 4.3 10.3 1.0
CZ A:ARG52 4.4 14.4 1.0
CA A:CYS49 4.5 9.4 1.0
CG A:ARG92 4.6 18.0 1.0
NH1 A:ARG52 4.6 14.1 1.0
O A:HOH354 4.6 8.5 1.0
N A:CYS49 4.7 9.3 1.0
CA A:ALA45 4.8 10.6 1.0
O A:HOH440 4.8 15.5 1.0
CB A:ARG92 4.8 14.6 1.0
N A:HIS46 4.8 10.6 1.0

Chlorine binding site 2 out of 6 in 6kqu

Go back to Chlorine Binding Sites List in 6kqu
Chlorine binding site 2 out of 6 in the Crystal Structure of Phospholipase A2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:34.3
occ:1.00
 C11 A:B3P211 3.5 20.8 0.5
N A:VAL69 3.5 21.6 1.0
O2 A:GOL202 3.5 37.1 1.0
C2 A:GOL202 3.6 38.6 1.0
CA A:SER68 3.6 15.8 1.0
C3 A:GOL202 3.8 38.7 1.0
CB A:SER68 3.9 15.0 1.0
O3 A:B3P211 4.1 18.3 0.5
C A:SER68 4.1 19.2 1.0
CE A:LYS11 4.1 34.3 1.0
O A:PHE67 4.2 12.0 1.0
O3 A:GOL202 4.3 39.6 1.0
O A:VAL69 4.4 34.3 1.0
C10 A:B3P211 4.4 21.9 0.5
CA A:VAL69 4.6 26.4 1.0
C8 A:B3P211 4.7 20.3 0.5
NZ A:LYS11 4.7 36.2 1.0
N A:SER68 4.7 13.9 1.0
CB A:VAL69 4.8 27.4 1.0
C A:VAL69 4.9 29.5 1.0
C A:PHE67 4.9 12.6 1.0
CD A:LYS11 4.9 32.2 1.0
C1 A:GOL202 5.0 41.0 1.0

Chlorine binding site 3 out of 6 in 6kqu

Go back to Chlorine Binding Sites List in 6kqu
Chlorine binding site 3 out of 6 in the Crystal Structure of Phospholipase A2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:22.4
occ:1.00
 O A:HOH412 3.0 12.7 1.0
O A:HOH424 3.1 29.9 1.0
N A:ARG106 3.2 14.7 1.0
O A:HOH406 3.3 26.6 1.0
CZ A:ARG106 3.7 18.2 1.0
CB A:ARG106 3.7 16.1 1.0
CA A:ASN105 3.8 14.3 1.0
OD1 A:ASN105 3.8 13.8 1.0
CG A:ARG106 3.8 16.2 1.0
NH1 A:ARG106 3.9 18.7 1.0
NH2 A:ARG106 4.0 17.8 1.0
C A:ASN105 4.0 14.0 1.0
O A:TYR104 4.0 14.0 1.0
NE A:ARG106 4.0 16.8 1.0
CA A:ARG106 4.0 14.8 1.0
O A:HOH310 4.2 12.9 1.0
CG A:ASN105 4.4 14.9 1.0
CD A:ARG106 4.5 16.6 1.0
CB A:ASN105 4.7 14.3 1.0
N A:ASN105 4.7 13.4 1.0
C A:TYR104 4.7 13.8 1.0
O A:HOH386 4.8 26.6 1.0

Chlorine binding site 4 out of 6 in 6kqu

Go back to Chlorine Binding Sites List in 6kqu
Chlorine binding site 4 out of 6 in the Crystal Structure of Phospholipase A2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:27.8
occ:1.00
 N A:ILE74 3.1 19.8 1.0
CA A:GLY73 3.4 26.6 1.0
CE A:LYS91 3.5 13.0 1.0
C A:GLY73 3.8 23.1 1.0
NZ A:LYS91 3.8 13.2 1.0
CD1 A:LEU95 4.0 12.2 1.0
O A:HOH357 4.0 31.0 1.0
CA A:ILE74 4.1 17.0 1.0
CB A:ILE74 4.1 16.8 1.0
O A:ILE74 4.2 14.6 1.0
CD2 A:LEU95 4.3 12.2 1.0
CG1 A:ILE74 4.3 17.1 1.0
O A:ARG72 4.6 31.6 1.0
C A:ILE74 4.6 15.0 1.0
CG A:LEU95 4.7 11.7 1.0
N A:GLY73 4.7 30.9 1.0
CD A:LYS91 4.7 12.7 1.0
CD1 A:ILE74 4.7 17.0 1.0
O A:GLY73 5.0 22.9 1.0

Chlorine binding site 5 out of 6 in 6kqu

Go back to Chlorine Binding Sites List in 6kqu
Chlorine binding site 5 out of 6 in the Crystal Structure of Phospholipase A2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:28.3
occ:1.00
 NE2 A:GLN38 3.1 17.7 1.0
O A:HOH338 3.1 18.4 1.0
CA A:ASP37 3.6 10.8 1.0
C A:ASP37 3.6 10.7 1.0
N A:GLN38 3.7 11.6 1.0
CD1 A:TRP41 3.9 13.7 1.0
NE1 A:TRP41 4.0 14.1 1.0
CD A:GLN38 4.1 17.4 1.0
CG A:GLN38 4.1 15.9 1.0
O A:ASP37 4.2 9.5 1.0
N A:ASP37 4.4 11.0 1.0
CA A:GLN38 4.4 12.5 1.0
O A:HOH355 4.4 14.8 1.0
O A:HOH370 4.6 26.6 1.0
CB A:ASP37 4.6 11.0 1.0
O A:VAL36 4.7 11.6 1.0
O A:HOH433 4.7 32.4 1.0
C A:VAL36 4.8 11.6 1.0
CB A:GLN38 4.9 13.7 1.0
O A:HOH376 4.9 22.4 1.0

Chlorine binding site 6 out of 6 in 6kqu

Go back to Chlorine Binding Sites List in 6kqu
Chlorine binding site 6 out of 6 in the Crystal Structure of Phospholipase A2


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 Phospholipase A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:26.9
occ:1.00
 NZ A:LYS15 3.3 20.1 1.0
NH1 A:ARG106 3.3 18.7 1.0
O A:HOH406 3.3 26.6 1.0
NE2 A:GLN19 3.7 23.0 1.0
CG A:ARG106 3.8 16.2 1.0
CD A:ARG106 3.9 16.6 1.0
CE A:LYS15 4.0 19.9 1.0
CD A:LYS15 4.2 20.6 1.0
CE1 A:TYR104 4.2 13.2 1.0
CZ A:ARG106 4.4 18.2 1.0
CD1 A:TYR104 4.4 13.6 1.0
NE A:ARG106 4.6 16.8 1.0
O A:HOH330 4.6 20.1 1.0
CG A:LYS15 4.8 20.6 1.0
CD A:GLN19 4.9 23.3 1.0

Reference:

S.Hou, Y.Zhang, J.Xu, J.Bai, J.Liu, J.Xie, T.Xu. Residue ASN21 Acts As A Switch For Calcium Binding to Modulate the Enzymatic Activity of Human Phospholipase A2 Group Iie. Biochimie V. 176 117 2020.
ISSN: ISSN 0300-9084
PubMed: 32659444
DOI: 10.1016/J.BIOCHI.2020.07.003
Page generated: Sun Jul 28 02:33:18 2024

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