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Chlorine in PDB 6so4: Fragment RZ132 in Complex with Map Kinase P38-Alpha

Enzymatic activity of Fragment RZ132 in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Fragment RZ132 in Complex with Map Kinase P38-Alpha:
2.7.11.24;

Protein crystallography data

The structure of Fragment RZ132 in Complex with Map Kinase P38-Alpha, PDB code: 6so4 was solved by C.E.Nichols, G.F.De Nicola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.07 / 1.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.784, 86.323, 126.699, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 22.8

Other elements in 6so4:

The structure of Fragment RZ132 in Complex with Map Kinase P38-Alpha also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Fragment RZ132 in Complex with Map Kinase P38-Alpha (pdb code 6so4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Fragment RZ132 in Complex with Map Kinase P38-Alpha, PDB code: 6so4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6so4

Go back to Chlorine Binding Sites List in 6so4
Chlorine binding site 1 out of 6 in the Fragment RZ132 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Fragment RZ132 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:40.8
occ:1.00
 O A:HOH774 2.7 29.6 1.0
O A:HOH635 3.0 28.8 1.0
O A:HOH737 3.0 32.4 1.0
N A:ARG23 3.1 18.7 1.0
N A:GLU22 3.4 20.3 1.0
CB A:ARG23 3.6 24.1 1.0
CB A:PRO6 3.7 32.8 1.0
CB A:PRO21 3.7 18.8 1.0
CA A:ARG23 3.9 22.5 1.0
C A:GLU22 3.9 19.4 1.0
CA A:GLU22 4.0 22.0 1.0
CB A:GLU22 4.0 19.8 1.0
CG A:ARG23 4.0 22.6 1.0
C A:PRO21 4.0 20.0 1.0
CA A:PRO21 4.3 18.7 1.0
CD A:ARG23 4.4 22.1 1.0
O A:THR7 4.4 24.4 1.0
O A:HOH704 4.7 28.5 1.0
CA A:PRO6 4.7 28.9 1.0
CG A:PRO6 4.8 34.3 1.0
O A:PRO21 4.8 19.2 1.0
CG A:GLU22 4.9 22.8 1.0
N A:THR7 4.9 26.9 1.0

Chlorine binding site 2 out of 6 in 6so4

Go back to Chlorine Binding Sites List in 6so4
Chlorine binding site 2 out of 6 in the Fragment RZ132 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Fragment RZ132 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:37.6
occ:1.00
 N A:ASN100 3.2 26.0 1.0
N A:ASP101 3.2 24.8 1.0
OG1 A:THR91 3.4 24.1 1.0
O A:GLU98 3.6 36.2 1.0
CB A:ALA93 3.7 24.9 1.0
CA A:ASN100 3.9 27.2 1.0
N A:ALA93 3.9 26.2 1.0
CB A:ASP101 3.9 29.1 1.0
C A:ASN100 4.0 29.7 1.0
CB A:ASN100 4.0 33.0 1.0
CA A:ASP101 4.0 27.7 1.0
CG A:PRO92 4.1 26.7 1.0
CD A:PRO92 4.1 21.5 1.0
C A:PHE99 4.1 33.7 1.0
O A:ASP101 4.2 24.5 1.0
CA A:ALA93 4.2 27.6 1.0
CA A:PHE99 4.2 27.1 1.0
OD2 A:ASP101 4.5 36.0 1.0
CG A:ASP101 4.5 36.2 1.0
C A:ASP101 4.6 20.1 1.0
C A:GLU98 4.6 37.3 1.0
N A:PRO92 4.7 20.4 1.0
OD1 A:ASN100 4.7 48.0 1.0
C A:PRO92 4.7 28.1 1.0
CD1 A:PHE99 4.7 25.4 1.0
CG A:ASN100 4.8 44.0 1.0
CB A:THR91 4.8 21.3 1.0
N A:PHE99 4.9 30.7 1.0

Chlorine binding site 3 out of 6 in 6so4

Go back to Chlorine Binding Sites List in 6so4
Chlorine binding site 3 out of 6 in the Fragment RZ132 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Fragment RZ132 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:38.3
occ:0.68
 O A:HOH511 2.9 35.4 1.0
O A:HOH524 3.0 37.6 1.0
N A:GLY85 3.2 24.1 1.0
CE A:LYS165 3.6 32.2 1.0
CD2 A:HIS107 3.8 40.6 1.0
CD A:LYS165 3.8 28.4 1.0
NZ A:LYS165 3.9 35.1 1.0
O A:VAL83 4.0 19.6 1.0
CA A:GLY85 4.0 25.8 1.0
CA A:ILE84 4.1 21.5 1.0
C A:ILE84 4.1 21.6 1.0
O A:GLY85 4.3 23.1 1.0
O A:HOH747 4.4 42.4 1.0
C A:GLY85 4.5 22.8 1.0
CG A:HIS107 4.5 32.7 1.0
CB A:HIS107 4.7 28.1 1.0
O A:HOH605 4.7 20.6 1.0
CG1 A:ILE84 4.8 27.4 1.0
NE2 A:HIS107 4.8 38.2 1.0
C A:VAL83 4.8 17.7 1.0
N A:ILE84 4.9 18.4 1.0

Chlorine binding site 4 out of 6 in 6so4

Go back to Chlorine Binding Sites List in 6so4
Chlorine binding site 4 out of 6 in the Fragment RZ132 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Fragment RZ132 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:26.9
occ:0.60
 O A:HOH583 3.0 32.7 1.0
N A:ASP324 3.0 20.7 1.0
NH2 A:ARG73 3.5 20.2 1.0
CB A:ASP324 3.6 20.4 1.0
CA A:TYR323 3.7 18.7 1.0
O A:PRO322 3.8 21.6 1.0
C A:TYR323 3.9 25.1 1.0
CA A:ASP324 3.9 21.4 1.0
CD1 A:TYR323 4.2 22.1 1.0
O A:ASP324 4.5 20.6 1.0
O A:HOH545 4.5 31.1 1.0
N A:TYR323 4.5 19.5 1.0
C A:PRO322 4.6 19.7 1.0
CE1 A:HIS77 4.7 25.3 1.0
ND1 A:HIS77 4.7 24.0 1.0
C A:ASP324 4.7 19.2 1.0
CZ A:ARG73 4.7 20.9 1.0
CB A:TYR323 4.8 20.0 1.0
CG A:TYR323 4.8 19.0 1.0
CE1 A:TYR323 4.9 21.4 1.0

Chlorine binding site 5 out of 6 in 6so4

Go back to Chlorine Binding Sites List in 6so4
Chlorine binding site 5 out of 6 in the Fragment RZ132 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Fragment RZ132 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:28.0
occ:0.75
 O A:HOH607 3.0 31.0 1.0
OG A:SER154 3.2 20.1 1.0
N A:SER154 3.2 18.9 1.0
CB A:SER154 3.4 22.5 1.0
ND2 A:ASN114 3.6 40.3 1.0
CD A:PRO153 3.7 15.8 1.0
O A:HOH717 3.7 45.0 1.0
N A:PRO153 3.8 16.2 1.0
CG A:LYS152 3.8 20.4 1.0
CB A:LYS152 3.9 18.6 1.0
CA A:SER154 3.9 21.9 1.0
CD A:LYS152 4.0 23.1 1.0
CB A:PRO153 4.1 20.6 1.0
C A:PRO153 4.1 18.3 1.0
CA A:PRO153 4.2 18.0 1.0
C A:LYS152 4.3 17.8 1.0
OD1 A:ASN114 4.4 48.5 1.0
CG A:PRO153 4.4 15.6 1.0
CE1 A:TYR188 4.4 14.8 1.0
CB A:ALA184 4.4 22.5 1.0
CG A:ASN114 4.5 44.2 1.0
CA A:LYS152 4.7 17.6 1.0
CE A:LYS152 4.8 26.8 1.0
OH A:TYR188 4.8 18.2 1.0
CZ A:TYR188 4.9 17.5 1.0
O A:LYS152 5.0 18.6 1.0

Chlorine binding site 6 out of 6 in 6so4

Go back to Chlorine Binding Sites List in 6so4
Chlorine binding site 6 out of 6 in the Fragment RZ132 in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Fragment RZ132 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:39.2
occ:0.64
 N A:GLN264 3.1 26.2 1.0
CA A:ALA263 3.6 27.5 1.0
C A:ALA263 3.8 25.6 1.0
CB A:ALA263 3.8 28.6 1.0
CG A:GLN264 4.0 30.5 1.0
CB A:GLN264 4.0 27.9 1.0
CA A:GLN264 4.1 22.6 1.0
O A:GLN264 4.6 24.5 1.0
NE2 A:GLN264 4.6 34.0 1.0
CD A:GLN264 4.8 38.9 1.0
C A:GLN264 4.9 24.6 1.0
N A:ALA263 4.9 25.1 1.0
O A:LEU262 5.0 25.8 1.0

Reference:

G.F.De Nicola, C.E.Nichols. Targeting the P38 / TAB1 Interface By Single Fragment in-Crystal Screening and Structure-Based Drug Design. To Be Published.
Page generated: Mon Jul 29 15:03:26 2024

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