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Chlorine in PDB 6soi: Fragment N13788A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Fragment N13788A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Fragment N13788A in Complex with Map Kinase P38-Alpha:
2.7.11.24;

Protein crystallography data

The structure of Fragment N13788A in Complex with Map Kinase P38-Alpha, PDB code: 6soi 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) 70.98 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.865, 85.721, 126.613, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 23.4

Other elements in 6soi:

The structure of Fragment N13788A 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 N13788A in Complex with Map Kinase P38-Alpha (pdb code 6soi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Fragment N13788A in Complex with Map Kinase P38-Alpha, PDB code: 6soi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6soi

Go back to Chlorine Binding Sites List in 6soi
Chlorine binding site 1 out of 5 in the Fragment N13788A 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 N13788A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:35.7
occ:1.00
 N A:ASN100 3.3 30.1 1.0
N A:ASP101 3.3 26.0 1.0
OG1 A:THR91 3.4 23.6 1.0
O A:GLU98 3.6 35.4 1.0
CB A:ALA93 3.6 26.8 1.0
N A:ALA93 3.8 27.1 1.0
CA A:ASN100 3.9 33.0 1.0
CG A:PRO92 4.0 29.1 1.0
CB A:ASP101 4.0 28.6 1.0
CB A:ASN100 4.1 35.9 1.0
C A:ASN100 4.1 31.5 1.0
CA A:ALA93 4.1 28.5 1.0
CD A:PRO92 4.2 23.6 1.0
CA A:ASP101 4.2 28.0 1.0
C A:PHE99 4.2 33.8 1.0
O A:ASP101 4.2 24.1 1.0
CA A:PHE99 4.2 32.3 1.0
ND2 A:ASN100 4.4 45.2 1.0
N A:PRO92 4.6 23.9 1.0
OD2 A:ASP101 4.6 36.5 1.0
CG A:ASP101 4.6 36.4 1.0
C A:PRO92 4.6 29.0 1.0
C A:GLU98 4.6 37.5 1.0
C A:ASP101 4.7 20.9 1.0
CG A:ASN100 4.8 43.4 1.0
CD1 A:PHE99 4.8 25.4 1.0
CB A:THR91 4.9 24.6 1.0
CB A:PRO92 4.9 27.4 1.0
N A:PHE99 4.9 33.3 1.0
CA A:PRO92 5.0 26.1 1.0

Chlorine binding site 2 out of 5 in 6soi

Go back to Chlorine Binding Sites List in 6soi
Chlorine binding site 2 out of 5 in the Fragment N13788A 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 N13788A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:45.2
occ:1.00
 O A:HOH629 3.0 36.8 1.0
O A:HOH507 3.1 34.0 1.0
N A:GLY85 3.2 23.8 1.0
CD2 A:HIS107 3.6 36.0 1.0
CE A:LYS165 3.7 37.2 1.0
CD A:LYS165 3.8 29.7 1.0
O A:VAL83 4.0 20.4 1.0
CA A:GLY85 4.0 24.7 1.0
CD1 A:ILE84 4.0 37.3 1.0
CA A:ILE84 4.1 21.5 1.0
C A:ILE84 4.1 22.1 1.0
NZ A:LYS165 4.2 37.6 1.0
O A:GLY85 4.3 24.1 1.0
NE2 A:HIS107 4.5 37.3 1.0
CG A:HIS107 4.5 32.7 1.0
C A:GLY85 4.5 23.8 1.0
O A:HOH582 4.7 20.2 1.0
CG1 A:ILE84 4.8 26.5 1.0
CB A:HIS107 4.8 31.8 1.0
C A:VAL83 4.8 18.8 1.0
N A:ILE84 4.9 16.6 1.0

Chlorine binding site 3 out of 5 in 6soi

Go back to Chlorine Binding Sites List in 6soi
Chlorine binding site 3 out of 5 in the Fragment N13788A 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 N13788A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:25.4
occ:0.57
 O A:HOH580 2.9 31.4 1.0
N A:ASP324 3.1 19.5 1.0
NH2 A:ARG73 3.5 21.2 1.0
CB A:ASP324 3.6 20.0 1.0
O A:PRO322 3.8 21.2 1.0
CA A:TYR323 3.8 18.2 1.0
CA A:ASP324 3.9 23.6 1.0
C A:TYR323 3.9 22.5 1.0
CD1 A:TYR323 4.2 20.6 1.0
O A:ASP324 4.4 21.4 1.0
C A:PRO322 4.6 20.3 1.0
O A:HOH590 4.6 31.3 1.0
N A:TYR323 4.6 18.1 1.0
CZ A:ARG73 4.6 21.3 1.0
ND1 A:HIS77 4.7 24.9 1.0
C A:ASP324 4.7 19.7 1.0
CE1 A:HIS77 4.7 25.3 1.0
CE1 A:TYR323 4.8 21.6 1.0
CG A:TYR323 4.8 19.8 1.0
CB A:TYR323 4.9 20.8 1.0

Chlorine binding site 4 out of 5 in 6soi

Go back to Chlorine Binding Sites List in 6soi
Chlorine binding site 4 out of 5 in the Fragment N13788A 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 N13788A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:32.7
occ:1.00
 O A:HOH650 2.9 31.2 1.0
OG A:SER154 3.2 22.0 1.0
N A:SER154 3.3 20.5 1.0
CB A:SER154 3.6 21.7 1.0
O A:HOH706 3.6 38.8 1.0
ND2 A:ASN114 3.7 36.6 1.0
CD A:PRO153 3.8 17.1 1.0
N A:PRO153 3.8 16.3 1.0
CG A:LYS152 3.9 17.8 1.0
CB A:LYS152 3.9 18.7 1.0
CD A:LYS152 4.0 23.3 1.0
CA A:SER154 4.1 20.4 1.0
CB A:PRO153 4.2 19.4 1.0
C A:PRO153 4.2 20.0 1.0
CA A:PRO153 4.3 17.8 1.0
CB A:ALA184 4.3 22.8 1.0
C A:LYS152 4.4 17.4 1.0
CE1 A:TYR188 4.4 16.7 1.0
CG A:PRO153 4.5 20.2 1.0
CG A:ASN114 4.6 37.6 1.0
OD1 A:ASN114 4.7 42.1 1.0
CE A:LYS152 4.7 25.4 1.0
CA A:LYS152 4.8 16.2 1.0
OH A:TYR188 4.9 20.6 1.0
CZ A:TYR188 4.9 18.8 1.0

Chlorine binding site 5 out of 5 in 6soi

Go back to Chlorine Binding Sites List in 6soi
Chlorine binding site 5 out of 5 in the Fragment N13788A 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 N13788A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:49.1
occ:1.00
 N A:GLN264 3.2 27.8 1.0
CA A:ALA263 3.6 26.5 1.0
CB A:ALA263 3.8 29.3 1.0
C A:ALA263 3.9 25.0 1.0
CB A:GLN264 4.1 28.3 1.0
CA A:GLN264 4.2 25.1 1.0
CG A:GLN264 4.2 35.9 1.0
O A:GLN264 4.8 27.1 1.0
NE2 A:GLN264 4.8 37.7 1.0
N A:ALA263 4.8 27.1 1.0
O A:LEU262 4.9 28.4 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: Sat Jul 12 19:51:17 2025

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