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Chlorine in PDB 6so1: Fragment N13569A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Fragment N13569A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Fragment N13569A in Complex with Map Kinase P38-Alpha:
2.7.11.24;

Protein crystallography data

The structure of Fragment N13569A in Complex with Map Kinase P38-Alpha, PDB code: 6so1 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) 29.18 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.683, 85.883, 126.807, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 20.4

Other elements in 6so1:

The structure of Fragment N13569A 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 N13569A in Complex with Map Kinase P38-Alpha (pdb code 6so1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Fragment N13569A in Complex with Map Kinase P38-Alpha, PDB code: 6so1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6so1

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Chlorine binding site 1 out of 7 in the Fragment N13569A 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 N13569A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:44.4
occ:1.00
 O A:HOH766 2.8 29.9 1.0
O A:HOH722 2.9 34.7 1.0
O A:HOH640 2.9 30.7 1.0
N A:ARG23 3.0 23.0 1.0
N A:GLU22 3.4 23.1 1.0
CB A:ARG23 3.6 29.7 1.0
CB A:PRO21 3.8 21.9 1.0
CA A:ARG23 3.8 25.5 1.0
C A:GLU22 3.8 23.9 1.0
CB A:PRO6 3.8 34.7 1.0
CA A:GLU22 3.8 24.1 1.0
CB A:GLU22 3.9 23.5 1.0
C A:PRO21 3.9 23.0 1.0
CG A:ARG23 4.0 26.8 1.0
CA A:PRO21 4.3 20.7 1.0
O A:THR7 4.4 27.9 1.0
CD A:ARG23 4.4 25.7 1.0
O A:PRO21 4.7 21.9 1.0
CG A:GLU22 4.7 26.6 1.0
CA A:PRO6 4.8 33.0 1.0
O A:HOH664 4.9 34.0 1.0
OE1 A:GLU22 4.9 26.7 1.0
N A:THR7 4.9 28.6 1.0
O A:GLU22 4.9 23.7 1.0
CG A:PRO6 4.9 34.3 1.0

Chlorine binding site 2 out of 7 in 6so1

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Chlorine binding site 2 out of 7 in the Fragment N13569A 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 N13569A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:40.8
occ:1.00
 N A:ASN100 3.1 31.9 1.0
N A:ASP101 3.1 29.8 1.0
OG1 A:THR91 3.4 27.4 1.0
O A:GLU98 3.6 37.2 1.0
CB A:ALA93 3.7 29.5 1.0
CA A:ASN100 3.8 34.4 1.0
N A:ALA93 3.8 29.5 1.0
CB A:ASP101 3.9 30.1 1.0
C A:ASN100 3.9 33.4 1.0
CB A:ASN100 3.9 40.0 1.0
CA A:ASP101 4.0 29.7 1.0
CG A:PRO92 4.0 29.5 1.0
C A:PHE99 4.1 34.3 1.0
CD A:PRO92 4.1 26.0 1.0
O A:ASP101 4.2 26.8 1.0
CA A:ALA93 4.2 30.2 1.0
CA A:PHE99 4.2 30.6 1.0
OD2 A:ASP101 4.4 37.9 1.0
CG A:ASP101 4.4 37.4 1.0
C A:GLU98 4.6 38.0 1.0
C A:ASP101 4.6 24.6 1.0
N A:PRO92 4.6 24.8 1.0
CD1 A:PHE99 4.7 27.6 1.0
C A:PRO92 4.7 33.0 1.0
CB A:THR91 4.8 24.9 1.0
N A:PHE99 4.9 34.9 1.0
CG A:ASN100 5.0 44.8 1.0
CB A:PRO92 5.0 28.0 1.0
OD1 A:ASN100 5.0 47.9 1.0

Chlorine binding site 3 out of 7 in 6so1

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Chlorine binding site 3 out of 7 in the Fragment N13569A 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 N13569A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:42.4
occ:0.77
 O A:HOH510 2.9 34.2 1.0
O A:HOH541 3.0 36.7 1.0
N A:GLY85 3.2 26.3 1.0
CE A:LYS165 3.6 36.2 1.0
ND1 A:HIS107 3.7 41.1 1.0
CD A:LYS165 3.8 33.1 1.0
CD1 A:ILE84 3.8 39.2 1.0
NZ A:LYS165 3.9 38.5 1.0
CA A:GLY85 4.0 26.8 1.0
O A:VAL83 4.0 21.8 1.0
CA A:ILE84 4.1 24.4 1.0
C A:ILE84 4.1 24.3 1.0
O A:GLY85 4.3 25.9 1.0
O A:HOH739 4.4 38.6 1.0
C A:GLY85 4.5 24.4 1.0
CE1 A:HIS107 4.5 38.2 1.0
CG A:HIS107 4.7 36.6 1.0
CB A:HIS107 4.8 33.1 1.0
CE A:MET109 4.8 43.9 1.0
CG1 A:ILE84 4.8 29.9 1.0
O A:HOH578 4.8 23.8 1.0
C A:VAL83 4.9 21.4 1.0
N A:ILE84 4.9 20.8 1.0

Chlorine binding site 4 out of 7 in 6so1

Go back to Chlorine Binding Sites List in 6so1
Chlorine binding site 4 out of 7 in the Fragment N13569A 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 N13569A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:32.4
occ:0.57
 O A:HOH621 2.8 34.8 1.0
N A:ASP324 3.0 22.2 1.0
NH2 A:ARG73 3.6 25.5 1.0
CB A:ASP324 3.6 21.5 1.0
O A:PRO322 3.7 24.3 1.0
CA A:TYR323 3.7 22.9 1.0
C A:TYR323 3.9 24.6 1.0
CA A:ASP324 3.9 23.0 1.0
CD1 A:TYR323 4.3 22.8 1.0
O A:HOH521 4.4 28.2 1.0
O A:HOH742 4.4 36.5 1.0
C A:PRO322 4.4 22.1 1.0
N A:TYR323 4.5 23.0 1.0
O A:HOH756 4.5 29.8 1.0
O A:ASP324 4.6 25.3 1.0
CE1 A:HIS77 4.6 25.8 1.0
ND1 A:HIS77 4.7 23.4 1.0
C A:ASP324 4.8 25.2 1.0
CZ A:ARG73 4.8 25.1 1.0
CB A:TYR323 4.8 21.4 1.0
CG A:TYR323 4.9 22.0 1.0
CE1 A:TYR323 5.0 25.8 1.0

Chlorine binding site 5 out of 7 in 6so1

Go back to Chlorine Binding Sites List in 6so1
Chlorine binding site 5 out of 7 in the Fragment N13569A 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 N13569A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:32.9
occ:0.76
 O A:HOH627 2.9 33.4 1.0
O A:HOH656 3.0 39.1 1.0
N A:SER154 3.2 22.5 1.0
OG A:SER154 3.3 25.3 1.0
ND2 A:ASN114 3.5 36.7 1.0
CD A:PRO153 3.5 20.9 1.0
CB A:SER154 3.6 26.6 1.0
N A:PRO153 3.7 20.1 1.0
CB A:LYS152 3.9 22.8 1.0
CG A:LYS152 3.9 23.5 1.0
CA A:SER154 4.0 24.9 1.0
CD A:LYS152 4.0 26.8 1.0
C A:PRO153 4.1 22.3 1.0
CB A:PRO153 4.1 24.8 1.0
CA A:PRO153 4.2 19.4 1.0
C A:LYS152 4.2 21.3 1.0
CG A:PRO153 4.3 21.5 1.0
CB A:ALA184 4.4 25.6 1.0
CE1 A:TYR188 4.4 17.1 1.0
CG A:ASN114 4.5 41.5 1.0
OD1 A:ASN114 4.6 45.5 1.0
CA A:LYS152 4.6 22.4 1.0
OH A:TYR188 4.8 22.1 1.0
CE A:LYS152 4.8 28.7 1.0
CZ A:TYR188 4.9 19.7 1.0
O A:LYS152 4.9 21.7 1.0

Chlorine binding site 6 out of 7 in 6so1

Go back to Chlorine Binding Sites List in 6so1
Chlorine binding site 6 out of 7 in the Fragment N13569A 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 N13569A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:39.3
occ:0.73
 N A:TYR323 3.2 23.0 1.0
O A:ALA144 3.5 25.5 1.0
O A:TYR323 3.7 26.3 1.0
C A:ALA144 3.7 25.8 1.0
CA A:PRO322 3.8 21.7 1.0
O A:HOH524 3.8 30.3 1.0
CA A:ALA144 3.9 24.6 1.0
C A:PRO322 4.0 22.1 1.0
CA A:TYR323 4.1 22.9 1.0
C A:TYR323 4.3 24.6 1.0
CB A:PRO322 4.3 26.9 1.0
O A:SER143 4.4 28.4 1.0
CB A:TYR323 4.4 21.4 1.0
N A:ASP145 4.5 23.6 1.0
OD2 A:ASP145 4.5 41.9 1.0
CB A:ASP145 4.5 28.4 1.0
CB A:ALA144 4.7 28.1 1.0
CG A:ASP145 4.7 39.4 1.0
O A:HOH735 4.8 35.5 1.0
N A:ALA144 5.0 22.5 1.0

Chlorine binding site 7 out of 7 in 6so1

Go back to Chlorine Binding Sites List in 6so1
Chlorine binding site 7 out of 7 in the Fragment N13569A 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 7 of Fragment N13569A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:39.0
occ:0.65
 N A:ASN269 2.9 19.7 1.0
CB A:ASN269 3.6 18.7 1.0
CB A:MET268 3.7 21.1 1.0
CA A:MET268 3.7 18.4 1.0
CA A:ASN269 3.8 19.5 1.0
C A:MET268 3.8 19.1 1.0
CE A:MET268 4.0 30.8 1.0
CG A:MET268 4.0 21.6 1.0
O A:ASN269 4.1 20.3 1.0
C A:ASN269 4.4 21.1 1.0
ND2 A:ASN272 4.8 22.0 1.0
CB A:ASN272 4.8 22.6 1.0
O A:HOH740 4.8 31.2 1.0
SD A:MET268 4.9 27.8 1.0
CG A:ASN269 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: Sat Jul 12 19:50:02 2025

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