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Chlorine in PDB 6sod: Fragment N14056A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Fragment N14056A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Fragment N14056A in Complex with Map Kinase P38-Alpha:
2.7.11.24;

Protein crystallography data

The structure of Fragment N14056A in Complex with Map Kinase P38-Alpha, PDB code: 6sod 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) 63.17 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.930, 85.310, 126.340, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 20.4

Other elements in 6sod:

The structure of Fragment N14056A 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 N14056A in Complex with Map Kinase P38-Alpha (pdb code 6sod). 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 N14056A in Complex with Map Kinase P38-Alpha, PDB code: 6sod:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6sod

Go back to Chlorine Binding Sites List in 6sod
Chlorine binding site 1 out of 7 in the Fragment N14056A 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 N14056A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:50.1
occ:1.00
 N A:ASP101 3.2 36.6 1.0
N A:ASN100 3.2 39.0 1.0
OG1 A:THR91 3.5 32.1 1.0
O A:GLU98 3.7 44.2 1.0
CB A:ALA93 3.7 38.2 1.0
CB A:ASP101 3.8 41.0 1.0
N A:ALA93 3.9 36.5 1.0
CA A:ASN100 3.9 39.9 1.0
C A:ASN100 4.0 43.7 1.0
CA A:ASP101 4.0 39.8 1.0
CD A:PRO92 4.0 31.1 1.0
CG A:PRO92 4.1 37.2 1.0
CB A:ASN100 4.2 43.3 1.0
O A:ASP101 4.2 35.1 1.0
C A:PHE99 4.2 42.2 1.0
CA A:ALA93 4.2 41.1 1.0
CA A:PHE99 4.2 40.1 1.0
OD2 A:ASP101 4.3 48.9 1.0
CG A:ASP101 4.4 47.2 1.0
C A:ASP101 4.6 32.5 1.0
N A:PRO92 4.6 29.9 1.0
C A:GLU98 4.7 46.9 1.0
C A:PRO92 4.7 38.6 1.0
CD1 A:PHE99 4.7 35.7 1.0
CB A:THR91 4.9 31.3 1.0
N A:PHE99 5.0 43.1 1.0

Chlorine binding site 2 out of 7 in 6sod

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Chlorine binding site 2 out of 7 in the Fragment N14056A 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 N14056A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:52.7
occ:1.00
 O A:HOH589 2.9 43.7 1.0
O A:HOH541 3.0 45.5 1.0
N A:GLY85 3.3 30.9 1.0
CE A:LYS165 3.5 44.2 1.0
ND1 A:HIS107 3.6 51.0 1.0
CD A:LYS165 3.8 41.3 1.0
CA A:ILE84 4.0 29.7 1.0
O A:VAL83 4.1 29.6 1.0
CA A:GLY85 4.1 32.4 1.0
C A:ILE84 4.1 29.4 1.0
NZ A:LYS165 4.2 44.0 1.0
O A:GLY85 4.3 33.0 1.0
CE1 A:HIS107 4.5 47.6 1.0
C A:GLY85 4.5 34.2 1.0
CG1 A:ILE84 4.6 33.6 1.0
CG A:HIS107 4.6 42.6 1.0
CB A:HIS107 4.7 40.9 1.0
CE A:MET109 4.8 53.1 1.0
O A:HOH572 4.9 28.3 1.0
C A:VAL83 4.9 24.6 1.0
CB A:ILE84 4.9 31.6 1.0
N A:ILE84 5.0 26.7 1.0

Chlorine binding site 3 out of 7 in 6sod

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Chlorine binding site 3 out of 7 in the Fragment N14056A 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 N14056A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:49.3
occ:1.00
 N A:ASP324 3.0 30.0 1.0
O A:HOH564 3.1 47.7 1.0
CB A:ASP324 3.5 28.5 1.0
NH2 A:ARG73 3.6 31.8 1.0
O A:PRO322 3.7 29.1 1.0
CA A:TYR323 3.8 29.4 1.0
CA A:ASP324 3.8 30.5 1.0
C A:TYR323 3.9 33.9 1.0
O A:HOH681 4.4 39.6 1.0
CD1 A:TYR323 4.4 30.6 1.0
O A:HOH542 4.4 35.7 1.0
C A:PRO322 4.5 29.9 1.0
O A:ASP324 4.5 31.9 1.0
N A:TYR323 4.5 26.5 1.0
O A:HOH676 4.5 46.0 1.0
C A:ASP324 4.7 27.6 1.0
CE1 A:HIS77 4.7 35.3 1.0
ND1 A:HIS77 4.7 35.9 1.0
CZ A:ARG73 4.8 31.9 1.0
CG A:ASP324 4.9 34.6 1.0
CB A:TYR323 4.9 27.4 1.0

Chlorine binding site 4 out of 7 in 6sod

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Chlorine binding site 4 out of 7 in the Fragment N14056A 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 N14056A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:42.7
occ:1.00
 O A:HOH606 3.0 40.1 1.0
OG A:SER154 3.2 30.8 1.0
N A:SER154 3.2 28.1 1.0
O A:HOH661 3.3 50.0 1.0
CB A:SER154 3.5 31.2 1.0
ND2 A:ASN114 3.5 45.8 1.0
CD A:PRO153 3.6 24.9 1.0
N A:PRO153 3.8 23.9 1.0
CA A:SER154 4.0 32.5 1.0
CB A:LYS152 4.0 26.8 1.0
CG A:LYS152 4.0 28.2 1.0
CD A:LYS152 4.1 32.5 1.0
CB A:PRO153 4.1 32.2 1.0
C A:PRO153 4.2 29.9 1.0
CA A:PRO153 4.3 26.9 1.0
CG A:PRO153 4.3 27.4 1.0
OD1 A:ASN114 4.3 52.0 1.0
C A:LYS152 4.3 24.0 1.0
CG A:ASN114 4.3 50.9 1.0
CB A:ALA184 4.4 36.1 1.0
CE1 A:TYR188 4.5 25.4 1.0
CE A:LYS152 4.8 36.9 1.0
CA A:LYS152 4.8 26.6 1.0
OH A:TYR188 4.9 26.5 1.0
CZ A:TYR188 5.0 24.6 1.0
O A:LYS152 5.0 25.9 1.0

Chlorine binding site 5 out of 7 in 6sod

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Chlorine binding site 5 out of 7 in the Fragment N14056A 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 N14056A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:67.0
occ:1.00
 O A:GLU163 3.8 37.6 1.0
CG A:LYS165 4.2 33.5 1.0
CE A:LYS165 4.3 44.2 1.0
ND2 A:ASN159 4.3 47.6 1.0
C A:GLU163 4.3 37.2 1.0
O A:HOH631 4.4 43.9 1.0
O A:ALA157 4.4 32.7 1.0
SD A:MET109 4.5 59.5 1.0
CB A:ASN159 4.5 44.8 1.0
CB A:LYS165 4.5 30.6 1.0
N A:LYS165 4.6 27.4 1.0
CG A:ASN159 4.6 47.6 1.0
CD A:LYS165 4.6 41.3 1.0
N A:ASN159 4.6 42.0 1.0
C A:LEU164 4.7 27.8 1.0
N A:LEU164 4.7 31.3 1.0
C A:ALA157 4.8 34.3 1.0
CA A:LEU164 4.8 29.4 1.0
NZ A:LYS165 4.8 44.0 1.0
CB A:GLU163 4.8 41.6 1.0
C A:VAL158 4.8 42.6 1.0
CA A:VAL158 4.9 38.8 1.0
CB A:ALA157 4.9 33.5 1.0
N A:VAL158 5.0 30.8 1.0

Chlorine binding site 6 out of 7 in 6sod

Go back to Chlorine Binding Sites List in 6sod
Chlorine binding site 6 out of 7 in the Fragment N14056A 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 N14056A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:35.0
occ:0.65
 N A:ASN269 3.0 27.3 1.0
CB A:ASN269 3.5 32.1 1.0
CB A:MET268 3.7 27.6 1.0
CA A:ASN269 3.8 28.4 1.0
CA A:MET268 3.9 26.3 1.0
C A:MET268 3.9 29.1 1.0
CE A:MET268 4.0 34.8 1.0
O A:ASN269 4.0 23.7 1.0
CG A:MET268 4.1 29.9 1.0
ND2 A:ASN272 4.4 48.9 1.0
C A:ASN269 4.4 27.7 1.0
CB A:ASN272 4.4 30.0 1.0
O A:HOH678 4.7 38.0 1.0
CG A:ASN269 4.9 37.1 1.0
SD A:MET268 4.9 33.8 1.0
CG A:ASN272 5.0 42.2 1.0

Chlorine binding site 7 out of 7 in 6sod

Go back to Chlorine Binding Sites List in 6sod
Chlorine binding site 7 out of 7 in the Fragment N14056A 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 N14056A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:77.0
occ:1.00
 OD1 A:ASN196 3.3 57.9 1.0
CA A:MET198 3.8 48.8 1.0
O A:ASN196 3.9 49.1 1.0
C A:MET198 3.9 53.1 1.0
N A:MET198 3.9 44.9 1.0
CG A:ASN196 4.1 55.8 1.0
N A:HIS199 4.3 53.9 1.0
O A:MET198 4.3 47.3 1.0
ND2 A:ASN196 4.3 58.6 1.0
CB A:SER251 4.3 61.8 1.0
C A:TRP197 4.4 49.0 1.0
OG A:SER251 4.4 60.8 1.0
O A:TRP197 4.5 44.2 1.0
C A:ASN196 4.6 43.5 1.0
O A:HOH611 4.8 55.2 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 15:03:31 2024

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