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Chlorine in PDB 5r9m: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha:
2.7.11.24;

Protein crystallography data

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha, PDB code: 5r9m was solved by G.F.De Nicola, C.E.Nichols, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.25 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.989, 85.920, 126.719, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 19.9

Other elements in 5r9m:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A 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 Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha (pdb code 5r9m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha, PDB code: 5r9m:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5r9m

Go back to Chlorine Binding Sites List in 5r9m
Chlorine binding site 1 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A 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 Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:39.6
occ:0.66
 O A:HOH740 2.9 38.2 1.0
N A:ARG23 3.0 26.8 1.0
O A:HOH710 3.1 40.2 1.0
O A:HOH650 3.1 35.7 1.0
N A:GLU22 3.4 27.6 1.0
CB A:ARG23 3.6 31.1 1.0
CB A:PRO6 3.7 38.2 1.0
CB A:PRO21 3.7 26.5 1.0
CA A:ARG23 3.8 27.0 1.0
C A:GLU22 3.9 28.0 1.0
CG A:ARG23 3.9 29.4 1.0
CA A:GLU22 3.9 29.2 1.0
CB A:GLU22 3.9 26.3 1.0
C A:PRO21 4.0 28.5 1.0
CA A:PRO21 4.3 25.0 1.0
CD A:ARG23 4.3 29.8 1.0
O A:THR7 4.5 30.9 1.0
O A:HOH671 4.7 35.7 1.0
O A:PRO21 4.8 25.2 1.0
CA A:PRO6 4.8 36.4 1.0
CG A:PRO6 4.8 41.5 1.0
CG A:GLU22 4.8 31.2 1.0
N A:THR7 5.0 32.8 1.0
O A:GLU22 5.0 26.9 1.0

Chlorine binding site 2 out of 6 in 5r9m

Go back to Chlorine Binding Sites List in 5r9m
Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A 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 Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:43.6
occ:1.00
 N A:ASN100 3.2 37.0 1.0
N A:ASP101 3.2 32.6 1.0
OG1 A:THR91 3.3 28.8 1.0
CB A:ALA93 3.7 34.3 1.0
O A:GLU98 3.7 41.9 1.0
N A:ALA93 3.8 32.5 1.0
CB A:ASP101 3.9 38.1 1.0
CA A:ASN100 3.9 39.9 1.0
CG A:PRO92 4.0 34.3 1.0
C A:ASN100 4.0 39.1 1.0
CD A:PRO92 4.1 27.3 1.0
CA A:ASP101 4.1 34.9 1.0
CB A:ASN100 4.1 42.8 1.0
CA A:ALA93 4.1 35.3 1.0
O A:ASP101 4.2 30.1 1.0
C A:PHE99 4.2 41.8 1.0
CA A:PHE99 4.2 37.4 1.0
OD2 A:ASP101 4.5 43.1 1.0
CG A:ASP101 4.5 43.4 1.0
N A:PRO92 4.6 29.6 1.0
C A:ASP101 4.6 27.0 1.0
C A:PRO92 4.6 37.4 1.0
C A:GLU98 4.7 44.1 1.0
CD1 A:PHE99 4.7 31.7 1.0
ND2 A:ASN100 4.7 48.5 1.0
CB A:THR91 4.8 30.2 1.0
N A:PHE99 4.9 40.8 1.0
CG A:ASN100 5.0 49.7 1.0
CB A:PRO92 5.0 31.9 1.0
CA A:PRO92 5.0 31.3 1.0

Chlorine binding site 3 out of 6 in 5r9m

Go back to Chlorine Binding Sites List in 5r9m
Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A 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 Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:48.5
occ:1.00
 O A:HOH520 3.0 38.1 1.0
O A:HOH517 3.1 40.8 1.0
N A:GLY85 3.3 29.5 1.0
CE A:LYS165 3.6 41.1 1.0
ND1 A:HIS107 3.6 45.3 1.0
CD A:LYS165 3.7 36.9 1.0
NZ A:LYS165 3.9 43.4 1.0
CA A:ILE84 3.9 27.7 1.0
O A:VAL83 4.1 27.2 1.0
C A:ILE84 4.1 28.1 1.0
CA A:GLY85 4.2 31.7 1.0
O A:GLY85 4.3 28.3 1.0
CG1 A:ILE84 4.4 32.7 1.0
CE A:MET109 4.5 47.4 1.0
CE1 A:HIS107 4.5 44.3 1.0
CG A:HIS107 4.6 38.4 1.0
CB A:HIS107 4.6 36.5 1.0
C A:GLY85 4.6 29.0 1.0
CB A:ILE84 4.8 30.9 1.0
C A:VAL83 4.9 23.9 1.0
N A:ILE84 4.9 24.6 1.0
O A:HOH582 4.9 26.5 1.0

Chlorine binding site 4 out of 6 in 5r9m

Go back to Chlorine Binding Sites List in 5r9m
Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A 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 Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:33.9
occ:0.62
 O A:HOH544 3.0 42.8 1.0
N A:ASP324 3.2 28.8 1.0
NH2 A:ARG73 3.5 28.9 1.0
CB A:ASP324 3.8 28.8 1.0
O A:PRO322 3.8 28.9 1.0
CA A:TYR323 3.9 28.8 1.0
C A:TYR323 4.0 31.5 1.0
CA A:ASP324 4.1 29.2 1.0
CD1 A:TYR323 4.2 27.6 1.0
CE1 A:HIS77 4.5 31.9 1.0
O A:ASP324 4.6 29.3 1.0
ND1 A:HIS77 4.6 29.2 1.0
C A:PRO322 4.6 29.5 1.0
N A:TYR323 4.7 27.5 1.0
CZ A:ARG73 4.7 27.8 1.0
CE1 A:TYR323 4.8 29.2 1.0
C A:ASP324 4.8 26.4 1.0
CG A:TYR323 4.9 27.0 1.0
CB A:TYR323 4.9 25.8 1.0

Chlorine binding site 5 out of 6 in 5r9m

Go back to Chlorine Binding Sites List in 5r9m
Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A 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 Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:37.5
occ:1.00
 O A:HOH648 2.9 40.1 1.0
OG A:SER154 3.2 27.8 1.0
N A:SER154 3.3 25.1 1.0
CB A:SER154 3.6 27.9 1.0
CD A:PRO153 3.7 22.7 1.0
ND2 A:ASN114 3.8 40.4 1.0
N A:PRO153 3.8 22.6 1.0
O A:HOH692 3.9 46.7 1.0
CG A:LYS152 3.9 24.9 1.0
CB A:LYS152 4.0 24.2 1.0
CD A:LYS152 4.0 26.7 1.0
CA A:SER154 4.1 28.6 1.0
CB A:PRO153 4.2 29.2 1.0
C A:PRO153 4.3 24.8 1.0
CG A:PRO153 4.3 24.2 1.0
CA A:PRO153 4.3 23.6 1.0
C A:LYS152 4.4 23.2 1.0
CB A:ALA184 4.4 30.1 1.0
CE1 A:TYR188 4.5 22.3 1.0
CE A:LYS152 4.7 29.1 1.0
CG A:ASN114 4.7 45.7 1.0
CA A:LYS152 4.8 23.7 1.0
OD1 A:ASN114 4.8 47.8 1.0
OH A:TYR188 4.9 28.0 1.0
CZ A:TYR188 5.0 24.0 1.0
O A:HOH515 5.0 41.0 1.0

Chlorine binding site 6 out of 6 in 5r9m

Go back to Chlorine Binding Sites List in 5r9m
Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A 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 Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13418A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:49.4
occ:0.78
 N A:GLN264 3.1 32.4 1.0
CA A:ALA263 3.5 33.4 1.0
CB A:ALA263 3.8 35.0 1.0
C A:ALA263 3.8 35.2 1.0
CB A:GLN264 4.1 36.0 1.0
CG A:GLN264 4.1 40.8 1.0
CA A:GLN264 4.2 32.1 1.0
O A:GLN264 4.7 31.7 1.0
NE2 A:GLN264 4.8 43.5 1.0
N A:ALA263 4.8 30.6 1.0
O A:LEU262 4.9 34.0 1.0
C A:GLN264 5.0 32.7 1.0
CD A:GLN264 5.0 45.9 1.0

Reference:

C.Nichols, J.Ng, A.Keshu, G.Kelly, M.R.Conte, M.S.Marber, F.Fraternali, G.F.De Nicola. Mining the Pdb For Tractable Cases Where X-Ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated By IL1 Beta-IL1R and P38 Alpha-TAB1 Complexes. J.Med.Chem. V. 63 7559 2020.
ISSN: ISSN 0022-2623
PubMed: 32543856
DOI: 10.1021/ACS.JMEDCHEM.0C00403
Page generated: Fri Jul 26 16:07:07 2024

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