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Chlorine in PDB 5r9x: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13611A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13611A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13611A 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 N13611A in Complex with Map Kinase P38-Alpha, PDB code: 5r9x 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) 29.88 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.077, 86.514, 127.258, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.2

Other elements in 5r9x:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13611A 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 N13611A in Complex with Map Kinase P38-Alpha (pdb code 5r9x). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13611A in Complex with Map Kinase P38-Alpha, PDB code: 5r9x:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5r9x

Go back to Chlorine Binding Sites List in 5r9x
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13611A 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 N13611A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:50.0
occ:1.00
 O A:HOH736 2.7 34.4 1.0
O A:HOH644 3.0 31.7 1.0
O A:HOH707 3.0 38.7 1.0
N A:ARG23 3.1 25.6 1.0
N A:GLU22 3.5 25.6 1.0
CB A:ARG23 3.6 28.6 1.0
CB A:PRO21 3.8 23.4 1.0
CB A:PRO6 3.8 34.6 1.0
CA A:ARG23 3.9 25.1 1.0
C A:GLU22 3.9 24.8 1.0
CB A:GLU22 3.9 25.1 1.0
CA A:GLU22 3.9 26.1 1.0
C A:PRO21 4.0 26.6 1.0
CG A:ARG23 4.0 28.5 1.0
CA A:PRO21 4.3 23.7 1.0
O A:THR7 4.4 29.3 1.0
CD A:ARG23 4.5 27.0 1.0
O A:PRO21 4.7 22.1 1.0
O A:HOH662 4.8 33.8 1.0
CG A:GLU22 4.8 27.5 1.0
CG A:PRO6 4.8 37.7 1.0
CA A:PRO6 4.8 31.0 1.0
N A:THR7 5.0 28.9 1.0

Chlorine binding site 2 out of 5 in 5r9x

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Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13611A 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 N13611A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:43.9
occ:1.00
 N A:ASP101 3.2 31.6 1.0
N A:ASN100 3.3 34.6 0.5
OG1 A:THR91 3.4 27.2 1.0
CB A:ALA93 3.7 30.0 1.0
O A:GLU98 3.7 38.4 1.0
CB A:ASP101 3.8 34.1 1.0
N A:ALA93 3.9 30.1 1.0
C A:ASN100 3.9 33.0 0.5
CA A:ASN100 4.0 35.0 0.5
CA A:ASP101 4.0 32.1 1.0
CD A:PRO92 4.1 26.3 1.0
O A:ASP101 4.1 29.8 1.0
CB A:ASN100 4.2 38.7 0.5
C A:PHE99 4.2 36.4 1.0
CG A:PRO92 4.2 29.6 1.0
CA A:ALA93 4.3 31.1 1.0
CA A:PHE99 4.3 34.7 1.0
CG A:ASP101 4.4 37.9 1.0
OD2 A:ASP101 4.4 38.4 1.0
C A:ASP101 4.6 27.8 1.0
N A:PRO92 4.6 26.1 1.0
C A:GLU98 4.7 39.9 1.0
C A:PRO92 4.7 34.5 1.0
ND2 A:ASN100 4.8 43.2 0.5
CD1 A:PHE99 4.8 30.6 1.0
CB A:THR91 4.8 25.9 1.0
CG A:ASN100 4.9 42.4 0.5
N A:PHE99 5.0 37.7 1.0

Chlorine binding site 3 out of 5 in 5r9x

Go back to Chlorine Binding Sites List in 5r9x
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13611A 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 N13611A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:53.5
occ:1.00
 O A:HOH507 2.9 39.5 1.0
O A:HOH524 3.2 41.0 1.0
N A:GLY85 3.3 26.4 1.0
CE A:LYS165 3.7 40.0 1.0
ND1 A:HIS107 3.7 45.1 1.0
NZ A:LYS165 3.8 44.4 1.0
CD A:LYS165 3.8 35.6 1.0
O A:VAL83 4.0 22.7 1.0
CD1 A:ILE84 4.0 45.6 1.0
CA A:GLY85 4.1 29.2 1.0
CA A:ILE84 4.1 25.0 1.0
C A:ILE84 4.1 26.7 1.0
O A:GLY85 4.4 26.4 1.0
CE1 A:HIS107 4.5 42.6 1.0
C A:GLY85 4.6 27.8 1.0
CG A:HIS107 4.7 37.2 1.0
CE A:MET109 4.8 61.5 1.0
CB A:HIS107 4.8 36.8 1.0
O A:HOH565 4.8 24.1 1.0
C A:VAL83 4.8 21.2 1.0
CG1 A:ILE84 4.9 33.6 1.0
N A:ILE84 4.9 22.4 1.0

Chlorine binding site 4 out of 5 in 5r9x

Go back to Chlorine Binding Sites List in 5r9x
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13611A 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 N13611A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:46.0
occ:1.00
 N A:ASP324 3.0 23.7 1.0
CB A:ASP324 3.6 25.1 1.0
NH2 A:ARG73 3.6 27.3 1.0
CA A:TYR323 3.7 24.9 1.0
O A:PRO322 3.8 24.0 1.0
C A:TYR323 3.8 26.9 1.0
CA A:ASP324 3.9 24.3 1.0
CD1 A:TYR323 4.3 26.5 1.0
O A:ASP324 4.4 26.0 1.0
C A:PRO322 4.5 23.1 1.0
N A:TYR323 4.5 23.7 1.0
C A:ASP324 4.7 23.5 1.0
NE2 A:HIS77 4.8 32.0 1.0
CD2 A:HIS77 4.8 23.5 1.0
CZ A:ARG73 4.8 26.7 1.0
CB A:TYR323 4.9 25.6 1.0
CG A:TYR323 4.9 25.8 1.0
CE1 A:TYR323 5.0 27.9 1.0

Chlorine binding site 5 out of 5 in 5r9x

Go back to Chlorine Binding Sites List in 5r9x
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13611A 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 N13611A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:38.0
occ:1.00
 O A:HOH631 2.9 34.9 1.0
OG A:SER154 3.3 24.4 1.0
N A:SER154 3.3 23.3 1.0
ND2 A:ASN114 3.5 49.9 0.5
CB A:SER154 3.6 25.8 1.0
CD A:PRO153 3.6 21.0 1.0
N A:PRO153 3.8 20.5 1.0
O A:HOH683 3.9 52.1 1.0
CG A:LYS152 3.9 22.6 1.0
CD A:LYS152 4.0 24.9 1.0
CB A:LYS152 4.0 21.5 1.0
CA A:SER154 4.1 25.7 1.0
CB A:PRO153 4.2 24.8 1.0
C A:PRO153 4.2 21.8 1.0
CA A:PRO153 4.3 20.8 1.0
C A:LYS152 4.3 22.2 1.0
CG A:PRO153 4.4 21.5 1.0
CB A:ALA184 4.4 27.2 1.0
CE1 A:TYR188 4.4 17.7 1.0
CG A:ASN114 4.5 51.1 0.5
OD1 A:ASN114 4.7 54.6 0.5
CA A:LYS152 4.7 21.0 1.0
CE A:LYS152 4.8 28.7 1.0
OH A:TYR188 4.9 23.5 1.0
CZ A:TYR188 4.9 20.5 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 16:11:19 2024

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