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Chlorine in PDB 5ra8: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B 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 N05711B in Complex with Map Kinase P38-Alpha, PDB code: 5ra8 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) 29.73 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.887, 86.638, 126.501, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21

Other elements in 5ra8:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B in Complex with Map Kinase P38-Alpha also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Fluorine (F) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B in Complex with Map Kinase P38-Alpha (pdb code 5ra8). 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 N05711B in Complex with Map Kinase P38-Alpha, PDB code: 5ra8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5ra8

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Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B 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 N05711B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:44.6
occ:1.00
 O A:HOH753 2.6 30.2 1.0
O A:HOH594 2.9 31.6 1.0
O A:HOH716 3.0 37.6 1.0
N A:ARG23 3.1 22.2 1.0
N A:GLU22 3.6 21.7 1.0
CB A:PRO6 3.7 34.7 1.0
CB A:ARG23 3.7 28.9 1.0
CB A:PRO21 3.8 22.5 1.0
CA A:ARG23 4.0 23.5 1.0
C A:GLU22 4.0 22.4 1.0
CG A:ARG23 4.0 26.3 1.0
CB A:GLU22 4.1 22.1 1.0
CA A:GLU22 4.1 21.9 1.0
C A:PRO21 4.1 23.1 1.0
CA A:PRO21 4.4 21.8 1.0
CD A:ARG23 4.5 28.0 1.0
O A:THR7 4.5 28.3 1.0
O A:HOH701 4.7 31.4 1.0
CA A:PRO6 4.7 32.1 1.0
CG A:PRO6 4.8 34.1 1.0
CG A:GLU22 4.8 24.8 1.0
N A:THR7 4.9 27.1 1.0
O A:PRO21 4.9 20.7 1.0
OE1 A:GLU22 5.0 24.8 1.0

Chlorine binding site 2 out of 5 in 5ra8

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Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B 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 N05711B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:47.6
occ:1.00
 N A:ASP101 3.2 29.9 1.0
N A:ASN100 3.3 31.9 1.0
OG1 A:THR91 3.4 27.7 1.0
CB A:ALA93 3.8 28.3 1.0
O A:GLU98 3.8 38.0 1.0
CB A:ASP101 3.9 31.3 1.0
CA A:ASN100 4.0 36.1 1.0
C A:ASN100 4.0 33.9 1.0
N A:ALA93 4.0 31.4 1.0
CA A:ASP101 4.0 29.0 1.0
CB A:ASN100 4.1 42.1 1.0
O A:ASP101 4.1 28.6 1.0
CD A:PRO92 4.1 27.2 1.0
CG A:PRO92 4.1 30.9 1.0
C A:PHE99 4.2 34.7 1.0
CA A:PHE99 4.3 32.1 1.0
CA A:ALA93 4.3 30.0 1.0
CG A:ASP101 4.4 37.7 1.0
OD2 A:ASP101 4.4 37.2 1.0
C A:ASP101 4.6 25.0 1.0
N A:PRO92 4.7 26.8 1.0
C A:GLU98 4.8 41.6 1.0
CB A:THR91 4.8 24.4 1.0
C A:PRO92 4.9 31.0 1.0
CD1 A:PHE99 4.9 26.7 1.0

Chlorine binding site 3 out of 5 in 5ra8

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Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B 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 N05711B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:76.5
occ:1.00
 O A:HOH509 2.9 43.5 1.0
O A:HOH518 3.0 42.7 1.0
ND1 A:HIS107 3.4 49.0 1.0
N A:GLY85 3.5 25.6 1.0
CE A:LYS165 3.5 41.6 1.0
CD A:LYS165 3.7 36.6 1.0
NZ A:LYS165 3.8 44.2 1.0
O A:VAL83 4.1 21.7 1.0
CE1 A:HIS107 4.2 43.2 1.0
CA A:GLY85 4.3 27.5 1.0
C A:ILE84 4.3 24.5 1.0
CD1 A:ILE84 4.3 38.3 1.0
CA A:ILE84 4.3 23.9 1.0
O A:GLY85 4.4 25.9 1.0
CG A:HIS107 4.4 40.9 1.0
CB A:HIS107 4.6 37.0 1.0
CE A:MET109 4.6 59.8 0.5
C A:GLY85 4.7 26.6 1.0
C A:VAL83 5.0 20.3 1.0
O A:HOH601 5.0 20.8 1.0

Chlorine binding site 4 out of 5 in 5ra8

Go back to Chlorine Binding Sites List in 5ra8
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B 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 N05711B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:43.4
occ:1.00
 O A:HOH705 2.9 38.0 1.0
N A:ASP324 3.0 24.4 1.0
NH2 A:ARG73 3.6 24.1 1.0
CB A:ASP324 3.6 24.9 1.0
O A:PRO322 3.8 24.6 1.0
CA A:TYR323 3.8 25.5 1.0
CA A:ASP324 3.9 24.6 1.0
C A:TYR323 3.9 27.3 1.0
O A:ASP324 4.3 25.5 1.0
CD1 A:TYR323 4.5 25.3 1.0
C A:PRO322 4.5 24.7 1.0
O A:HOH741 4.5 25.8 1.0
O A:HOH548 4.5 29.4 1.0
N A:TYR323 4.5 21.1 1.0
C A:ASP324 4.6 22.4 1.0
O A:HOH735 4.6 40.1 1.0
CD2 A:HIS77 4.7 26.6 1.0
CZ A:ARG73 4.8 21.4 1.0
NE2 A:HIS77 4.9 30.4 1.0
CB A:TYR323 4.9 24.6 1.0
CG A:ASP324 5.0 29.6 1.0

Chlorine binding site 5 out of 5 in 5ra8

Go back to Chlorine Binding Sites List in 5ra8
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N05711B 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 N05711B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:32.8
occ:1.00
 O A:HOH627 2.8 40.1 1.0
O A:HOH609 3.0 31.8 1.0
N A:SER154 3.2 20.8 1.0
OG A:SER154 3.2 22.4 1.0
CB A:SER154 3.6 22.6 1.0
CD A:PRO153 3.6 20.2 1.0
ND2 A:ASN114 3.7 48.0 0.5
N A:PRO153 3.8 18.3 1.0
CB A:LYS152 3.9 20.1 1.0
CG A:LYS152 3.9 20.2 1.0
CA A:SER154 4.0 22.9 1.0
CD A:LYS152 4.1 21.3 1.0
CB A:PRO153 4.1 19.9 1.0
C A:PRO153 4.2 19.4 1.0
CA A:PRO153 4.3 18.5 1.0
CB A:ALA184 4.3 26.0 1.0
C A:LYS152 4.3 19.3 1.0
CG A:PRO153 4.4 18.8 1.0
OD1 A:ASN114 4.4 52.7 0.5
CG A:ASN114 4.4 50.8 0.5
CE1 A:TYR188 4.4 18.2 1.0
CA A:LYS152 4.7 19.2 1.0
CE A:LYS152 4.8 25.8 1.0
OH A:TYR188 4.8 20.9 1.0
CZ A:TYR188 4.9 18.3 1.0
O A:LYS152 5.0 19.8 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 16:15:11 2024

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