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Chlorine in PDB 5r8x: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11396A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11396A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11396A 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 N11396A in Complex with Map Kinase P38-Alpha, PDB code: 5r8x 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) 71.65 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.910, 86.614, 127.537, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 24.9

Other elements in 5r8x:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11396A 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 N11396A in Complex with Map Kinase P38-Alpha (pdb code 5r8x). 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 N11396A in Complex with Map Kinase P38-Alpha, PDB code: 5r8x:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5r8x

Go back to Chlorine Binding Sites List in 5r8x
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11396A 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 N11396A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:49.1
occ:1.00
 O A:HOH752 2.7 22.2 1.0
O A:HOH653 3.0 25.0 1.0
O A:HOH715 3.0 33.1 1.0
N A:ARG23 3.1 18.0 1.0
N A:GLU22 3.5 17.1 1.0
CB A:ARG23 3.7 20.3 1.0
CB A:PRO6 3.8 28.6 1.0
CB A:PRO21 3.8 16.4 1.0
CA A:ARG23 3.9 18.7 1.0
CB A:GLU22 3.9 18.2 1.0
C A:GLU22 3.9 16.6 1.0
CG A:ARG23 3.9 22.1 1.0
CA A:GLU22 4.0 18.0 1.0
C A:PRO21 4.1 17.5 1.0
CA A:PRO21 4.3 16.3 1.0
O A:THR7 4.4 21.2 1.0
CD A:ARG23 4.4 24.0 1.0
O A:HOH659 4.8 26.5 1.0
CA A:PRO6 4.8 25.0 1.0
CG A:GLU22 4.8 19.9 1.0
O A:PRO21 4.8 16.6 1.0
CG A:PRO6 4.9 26.9 1.0

Chlorine binding site 2 out of 5 in 5r8x

Go back to Chlorine Binding Sites List in 5r8x
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11396A 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 N11396A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:38.1
occ:1.00
 N A:ASP101 3.1 22.9 1.0
N A:ASN100 3.2 26.5 1.0
OG1 A:THR91 3.4 18.8 1.0
CB A:ASP101 3.7 28.9 1.0
O A:GLU98 3.7 30.7 1.0
CA A:ASN100 3.9 28.9 1.0
CB A:ALA93 3.9 24.0 1.0
CA A:ASP101 3.9 25.2 1.0
C A:ASN100 3.9 25.6 1.0
N A:ALA93 4.0 26.1 1.0
CB A:ASN100 4.0 33.0 1.0
CG A:PRO92 4.1 21.6 1.0
O A:ASP101 4.1 19.3 1.0
CD A:PRO92 4.1 19.3 1.0
C A:PHE99 4.2 27.8 1.0
CA A:PHE99 4.3 26.9 1.0
CA A:ALA93 4.4 25.5 1.0
CG A:ASP101 4.4 33.6 1.0
OD2 A:ASP101 4.4 34.3 1.0
C A:ASP101 4.5 20.0 1.0
N A:PRO92 4.6 18.9 1.0
C A:GLU98 4.7 33.6 1.0
C A:PRO92 4.8 25.9 1.0
CD1 A:PHE99 4.9 23.2 1.0
CB A:THR91 4.9 18.8 1.0
CB A:PRO92 4.9 19.9 1.0
N A:PHE99 5.0 28.4 1.0
CA A:PRO92 5.0 22.1 1.0

Chlorine binding site 3 out of 5 in 5r8x

Go back to Chlorine Binding Sites List in 5r8x
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11396A 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 N11396A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:45.8
occ:1.00
 O A:HOH506 2.9 30.6 1.0
O A:HOH561 3.1 32.7 1.0
N A:GLY85 3.3 19.0 1.0
CE A:LYS165 3.5 29.1 1.0
NZ A:LYS165 3.6 34.2 1.0
CD A:LYS165 3.7 26.5 1.0
ND1 A:HIS107 3.9 38.7 0.5
O A:VAL83 4.0 16.3 1.0
CA A:ILE84 4.1 19.4 1.0
CA A:GLY85 4.1 20.1 1.0
C A:ILE84 4.1 20.0 1.0
O A:GLY85 4.4 20.9 1.0
CB A:HIS107 4.6 34.6 0.5
CG A:HIS107 4.6 36.2 0.5
C A:GLY85 4.7 19.4 1.0
CE A:MET109 4.7 50.5 0.5
CD1 A:ILE84 4.7 33.0 1.0
CE1 A:HIS107 4.8 39.4 0.5
C A:VAL83 4.8 15.7 1.0
N A:ILE84 4.9 16.4 1.0
CG1 A:ILE84 4.9 28.1 1.0

Chlorine binding site 4 out of 5 in 5r8x

Go back to Chlorine Binding Sites List in 5r8x
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11396A 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 N11396A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:38.0
occ:1.00
 N A:ASP324 3.0 20.0 1.0
NH2 A:ARG73 3.6 19.5 1.0
CB A:ASP324 3.7 21.4 1.0
CA A:TYR323 3.7 19.2 1.0
O A:PRO322 3.8 19.3 1.0
C A:TYR323 3.8 21.4 1.0
CA A:ASP324 3.9 18.8 1.0
O A:HOH564 4.4 22.5 1.0
O A:HOH739 4.4 29.2 1.0
CD1 A:TYR323 4.4 19.8 1.0
C A:PRO322 4.5 18.8 1.0
N A:TYR323 4.5 18.8 1.0
O A:ASP324 4.5 19.6 1.0
CZ A:ARG73 4.7 17.6 1.0
C A:ASP324 4.8 17.7 1.0
CD2 A:HIS77 4.8 20.3 1.0
CB A:TYR323 4.9 19.0 1.0
NE2 A:HIS77 4.9 23.3 1.0
CG A:TYR323 4.9 20.0 1.0

Chlorine binding site 5 out of 5 in 5r8x

Go back to Chlorine Binding Sites List in 5r8x
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11396A 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 N11396A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:32.7
occ:1.00
 O A:HOH601 2.9 37.8 1.0
OG A:SER154 3.3 18.1 1.0
N A:SER154 3.3 16.7 1.0
ND2 A:ASN114 3.5 44.4 0.5
CD A:PRO153 3.6 16.2 1.0
CB A:SER154 3.6 18.6 1.0
N A:PRO153 3.8 16.0 1.0
CG A:LYS152 3.8 21.1 1.0
CB A:LYS152 4.0 18.7 1.0
CD A:LYS152 4.1 22.8 1.0
CA A:SER154 4.1 18.3 1.0
CB A:PRO153 4.2 16.5 1.0
CB A:ALA184 4.2 17.5 1.0
C A:PRO153 4.3 17.0 1.0
CA A:PRO153 4.3 15.3 1.0
CG A:PRO153 4.3 16.3 1.0
OD1 A:ASN114 4.3 47.8 0.5
C A:LYS152 4.4 16.2 1.0
CG A:ASN114 4.4 45.8 0.5
O A:HOH628 4.4 48.0 1.0
CE1 A:TYR188 4.4 12.6 1.0
CA A:LYS152 4.7 17.5 1.0
OH A:TYR188 4.7 15.8 1.0
CZ A:TYR188 4.9 13.3 1.0
CE A:LYS152 4.9 25.0 1.0
O A:HOH504 5.0 38.0 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 15:55:47 2024

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