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Chlorine in PDB 5r9v: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A 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 N13596A in Complex with Map Kinase P38-Alpha, PDB code: 5r9v 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) 29.34 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.842, 86.205, 127.628, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 19

Other elements in 5r9v:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A in Complex with Map Kinase P38-Alpha also contains other interesting chemical elements:

Fluorine (F) 3 atoms
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 N13596A in Complex with Map Kinase P38-Alpha (pdb code 5r9v). 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 N13596A in Complex with Map Kinase P38-Alpha, PDB code: 5r9v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5r9v

Go back to Chlorine Binding Sites List in 5r9v
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A 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 N13596A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:38.6
occ:1.00
 O A:HOH746 2.7 28.2 1.0
O A:HOH629 2.9 26.7 1.0
O A:HOH714 2.9 32.4 1.0
N A:ARG23 3.0 18.0 1.0
N A:GLU22 3.5 18.8 1.0
CB A:ARG23 3.6 23.9 1.0
CB A:PRO6 3.8 27.3 1.0
CB A:PRO21 3.8 17.6 1.0
CA A:ARG23 3.8 19.1 1.0
C A:GLU22 3.8 18.8 1.0
CA A:GLU22 3.9 17.7 1.0
CB A:GLU22 4.0 18.8 1.0
CG A:ARG23 4.0 23.5 1.0
C A:PRO21 4.1 18.0 1.0
CA A:PRO21 4.3 16.7 1.0
O A:THR7 4.4 21.5 1.0
CD A:ARG23 4.5 22.0 1.0
O A:PRO21 4.8 17.7 1.0
CA A:PRO6 4.8 24.6 1.0
O A:HOH668 4.8 28.0 1.0
CG A:GLU22 4.9 21.5 1.0
CG A:PRO6 4.9 30.2 1.0
OE1 A:GLU22 5.0 21.6 1.0
O A:GLU22 5.0 19.6 1.0

Chlorine binding site 2 out of 5 in 5r9v

Go back to Chlorine Binding Sites List in 5r9v
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A 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 N13596A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:35.3
occ:1.00
 N A:ASP101 3.2 24.6 1.0
N A:ASN100 3.2 25.4 1.0
OG1 A:THR91 3.4 21.8 1.0
CB A:ALA93 3.6 26.5 1.0
O A:GLU98 3.7 34.0 1.0
N A:ALA93 3.8 25.6 1.0
CB A:ASP101 3.8 26.5 1.0
CA A:ASN100 4.0 27.4 1.0
CA A:ASP101 4.0 24.8 1.0
C A:ASN100 4.0 24.9 1.0
CD A:PRO92 4.1 22.4 1.0
CB A:ASN100 4.1 33.6 1.0
CA A:ALA93 4.1 25.6 1.0
O A:ASP101 4.2 21.7 1.0
CG A:PRO92 4.2 27.4 1.0
C A:PHE99 4.2 28.3 1.0
CA A:PHE99 4.2 24.5 1.0
OD2 A:ASP101 4.4 33.0 1.0
CG A:ASP101 4.5 34.2 1.0
N A:PRO92 4.6 20.3 1.0
C A:ASP101 4.6 20.4 1.0
C A:GLU98 4.7 33.0 1.0
C A:PRO92 4.7 26.4 1.0
CB A:THR91 4.8 20.1 1.0
CD1 A:PHE99 4.8 23.5 1.0
ND2 A:ASN100 4.9 44.6 1.0
CB A:PRO92 4.9 24.9 1.0
N A:PHE99 5.0 28.1 1.0

Chlorine binding site 3 out of 5 in 5r9v

Go back to Chlorine Binding Sites List in 5r9v
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A 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 N13596A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:45.7
occ:1.00
 O A:HOH566 2.9 33.9 1.0
O A:HOH541 3.1 33.0 1.0
N A:GLY85 3.2 22.0 1.0
ND1 A:HIS107 3.6 35.2 1.0
CD A:LYS165 3.8 27.5 1.0
CE A:LYS165 3.9 32.5 1.0
CA A:ILE84 4.0 19.8 1.0
O A:VAL83 4.0 18.6 1.0
CA A:GLY85 4.0 24.9 1.0
NZ A:LYS165 4.0 35.4 1.0
C A:ILE84 4.0 22.5 1.0
CD1 A:ILE84 4.1 36.7 1.0
O A:GLY85 4.4 22.1 1.0
CE1 A:HIS107 4.4 34.1 1.0
C A:GLY85 4.6 20.1 1.0
CG A:HIS107 4.6 31.0 1.0
CG1 A:ILE84 4.7 26.4 1.0
CE A:MET109 4.7 52.7 1.0
CB A:HIS107 4.8 27.1 1.0
C A:VAL83 4.8 17.1 1.0
O A:HOH563 4.9 19.7 1.0
N A:ILE84 4.9 16.9 1.0
CB A:ILE84 5.0 23.0 1.0

Chlorine binding site 4 out of 5 in 5r9v

Go back to Chlorine Binding Sites List in 5r9v
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A 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 N13596A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:32.5
occ:1.00
 N A:ASP324 3.0 17.7 1.0
CB A:ASP324 3.6 19.3 1.0
NH2 A:ARG73 3.6 21.1 1.0
O A:PRO322 3.7 19.9 1.0
CA A:TYR323 3.8 17.6 1.0
C A:TYR323 3.8 18.7 1.0
CA A:ASP324 3.9 17.5 1.0
CD1 A:TYR323 4.3 19.8 1.0
C A:PRO322 4.4 17.6 1.0
O A:ASP324 4.5 20.1 1.0
O A:HOH734 4.5 23.5 1.0
O A:HOH530 4.5 25.8 1.0
O A:HOH722 4.5 35.5 1.0
N A:TYR323 4.5 18.4 1.0
C A:ASP324 4.7 18.7 1.0
NE2 A:HIS77 4.7 25.7 1.0
CZ A:ARG73 4.8 19.3 1.0
CD2 A:HIS77 4.8 17.4 1.0
CB A:TYR323 4.9 18.7 1.0
CE1 A:TYR323 5.0 24.4 1.0
CG A:TYR323 5.0 17.2 1.0

Chlorine binding site 5 out of 5 in 5r9v

Go back to Chlorine Binding Sites List in 5r9v
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13596A 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 N13596A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:30.0
occ:1.00
 O A:HOH631 2.9 28.6 1.0
ND2 A:ASN114 3.2 39.6 0.5
OG A:SER154 3.2 20.8 1.0
N A:SER154 3.3 18.5 1.0
CB A:SER154 3.5 20.2 1.0
CD A:PRO153 3.7 16.9 1.0
N A:PRO153 3.7 16.2 1.0
CG A:LYS152 3.9 19.4 1.0
CB A:LYS152 3.9 18.0 1.0
CD A:LYS152 4.0 19.3 1.0
CA A:SER154 4.0 19.3 1.0
CG A:ASN114 4.1 39.0 0.5
CB A:PRO153 4.2 18.4 1.0
C A:PRO153 4.2 17.8 1.0
CA A:PRO153 4.2 17.2 1.0
C A:LYS152 4.3 16.3 1.0
CB A:ALA184 4.3 20.0 1.0
OD1 A:ASN114 4.3 42.8 0.5
CG A:PRO153 4.4 17.7 1.0
CE1 A:TYR188 4.4 14.5 1.0
CA A:LYS152 4.7 16.8 1.0
CE A:LYS152 4.8 22.4 1.0
OH A:TYR188 4.9 16.8 1.0
CZ A:TYR188 4.9 13.7 1.0
O A:LYS152 5.0 17.0 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 16:10:55 2024

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