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Chlorine in PDB 5ra1: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08141B in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08141B in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08141B 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 N08141B in Complex with Map Kinase P38-Alpha, PDB code: 5ra1 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) 51.20 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.890, 86.580, 126.770, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.3

Other elements in 5ra1:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08141B 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 N08141B in Complex with Map Kinase P38-Alpha (pdb code 5ra1). 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 N08141B in Complex with Map Kinase P38-Alpha, PDB code: 5ra1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5ra1

Go back to Chlorine Binding Sites List in 5ra1
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08141B 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 N08141B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:43.3
occ:1.00
 O A:HOH745 2.7 31.4 1.0
O A:HOH623 2.9 28.1 1.0
O A:HOH712 2.9 31.4 1.0
N A:ARG23 3.0 21.3 1.0
N A:GLU22 3.5 20.5 1.0
CB A:ARG23 3.7 23.8 1.0
CB A:PRO6 3.7 31.3 1.0
CB A:PRO21 3.8 18.6 1.0
C A:GLU22 3.9 20.4 1.0
CA A:ARG23 3.9 21.5 1.0
CB A:GLU22 3.9 20.5 1.0
CA A:GLU22 4.0 20.5 1.0
C A:PRO21 4.0 20.1 1.0
CG A:ARG23 4.0 21.7 1.0
CA A:PRO21 4.3 19.6 1.0
O A:THR7 4.4 25.7 1.0
CD A:ARG23 4.5 23.6 1.0
O A:HOH666 4.7 29.8 1.0
O A:PRO21 4.7 18.7 1.0
CA A:PRO6 4.8 28.2 1.0
CG A:GLU22 4.8 24.1 1.0
CG A:PRO6 4.8 32.1 1.0
N A:THR7 4.9 25.4 1.0
OE1 A:GLU22 5.0 24.9 1.0

Chlorine binding site 2 out of 5 in 5ra1

Go back to Chlorine Binding Sites List in 5ra1
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08141B 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 N08141B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:42.6
occ:1.00
 N A:ASP101 3.2 28.5 1.0
N A:ASN100 3.3 29.7 1.0
OG1 A:THR91 3.3 24.3 1.0
CB A:ALA93 3.7 24.0 1.0
O A:GLU98 3.8 33.6 1.0
N A:ALA93 3.8 25.0 1.0
CB A:ASP101 3.9 27.5 1.0
CA A:ASN100 4.0 33.7 1.0
CA A:ASP101 4.0 26.9 1.0
C A:ASN100 4.0 32.5 1.0
O A:ASP101 4.1 25.7 1.0
CD A:PRO92 4.1 24.7 1.0
CG A:PRO92 4.2 27.2 1.0
CB A:ASN100 4.2 37.0 1.0
C A:PHE99 4.2 32.6 1.0
CA A:ALA93 4.2 26.0 1.0
CA A:PHE99 4.2 28.2 1.0
OD2 A:ASP101 4.4 38.2 1.0
CG A:ASP101 4.4 36.2 1.0
C A:ASP101 4.5 24.0 1.0
N A:PRO92 4.6 24.1 1.0
C A:PRO92 4.7 25.7 1.0
C A:GLU98 4.7 35.4 1.0
CB A:THR91 4.8 24.1 1.0
CD1 A:PHE99 4.8 21.8 1.0
ND2 A:ASN100 5.0 45.1 1.0
N A:PHE99 5.0 31.2 1.0
CB A:PRO92 5.0 24.5 1.0

Chlorine binding site 3 out of 5 in 5ra1

Go back to Chlorine Binding Sites List in 5ra1
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08141B 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 N08141B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:66.1
occ:1.00
 O A:HOH521 2.9 41.8 1.0
N A:GLY85 3.2 22.4 1.0
ND1 A:HIS107 3.5 40.0 1.0
CE A:LYS165 3.6 38.9 1.0
CD A:LYS165 3.6 32.0 1.0
NZ A:LYS165 3.9 42.9 1.0
O A:VAL83 4.0 19.1 1.0
C A:ILE84 4.1 22.4 0.5
CA A:GLY85 4.1 24.6 1.0
CA A:ILE84 4.2 21.5 0.5
O A:GLY85 4.3 23.5 1.0
CE1 A:HIS107 4.4 36.5 1.0
OG1 A:THR106 4.4 31.2 0.5
CE A:MET109 4.5 62.3 1.0
CG A:HIS107 4.5 32.6 1.0
CB A:HIS107 4.6 30.8 1.0
C A:GLY85 4.6 23.0 1.0
C A:VAL83 4.8 18.8 1.0
N A:ILE84 4.9 20.4 0.5
O A:HOH573 4.9 21.6 1.0

Chlorine binding site 4 out of 5 in 5ra1

Go back to Chlorine Binding Sites List in 5ra1
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08141B 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 N08141B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:39.7
occ:1.00
 N A:ASP324 3.0 20.4 1.0
CB A:ASP324 3.6 21.4 1.0
NH2 A:ARG73 3.6 22.7 1.0
O A:PRO322 3.6 22.3 1.0
CA A:TYR323 3.8 19.1 1.0
CA A:ASP324 3.8 21.0 1.0
C A:TYR323 3.9 22.7 1.0
O A:ASP324 4.3 22.6 1.0
C A:PRO322 4.4 20.7 1.0
O A:HOH736 4.4 24.9 1.0
O A:HOH517 4.5 26.2 1.0
O A:HOH727 4.5 34.5 1.0
N A:TYR323 4.5 19.0 1.0
CD1 A:TYR323 4.5 20.9 1.0
C A:ASP324 4.6 19.6 1.0
CD2 A:HIS77 4.8 22.2 1.0
CZ A:ARG73 4.8 20.5 1.0
NE2 A:HIS77 4.9 29.2 1.0
CB A:TYR323 4.9 19.9 1.0
CG A:ASP324 5.0 25.5 1.0

Chlorine binding site 5 out of 5 in 5ra1

Go back to Chlorine Binding Sites List in 5ra1
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08141B 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 N08141B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:31.6
occ:1.00
 O A:HOH551 3.0 30.0 1.0
OG A:SER154 3.3 22.3 1.0
N A:SER154 3.3 18.0 1.0
CB A:SER154 3.6 18.4 1.0
ND2 A:ASN114 3.6 42.8 0.5
CD A:PRO153 3.7 18.2 1.0
N A:PRO153 3.8 16.2 1.0
CG A:LYS152 3.9 19.6 1.0
CB A:LYS152 4.0 18.5 1.0
CA A:SER154 4.0 19.6 1.0
CD A:LYS152 4.0 20.6 1.0
CB A:PRO153 4.2 19.6 1.0
C A:PRO153 4.2 18.1 1.0
CA A:PRO153 4.3 17.7 1.0
CB A:ALA184 4.3 21.2 1.0
C A:LYS152 4.3 17.3 1.0
CE1 A:TYR188 4.5 17.0 1.0
CG A:PRO153 4.5 18.7 1.0
OD1 A:ASN114 4.5 45.0 0.5
CG A:ASN114 4.5 45.4 0.5
CA A:LYS152 4.7 17.2 1.0
CE A:LYS152 4.8 24.4 1.0
OH A:TYR188 4.8 18.3 1.0
CZ A:TYR188 4.9 17.2 1.0
O A:HOH503 5.0 41.4 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 16:11:41 2024

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