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Chlorine in PDB 5r98: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A 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 N14109A in Complex with Map Kinase P38-Alpha, PDB code: 5r98 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) 29.26 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.846, 85.944, 127.136, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20

Other elements in 5r98:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A 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 N14109A in Complex with Map Kinase P38-Alpha (pdb code 5r98). 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 N14109A in Complex with Map Kinase P38-Alpha, PDB code: 5r98:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5r98

Go back to Chlorine Binding Sites List in 5r98
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A 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 N14109A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:43.9
occ:1.00
 O A:HOH777 2.6 33.4 1.0
O A:HOH622 3.0 30.2 1.0
O A:HOH736 3.0 36.9 1.0
N A:ARG23 3.1 21.4 1.0
N A:GLU22 3.4 22.2 1.0
CB A:ARG23 3.6 27.3 1.0
CB A:PRO21 3.7 21.3 1.0
CB A:PRO6 3.7 31.5 1.0
CA A:ARG23 3.9 22.9 1.0
C A:GLU22 3.9 20.5 1.0
CA A:GLU22 3.9 24.7 1.0
C A:PRO21 4.0 21.9 1.0
CB A:GLU22 4.0 20.6 1.0
CG A:ARG23 4.1 27.6 1.0
CA A:PRO21 4.3 18.7 1.0
O A:THR7 4.4 25.8 1.0
CD A:ARG23 4.4 23.8 1.0
O A:PRO21 4.7 18.6 1.0
O A:HOH686 4.8 32.0 1.0
CA A:PRO6 4.8 29.6 1.0
CG A:PRO6 4.8 30.9 1.0
N A:THR7 4.9 23.8 1.0
CG A:GLU22 4.9 23.7 1.0

Chlorine binding site 2 out of 5 in 5r98

Go back to Chlorine Binding Sites List in 5r98
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A 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 N14109A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:39.5
occ:1.00
 N A:ASP101 3.2 26.8 1.0
N A:ASN100 3.2 26.5 1.0
OG1 A:THR91 3.5 25.5 1.0
O A:GLU98 3.7 37.1 1.0
CB A:ALA93 3.7 25.7 1.0
N A:ALA93 3.8 28.8 1.0
CB A:ASP101 3.9 29.4 1.0
CA A:ASN100 3.9 29.8 1.0
C A:ASN100 4.0 32.2 1.0
CG A:PRO92 4.0 30.6 1.0
CA A:ASP101 4.0 27.4 1.0
CD A:PRO92 4.0 25.4 1.0
CB A:ASN100 4.1 37.5 1.0
CA A:ALA93 4.2 27.8 1.0
O A:ASP101 4.2 26.8 1.0
C A:PHE99 4.2 31.0 1.0
CA A:PHE99 4.3 28.4 1.0
CG A:ASP101 4.4 39.1 1.0
OD2 A:ASP101 4.5 35.3 1.0
N A:PRO92 4.6 24.1 1.0
C A:ASP101 4.6 24.6 1.0
C A:PRO92 4.7 28.9 1.0
C A:GLU98 4.7 37.6 1.0
ND2 A:ASN100 4.7 49.9 1.0
CD1 A:PHE99 4.8 26.6 1.0
CB A:THR91 4.9 25.1 1.0
CB A:PRO92 4.9 27.1 1.0
CG A:ASN100 4.9 48.3 1.0
N A:PHE99 5.0 34.5 1.0
CA A:PRO92 5.0 27.1 1.0

Chlorine binding site 3 out of 5 in 5r98

Go back to Chlorine Binding Sites List in 5r98
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A 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 N14109A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:45.9
occ:1.00
 O A:HOH518 2.9 36.0 1.0
O A:HOH511 3.1 33.1 1.0
N A:GLY85 3.2 25.4 1.0
CD2 A:HIS107 3.6 31.7 1.0
CE A:LYS165 3.7 36.9 1.0
CD1 A:ILE84 3.8 38.8 1.0
CD A:LYS165 3.9 29.4 1.0
O A:VAL83 4.0 21.8 1.0
CA A:GLY85 4.0 26.7 1.0
CA A:ILE84 4.0 23.5 1.0
NZ A:LYS165 4.0 43.2 1.0
C A:ILE84 4.1 24.2 1.0
O A:GLY85 4.3 25.4 1.0
C A:GLY85 4.5 26.0 1.0
CG A:HIS107 4.5 33.1 1.0
NE2 A:HIS107 4.6 38.2 1.0
O A:HOH552 4.7 23.3 1.0
CB A:HIS107 4.7 29.1 1.0
CG1 A:ILE84 4.7 29.5 1.0
C A:VAL83 4.8 20.0 1.0
N A:ILE84 4.9 18.8 1.0
CE A:MET109 4.9 41.7 1.0

Chlorine binding site 4 out of 5 in 5r98

Go back to Chlorine Binding Sites List in 5r98
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A 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 N14109A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:35.8
occ:0.72
 O A:HOH567 2.9 33.1 1.0
N A:ASP324 3.0 22.6 1.0
NH2 A:ARG73 3.6 24.7 1.0
CB A:ASP324 3.6 21.3 1.0
O A:PRO322 3.7 23.3 1.0
CA A:TYR323 3.8 20.6 1.0
C A:TYR323 3.9 24.1 1.0
CA A:ASP324 3.9 21.2 1.0
CD1 A:TYR323 4.3 24.5 1.0
O A:HOH751 4.4 39.9 1.0
O A:HOH551 4.5 27.9 1.0
C A:PRO322 4.5 21.8 1.0
O A:ASP324 4.5 22.6 1.0
N A:TYR323 4.6 21.7 1.0
O A:HOH761 4.6 28.4 1.0
CE1 A:HIS77 4.7 26.4 1.0
C A:ASP324 4.7 21.6 1.0
ND1 A:HIS77 4.7 25.7 1.0
CZ A:ARG73 4.7 22.1 1.0
CB A:TYR323 4.9 20.6 1.0
CG A:TYR323 4.9 21.2 1.0

Chlorine binding site 5 out of 5 in 5r98

Go back to Chlorine Binding Sites List in 5r98
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14109A 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 N14109A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:35.1
occ:1.00
 O A:HOH620 3.0 31.3 1.0
O A:HOH713 3.1 41.9 1.0
OG A:SER154 3.2 23.4 1.0
N A:SER154 3.3 22.1 1.0
CB A:SER154 3.5 25.1 1.0
ND2 A:ASN114 3.5 40.5 1.0
CD A:PRO153 3.7 19.1 1.0
N A:PRO153 3.8 19.1 1.0
CG A:LYS152 3.8 21.4 1.0
CB A:LYS152 3.9 20.3 1.0
CD A:LYS152 3.9 25.7 1.0
CA A:SER154 4.0 23.2 1.0
CB A:PRO153 4.2 23.0 1.0
C A:PRO153 4.2 20.2 1.0
CA A:PRO153 4.3 20.1 1.0
C A:LYS152 4.3 20.7 1.0
CG A:ASN114 4.4 44.0 1.0
CG A:PRO153 4.4 20.1 1.0
CB A:ALA184 4.4 25.3 1.0
CE1 A:TYR188 4.4 17.8 1.0
OD1 A:ASN114 4.5 53.5 1.0
CE A:LYS152 4.7 25.2 1.0
CA A:LYS152 4.7 19.7 1.0
OH A:TYR188 4.8 22.7 1.0
CZ A:TYR188 4.9 21.7 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 16:00:09 2024

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