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Chlorine in PDB 5r99: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha, PDB code: 5r99 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) 29.57 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.841, 87.481, 125.653, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.6

Other elements in 5r99:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha (pdb code 5r99). 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 N13619A in Complex with Map Kinase P38-Alpha, PDB code: 5r99:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5r99

Go back to Chlorine Binding Sites List in 5r99
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:45.5
occ:1.00
 O A:HOH762 2.6 36.3 1.0
N A:ARG23 3.1 23.1 1.0
O A:HOH645 3.2 33.2 1.0
O A:HOH729 3.4 39.3 1.0
N A:GLU22 3.5 23.1 1.0
CB A:PRO6 3.6 35.9 1.0
CB A:ARG23 3.6 28.3 1.0
CB A:PRO21 3.7 25.7 1.0
CA A:ARG23 3.9 24.6 1.0
C A:GLU22 4.0 21.8 1.0
CG A:ARG23 4.0 24.2 1.0
CA A:GLU22 4.0 24.9 1.0
C A:PRO21 4.0 26.4 1.0
CB A:GLU22 4.0 22.1 1.0
CA A:PRO21 4.3 24.8 1.0
CD A:ARG23 4.3 30.1 1.0
O A:THR7 4.4 27.8 1.0
O A:HOH699 4.7 32.5 1.0
CA A:PRO6 4.7 33.1 1.0
CG A:PRO6 4.7 36.8 1.0
O A:PRO21 4.8 21.9 1.0
N A:THR7 4.9 27.4 1.0
CG A:GLU22 5.0 27.1 1.0

Chlorine binding site 2 out of 5 in 5r99

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Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:39.6
occ:1.00
 N A:ASN100 3.2 29.9 1.0
N A:ASP101 3.2 29.1 1.0
OG1 A:THR91 3.4 25.4 1.0
CB A:ALA93 3.7 30.4 1.0
O A:GLU98 3.7 35.2 1.0
N A:ALA93 3.8 28.5 1.0
CA A:ASN100 3.9 29.4 1.0
CG A:PRO92 3.9 32.5 1.0
CD A:PRO92 4.0 25.0 1.0
C A:ASN100 4.0 33.1 1.0
CB A:ASP101 4.0 30.7 1.0
CB A:ASN100 4.1 39.2 1.0
CA A:ASP101 4.1 28.5 1.0
C A:PHE99 4.1 39.8 1.0
CA A:ALA93 4.2 29.0 1.0
O A:ASP101 4.2 29.2 1.0
CA A:PHE99 4.2 30.3 1.0
OD2 A:ASP101 4.5 41.1 1.0
N A:PRO92 4.5 27.4 1.0
CG A:ASP101 4.6 42.8 1.0
C A:ASP101 4.7 21.1 1.0
C A:PRO92 4.7 33.6 1.0
OD1 A:ASN100 4.7 53.1 1.0
C A:GLU98 4.7 39.1 1.0
CD1 A:PHE99 4.7 28.5 1.0
CB A:THR91 4.8 26.2 1.0
CB A:PRO92 4.8 29.9 1.0
CG A:ASN100 4.9 52.5 1.0
CA A:PRO92 5.0 31.4 1.0
N A:PHE99 5.0 36.9 1.0

Chlorine binding site 3 out of 5 in 5r99

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Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:50.9
occ:1.00
 O A:HOH584 2.9 36.9 1.0
N A:GLY85 3.0 25.3 1.0
ND1 A:HIS107 3.1 40.3 1.0
NZ A:LYS165 3.1 31.0 0.6
OG1 A:THR106 3.6 26.2 1.0
CE1 A:HIS107 3.7 41.2 1.0
CA A:ILE84 3.8 24.4 1.0
CD A:LYS165 3.8 28.3 0.4
CE A:MET109 3.8 37.2 1.0
CD A:LYS165 3.8 28.4 0.6
CA A:GLY85 3.8 25.9 1.0
C A:ILE84 3.8 27.5 1.0
CE A:LYS165 3.9 32.5 0.6
O A:GLY85 3.9 24.4 1.0
O A:VAL83 3.9 23.6 1.0
CE A:LYS165 3.9 32.5 0.4
NZ A:LYS165 4.0 29.6 0.4
C A:GLY85 4.2 27.0 1.0
CG A:HIS107 4.3 33.8 1.0
CG1 A:ILE84 4.5 27.0 1.0
CB A:HIS107 4.7 29.4 1.0
C A:VAL83 4.7 20.8 1.0
N A:ILE84 4.7 20.6 1.0
CB A:ILE84 4.8 22.7 1.0
O A:HOH726 4.8 42.0 1.0
N A:HIS107 4.8 23.9 1.0
O A:HOH588 4.8 22.0 1.0
NE2 A:HIS107 4.9 37.8 1.0
O A:ILE84 5.0 25.1 1.0

Chlorine binding site 4 out of 5 in 5r99

Go back to Chlorine Binding Sites List in 5r99
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:33.4
occ:0.64
 N A:ASP324 2.9 25.1 1.0
O A:HOH577 3.1 41.7 1.0
CB A:ASP324 3.5 23.4 1.0
NH2 A:ARG73 3.5 25.6 1.0
CA A:TYR323 3.7 30.4 1.0
CA A:ASP324 3.8 25.5 1.0
C A:TYR323 3.8 28.7 1.0
O A:PRO322 3.8 26.7 1.0
CD1 A:TYR323 4.2 26.3 1.0
O A:ASP324 4.4 26.1 1.0
N A:TYR323 4.5 22.6 1.0
O A:HOH571 4.5 31.0 1.0
C A:ASP324 4.5 24.0 1.0
C A:PRO322 4.6 26.6 1.0
O A:HOH731 4.6 50.2 1.0
CE1 A:HIS77 4.6 29.6 1.0
ND1 A:HIS77 4.7 34.0 1.0
CZ A:ARG73 4.8 21.9 1.0
CB A:TYR323 4.8 25.1 1.0
CG A:TYR323 4.8 24.2 1.0
CE1 A:TYR323 4.9 25.2 1.0
CG A:ASP324 4.9 32.3 1.0

Chlorine binding site 5 out of 5 in 5r99

Go back to Chlorine Binding Sites List in 5r99
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:33.6
occ:1.00
 O A:HOH581 3.0 37.1 1.0
OG A:SER154 3.2 22.2 1.0
N A:SER154 3.2 23.1 1.0
CB A:SER154 3.5 23.9 1.0
O A:HOH696 3.5 39.8 1.0
CD A:PRO153 3.7 19.6 1.0
ND2 A:ASN114 3.8 38.4 1.0
N A:PRO153 3.8 20.2 1.0
CG A:LYS152 3.9 23.7 1.0
CA A:SER154 3.9 23.5 1.0
CB A:LYS152 4.0 24.9 1.0
CD A:LYS152 4.1 24.6 1.0
CB A:PRO153 4.2 27.6 1.0
C A:PRO153 4.2 22.4 1.0
CA A:PRO153 4.3 21.0 1.0
CG A:PRO153 4.4 20.8 1.0
CB A:ALA184 4.4 29.2 1.0
C A:LYS152 4.4 19.6 1.0
CE1 A:TYR188 4.5 17.5 1.0
CE A:LYS152 4.7 26.1 1.0
CG A:ASN114 4.7 44.0 1.0
OD1 A:ASN114 4.8 42.6 1.0
CA A:LYS152 4.8 20.9 1.0
OH A:TYR188 4.8 20.4 1.0
CZ A:TYR188 4.9 20.2 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 16:00:20 2024

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