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Chlorine in PDB 5r9b: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A 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 N13866A in Complex with Map Kinase P38-Alpha, PDB code: 5r9b 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) 29.30 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.982, 85.900, 127.152, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 19.9

Other elements in 5r9b:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A 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 N13866A in Complex with Map Kinase P38-Alpha (pdb code 5r9b). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A in Complex with Map Kinase P38-Alpha, PDB code: 5r9b:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5r9b

Go back to Chlorine Binding Sites List in 5r9b
Chlorine binding site 1 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A 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 N13866A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:36.5
occ:0.74
 O A:HOH747 2.6 39.6 1.0
O A:HOH634 3.1 37.2 1.0
N A:ARG23 3.2 21.7 1.0
N A:GLU22 3.5 25.4 1.0
CB A:ARG23 3.6 28.6 1.0
CB A:PRO21 3.7 23.3 1.0
CB A:PRO6 3.7 38.2 1.0
CG A:ARG23 3.9 25.9 1.0
CA A:ARG23 3.9 23.3 1.0
C A:GLU22 4.0 23.2 1.0
C A:PRO21 4.1 24.5 1.0
CA A:GLU22 4.1 26.7 1.0
CD A:ARG23 4.1 26.6 1.0
CB A:GLU22 4.2 25.8 1.0
CA A:PRO21 4.3 23.4 1.0
O A:HOH698 4.4 36.1 1.0
O A:THR7 4.6 30.1 1.0
CG A:PRO6 4.8 36.6 1.0
O A:PRO21 4.8 23.1 1.0
CA A:PRO6 4.8 37.6 1.0

Chlorine binding site 2 out of 6 in 5r9b

Go back to Chlorine Binding Sites List in 5r9b
Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A 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 N13866A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:45.6
occ:1.00
 N A:ASP101 3.3 31.2 1.0
N A:ASN100 3.3 34.9 1.0
OG1 A:THR91 3.4 28.5 1.0
O A:GLU98 3.7 40.6 1.0
CB A:ALA93 3.7 31.8 1.0
N A:ALA93 3.8 31.1 1.0
CB A:ASP101 3.9 32.6 1.0
CD A:PRO92 4.0 28.2 1.0
CG A:PRO92 4.0 34.5 1.0
CA A:ASN100 4.1 37.8 1.0
CA A:ASP101 4.1 33.6 1.0
C A:ASN100 4.1 39.1 1.0
CA A:ALA93 4.1 35.6 1.0
O A:ASP101 4.2 30.2 1.0
C A:PHE99 4.2 41.5 1.0
CA A:PHE99 4.2 37.6 1.0
CB A:ASN100 4.4 47.6 1.0
CG A:ASP101 4.5 43.7 1.0
OD2 A:ASP101 4.5 41.8 1.0
N A:PRO92 4.6 27.2 1.0
C A:PRO92 4.6 34.5 1.0
C A:ASP101 4.7 27.9 1.0
C A:GLU98 4.7 42.3 1.0
CD1 A:PHE99 4.8 30.9 1.0
CB A:THR91 4.8 27.8 1.0
CB A:PRO92 4.9 30.2 1.0
N A:PHE99 5.0 40.6 1.0

Chlorine binding site 3 out of 6 in 5r9b

Go back to Chlorine Binding Sites List in 5r9b
Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A 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 N13866A 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:HOH586 2.9 37.8 1.0
O A:HOH519 3.0 35.7 1.0
N A:GLY85 3.2 27.7 1.0
ND1 A:HIS107 3.6 42.3 1.0
CE A:LYS165 3.7 38.5 1.0
CD A:LYS165 3.9 34.8 1.0
O A:VAL83 3.9 22.6 1.0
CA A:ILE84 4.0 25.4 1.0
CA A:GLY85 4.0 28.1 1.0
CD1 A:ILE84 4.1 39.7 1.0
C A:ILE84 4.1 26.3 1.0
NZ A:LYS165 4.2 42.1 1.0
O A:GLY85 4.3 27.5 1.0
CE1 A:HIS107 4.4 35.4 1.0
O A:HOH727 4.5 41.4 1.0
C A:GLY85 4.5 26.5 1.0
CG A:HIS107 4.6 36.9 1.0
O A:HOH571 4.7 25.1 1.0
C A:VAL83 4.8 22.3 1.0
CB A:HIS107 4.8 32.1 1.0
CG1 A:ILE84 4.8 32.1 1.0
N A:ILE84 4.9 22.6 1.0
CE A:MET109 5.0 45.4 1.0

Chlorine binding site 4 out of 6 in 5r9b

Go back to Chlorine Binding Sites List in 5r9b
Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A 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 N13866A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:30.1
occ:0.57
 O A:HOH626 2.8 38.0 1.0
N A:ASP324 3.0 23.1 1.0
CB A:ASP324 3.6 23.9 1.0
NH2 A:ARG73 3.6 24.1 1.0
O A:PRO322 3.7 24.3 1.0
CA A:TYR323 3.7 24.1 1.0
C A:TYR323 3.8 26.1 1.0
CA A:ASP324 3.8 23.9 1.0
CD1 A:TYR323 4.3 25.4 1.0
O A:HOH729 4.4 42.0 1.0
C A:PRO322 4.5 23.6 1.0
O A:HOH526 4.5 30.1 1.0
N A:TYR323 4.5 23.5 1.0
O A:ASP324 4.5 25.2 1.0
O A:HOH744 4.6 31.4 1.0
C A:ASP324 4.7 22.8 1.0
CE1 A:HIS77 4.7 29.8 1.0
CZ A:ARG73 4.8 23.9 1.0
ND1 A:HIS77 4.8 27.2 1.0
CB A:TYR323 4.8 22.5 1.0
CG A:TYR323 4.9 22.1 1.0
CE1 A:TYR323 5.0 27.4 1.0

Chlorine binding site 5 out of 6 in 5r9b

Go back to Chlorine Binding Sites List in 5r9b
Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A 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 N13866A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:33.8
occ:1.00
 O A:HOH658 2.9 38.1 1.0
OG A:SER154 3.2 25.3 1.0
O A:HOH705 3.3 42.9 1.0
N A:SER154 3.3 23.6 1.0
ND2 A:ASN114 3.5 39.6 1.0
CB A:SER154 3.6 25.3 1.0
CD A:PRO153 3.6 22.0 1.0
N A:PRO153 3.8 21.2 1.0
CG A:LYS152 4.0 22.1 1.0
CD A:LYS152 4.0 25.9 1.0
CB A:LYS152 4.0 22.0 1.0
CA A:SER154 4.0 24.3 1.0
CB A:PRO153 4.1 22.8 1.0
O A:HOH723 4.2 47.9 1.0
C A:PRO153 4.2 22.6 1.0
CA A:PRO153 4.3 21.2 1.0
CB A:ALA184 4.3 26.6 1.0
CG A:PRO153 4.4 21.0 1.0
C A:LYS152 4.4 20.8 1.0
CG A:ASN114 4.4 40.5 1.0
OD1 A:ASN114 4.4 49.6 1.0
CE1 A:TYR188 4.4 20.9 1.0
CE A:LYS152 4.7 27.7 1.0
CA A:LYS152 4.8 21.4 1.0
OH A:TYR188 4.9 23.4 1.0
CZ A:TYR188 5.0 24.6 1.0

Chlorine binding site 6 out of 6 in 5r9b

Go back to Chlorine Binding Sites List in 5r9b
Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A 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 6 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13866A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:49.9
occ:1.00
 O A:HOH724 2.7 45.5 1.0
N A:GLN264 3.1 26.8 1.0
CA A:ALA263 3.7 30.4 1.0
C A:ALA263 3.9 27.9 1.0
CB A:GLN264 4.0 31.7 1.0
CB A:ALA263 4.0 34.7 1.0
CG A:GLN264 4.1 35.4 1.0
CA A:GLN264 4.1 26.9 1.0
NE2 A:GLN264 4.6 37.3 1.0
O A:GLN264 4.7 28.5 1.0
CD A:GLN264 4.9 40.6 1.0
O A:LEU262 4.9 29.8 1.0
N A:ALA263 4.9 27.3 1.0
C A:GLN264 5.0 27.0 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 16:03:07 2024

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