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Chlorine in PDB 5r9a: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A 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 N13838A in Complex with Map Kinase P38-Alpha, PDB code: 5r9a 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) 33.94 / 1.53
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.600, 86.390, 125.640, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 20.8

Other elements in 5r9a:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A 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 N13838A in Complex with Map Kinase P38-Alpha (pdb code 5r9a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha, PDB code: 5r9a:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5r9a

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Chlorine binding site 1 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A 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 N13838A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:41.4
occ:1.00
 O A:HOH761 2.7 34.1 1.0
O A:HOH609 2.9 30.8 1.0
O A:HOH723 3.1 34.1 1.0
N A:ARG23 3.1 19.9 1.0
N A:GLU22 3.4 21.5 1.0
CB A:ARG23 3.6 24.6 1.0
CB A:PRO21 3.7 21.2 1.0
CB A:PRO6 3.7 31.4 1.0
CA A:ARG23 3.9 20.7 1.0
C A:GLU22 3.9 19.2 1.0
CA A:GLU22 3.9 22.0 1.0
CB A:GLU22 3.9 20.5 1.0
C A:PRO21 4.0 22.4 1.0
CG A:ARG23 4.0 24.2 1.0
CA A:PRO21 4.2 19.4 1.0
O A:THR7 4.4 25.9 1.0
CD A:ARG23 4.4 25.9 1.0
O A:HOH698 4.7 30.4 1.0
O A:PRO21 4.8 22.1 1.0
CA A:PRO6 4.8 30.3 1.0
CG A:GLU22 4.8 24.3 1.0
CG A:PRO6 4.9 32.3 1.0
N A:THR7 4.9 26.0 1.0
OE1 A:GLU22 5.0 25.3 1.0

Chlorine binding site 2 out of 7 in 5r9a

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Chlorine binding site 2 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A 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 N13838A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:38.8
occ:1.00
 N A:ASN100 3.2 28.9 1.0
N A:ASP101 3.2 28.5 1.0
OG1 A:THR91 3.4 26.2 1.0
CB A:ALA93 3.6 28.1 1.0
O A:GLU98 3.6 37.3 1.0
N A:ALA93 3.7 26.8 1.0
CA A:ASN100 3.9 30.3 1.0
CG A:PRO92 4.0 28.5 1.0
CB A:ASP101 4.0 27.3 1.0
C A:ASN100 4.0 31.2 1.0
CD A:PRO92 4.0 23.6 1.0
CA A:ALA93 4.1 27.4 1.0
CB A:ASN100 4.1 36.7 1.0
CA A:ASP101 4.1 24.7 1.0
C A:PHE99 4.2 32.9 1.0
O A:ASP101 4.2 25.6 1.0
CA A:PHE99 4.2 30.9 1.0
CG A:ASP101 4.5 35.7 1.0
N A:PRO92 4.6 23.6 1.0
OD2 A:ASP101 4.6 34.3 1.0
C A:PRO92 4.6 30.8 1.0
C A:ASP101 4.6 22.8 1.0
C A:GLU98 4.6 38.4 1.0
CD1 A:PHE99 4.8 26.0 1.0
CB A:THR91 4.8 23.9 1.0
N A:PHE99 4.9 33.3 1.0
CB A:PRO92 4.9 25.7 1.0
CA A:PRO92 5.0 25.7 1.0

Chlorine binding site 3 out of 7 in 5r9a

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Chlorine binding site 3 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A 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 N13838A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:49.2
occ:1.00
 O A:HOH504 2.9 38.1 1.0
O A:HOH519 2.9 40.2 1.0
N A:GLY85 3.1 25.0 1.0
CE A:LYS165 3.5 40.6 1.0
CD2 A:HIS107 3.5 35.8 1.0
CD A:LYS165 3.6 32.6 1.0
NZ A:LYS165 3.7 42.6 1.0
O A:VAL83 3.9 21.5 1.0
CA A:GLY85 3.9 27.4 1.0
CA A:ILE84 3.9 22.0 1.0
C A:ILE84 3.9 25.3 1.0
O A:GLY85 4.2 24.8 1.0
C A:GLY85 4.4 23.6 1.0
CG A:HIS107 4.4 34.6 1.0
NE2 A:HIS107 4.5 40.8 1.0
CE A:MET109 4.6 45.6 1.0
CG1 A:ILE84 4.7 28.3 1.0
CB A:HIS107 4.7 29.0 1.0
C A:VAL83 4.7 19.8 1.0
O A:HOH593 4.7 22.0 1.0
N A:ILE84 4.8 20.1 1.0
CB A:ILE84 4.9 24.7 1.0

Chlorine binding site 4 out of 7 in 5r9a

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Chlorine binding site 4 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A 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 N13838A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:28.1
occ:0.56
 O A:HOH616 3.0 35.1 1.0
N A:ASP324 3.0 21.7 1.0
NH2 A:ARG73 3.5 22.3 1.0
CB A:ASP324 3.5 23.4 1.0
O A:PRO322 3.7 23.5 1.0
CA A:TYR323 3.8 23.5 1.0
CA A:ASP324 3.8 24.8 1.0
C A:TYR323 3.9 24.6 1.0
CD1 A:TYR323 4.3 23.3 1.0
O A:ASP324 4.4 24.8 1.0
O A:HOH749 4.5 29.2 1.0
O A:HOH743 4.5 43.4 1.0
C A:PRO322 4.5 21.2 1.0
N A:TYR323 4.5 22.5 1.0
O A:HOH599 4.6 31.0 1.0
C A:ASP324 4.6 23.5 1.0
CZ A:ARG73 4.7 23.6 1.0
ND1 A:HIS77 4.8 28.0 1.0
CE1 A:HIS77 4.8 28.0 1.0
CB A:TYR323 4.9 22.1 1.0
CG A:TYR323 4.9 21.0 1.0
CG A:ASP324 4.9 28.3 1.0

Chlorine binding site 5 out of 7 in 5r9a

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Chlorine binding site 5 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A 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 N13838A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:33.4
occ:1.00
 O A:HOH632 2.9 33.7 1.0
OG A:SER154 3.2 23.6 1.0
N A:SER154 3.2 22.1 1.0
O A:HOH669 3.5 42.6 1.0
ND2 A:ASN114 3.5 36.4 1.0
CB A:SER154 3.5 23.5 1.0
CD A:PRO153 3.7 20.0 1.0
N A:PRO153 3.8 18.3 1.0
CG A:LYS152 3.9 23.4 1.0
CB A:LYS152 3.9 23.1 1.0
CD A:LYS152 4.0 24.5 1.0
CA A:SER154 4.0 23.2 1.0
CB A:PRO153 4.1 21.6 1.0
C A:PRO153 4.2 21.4 1.0
CA A:PRO153 4.2 19.6 1.0
C A:LYS152 4.3 18.6 1.0
CG A:PRO153 4.3 21.5 1.0
CE1 A:TYR188 4.4 17.9 1.0
CG A:ASN114 4.4 38.9 1.0
CB A:ALA184 4.5 26.5 1.0
OD1 A:ASN114 4.5 46.1 1.0
CE A:LYS152 4.7 27.4 1.0
CA A:LYS152 4.7 20.1 1.0
OH A:TYR188 4.8 22.2 1.0
O A:HOH501 4.8 35.1 1.0
CZ A:TYR188 4.9 20.8 1.0

Chlorine binding site 6 out of 7 in 5r9a

Go back to Chlorine Binding Sites List in 5r9a
Chlorine binding site 6 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A 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 N13838A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:56.7
occ:1.00
 N A:HIS199 3.1 30.6 1.0
CB A:HIS199 3.8 39.1 1.0
CA A:MET198 3.8 26.6 1.0
CD2 A:HIS199 3.9 50.7 1.0
CB A:MET198 4.0 26.8 1.0
C A:MET198 4.0 25.0 1.0
CA A:HIS199 4.0 34.2 1.0
CG A:MET198 4.1 30.1 1.0
CG A:HIS199 4.1 48.1 1.0
CE A:MET198 4.5 35.8 1.0
O A:HIS199 4.6 31.2 1.0
N3 A:SQM401 4.8 32.2 0.8
C A:HIS199 4.8 30.9 1.0
OG A:SER251 4.9 36.8 1.0

Chlorine binding site 7 out of 7 in 5r9a

Go back to Chlorine Binding Sites List in 5r9a
Chlorine binding site 7 out of 7 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A 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 7 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13838A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:44.4
occ:1.00
 N A:GLN264 3.0 22.1 1.0
CA A:ALA263 3.6 23.4 1.0
C A:ALA263 3.8 21.8 1.0
CB A:GLN264 3.8 27.1 1.0
CG A:GLN264 3.9 28.5 1.0
CB A:ALA263 3.9 28.7 1.0
CA A:GLN264 4.0 22.5 1.0
NE2 A:GLN264 4.5 32.0 1.0
O A:GLN264 4.6 24.2 1.0
CD A:GLN264 4.7 30.6 1.0
O A:LEU262 4.8 24.6 1.0
C A:GLN264 4.8 21.8 1.0
N A:ALA263 4.8 24.3 1.0
O A:ALA263 5.0 24.2 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: Sat Jul 12 07:52:21 2025

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