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Chlorine in PDB 5ra3: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N10836B in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N10836B in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N10836B 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 N10836B in Complex with Map Kinase P38-Alpha, PDB code: 5ra3 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) 71.43 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.006, 86.109, 127.911, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 22.9

Other elements in 5ra3:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N10836B 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 N10836B in Complex with Map Kinase P38-Alpha (pdb code 5ra3). 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 N10836B in Complex with Map Kinase P38-Alpha, PDB code: 5ra3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5ra3

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Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N10836B 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 N10836B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:40.0
occ:1.00
 O A:HOH740 2.8 40.3 1.0
N A:ARG23 3.0 17.1 1.0
O A:HOH645 3.0 25.3 1.0
O A:HOH704 3.2 31.6 1.0
N A:GLU22 3.5 17.4 1.0
CB A:ARG23 3.7 18.9 1.0
CB A:PRO6 3.8 30.2 1.0
C A:GLU22 3.8 18.0 1.0
CB A:PRO21 3.8 15.2 1.0
CA A:ARG23 3.8 17.8 1.0
CB A:GLU22 3.9 19.2 1.0
CA A:GLU22 3.9 19.5 1.0
C A:PRO21 4.0 17.6 1.0
CG A:ARG23 4.1 19.5 1.0
CA A:PRO21 4.3 14.6 1.0
CD A:ARG23 4.4 20.1 1.0
O A:THR7 4.4 19.2 1.0
O A:HOH686 4.7 12.2 0.5
O A:PRO21 4.7 14.4 1.0
CG A:GLU22 4.8 21.4 1.0
CA A:PRO6 4.9 28.2 1.0
CG A:PRO6 4.9 30.8 1.0
O A:GLU22 5.0 16.8 1.0

Chlorine binding site 2 out of 5 in 5ra3

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Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N10836B 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 N10836B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:39.7
occ:1.00
 N A:ASP101 3.1 25.3 1.0
N A:ASN100 3.2 27.1 1.0
OG1 A:THR91 3.4 20.7 1.0
O A:GLU98 3.7 32.4 1.0
CB A:ASP101 3.7 28.6 1.0
CB A:ALA93 3.8 25.8 1.0
N A:ALA93 3.9 24.4 1.0
CA A:ASN100 3.9 28.1 1.0
CA A:ASP101 3.9 26.0 1.0
C A:ASN100 4.0 27.5 1.0
CB A:ASN100 4.1 34.8 1.0
CD A:PRO92 4.1 20.6 1.0
C A:PHE99 4.1 27.0 1.0
O A:ASP101 4.2 21.9 1.0
CA A:PHE99 4.2 25.4 1.0
CG A:PRO92 4.3 23.8 1.0
CA A:ALA93 4.3 26.7 1.0
OD2 A:ASP101 4.3 33.0 1.0
CG A:ASP101 4.3 35.0 1.0
C A:ASP101 4.6 20.7 1.0
C A:GLU98 4.6 34.5 1.0
N A:PRO92 4.7 19.8 1.0
CD1 A:PHE99 4.8 22.7 1.0
C A:PRO92 4.8 26.3 1.0
CB A:THR91 4.9 21.4 1.0
N A:PHE99 4.9 29.1 1.0
ND2 A:ASN100 4.9 41.8 1.0

Chlorine binding site 3 out of 5 in 5ra3

Go back to Chlorine Binding Sites List in 5ra3
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N10836B 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 N10836B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:57.2
occ:1.00
 O A:HOH610 2.9 22.9 0.5
O A:HOH542 3.1 30.1 0.5
N A:GLY85 3.2 21.3 1.0
CE A:LYS165 3.3 23.6 0.5
CD A:LYS165 3.5 22.4 0.5
ND1 A:HIS107 3.8 29.7 0.5
CA A:GLY85 4.0 22.4 1.0
O A:VAL83 4.1 14.8 1.0
C A:ILE84 4.1 18.9 1.0
CD1 A:ILE84 4.1 35.3 1.0
CA A:ILE84 4.1 18.8 1.0
CE A:MET109 4.3 39.3 0.5
NZ A:LYS165 4.4 24.5 0.5
O A:GLY85 4.4 21.1 1.0
CB A:HIS107 4.5 26.1 0.5
C A:GLY85 4.6 19.4 1.0
CG A:HIS107 4.6 28.2 0.5
CE1 A:HIS107 4.8 30.0 0.5
CG1 A:ILE84 4.8 26.8 1.0
C A:VAL83 4.9 15.8 1.0
CG A:LYS165 5.0 20.2 0.5
O A:HOH597 5.0 16.3 0.5

Chlorine binding site 4 out of 5 in 5ra3

Go back to Chlorine Binding Sites List in 5ra3
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N10836B 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 N10836B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:36.4
occ:1.00
 N A:ASP324 2.9 17.4 1.0
CB A:ASP324 3.6 19.6 1.0
NH2 A:ARG73 3.6 18.3 1.0
CA A:TYR323 3.8 16.1 1.0
O A:PRO322 3.8 17.3 1.0
C A:TYR323 3.8 18.0 1.0
CA A:ASP324 3.9 17.9 1.0
O A:HOH714 4.4 34.1 0.5
CD1 A:TYR323 4.4 19.7 1.0
O A:HOH730 4.4 17.2 0.5
O A:ASP324 4.4 18.9 1.0
O A:HOH537 4.5 22.6 0.5
C A:PRO322 4.5 16.4 1.0
N A:TYR323 4.5 15.9 1.0
C A:ASP324 4.7 17.1 1.0
CD2 A:HIS77 4.8 17.4 1.0
CZ A:ARG73 4.8 17.6 1.0
NE2 A:HIS77 4.8 23.4 1.0
CB A:TYR323 4.9 16.4 1.0
O A:TYR323 5.0 19.0 1.0

Chlorine binding site 5 out of 5 in 5ra3

Go back to Chlorine Binding Sites List in 5ra3
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N10836B 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 N10836B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:29.8
occ:1.00
 O A:HOH629 3.0 20.1 0.5
O A:HOH600 3.0 42.1 0.5
OG A:SER154 3.2 17.4 1.0
ND2 A:ASN114 3.3 26.1 0.5
N A:SER154 3.3 15.9 1.0
CB A:SER154 3.5 18.9 1.0
CD A:PRO153 3.7 16.2 1.0
CG A:LYS152 3.8 19.1 1.0
N A:PRO153 3.8 14.1 1.0
CD A:LYS152 4.0 21.7 1.0
CB A:LYS152 4.0 18.4 1.0
CA A:SER154 4.0 17.6 1.0
CG A:ASN114 4.1 25.9 0.5
CB A:PRO153 4.1 14.8 1.0
OD1 A:ASN114 4.2 29.3 0.5
C A:PRO153 4.2 14.7 1.0
CA A:PRO153 4.3 14.3 1.0
CB A:ALA184 4.3 19.2 1.0
C A:LYS152 4.4 15.0 1.0
CG A:PRO153 4.4 16.1 1.0
CE1 A:TYR188 4.5 13.7 0.5
CA A:LYS152 4.8 15.4 1.0
CE A:LYS152 4.8 22.9 1.0
OH A:TYR188 4.9 14.4 0.5
CZ A:TYR188 5.0 13.6 0.5

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 08:01:26 2025

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