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Chlorine in PDB 5ra0: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13421A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13421A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13421A 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 N13421A in Complex with Map Kinase P38-Alpha, PDB code: 5ra0 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) 63.22 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.950, 87.040, 126.290, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 25.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13421A in Complex with Map Kinase P38-Alpha (pdb code 5ra0). 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 N13421A in Complex with Map Kinase P38-Alpha, PDB code: 5ra0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5ra0

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Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13421A 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 N13421A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:47.6
occ:1.00
O A:HOH728 2.8 33.9 1.0
O A:HOH599 3.0 34.6 1.0
N A:ARG23 3.1 24.7 1.0
O A:HOH697 3.2 34.1 1.0
N A:GLU22 3.5 30.6 1.0
CB A:ARG23 3.7 27.0 1.0
CB A:PRO6 3.7 34.3 1.0
CB A:GLU22 3.8 28.0 1.0
CB A:PRO21 3.8 27.1 1.0
CA A:GLU22 3.9 26.9 1.0
C A:GLU22 3.9 27.1 1.0
CA A:ARG23 4.0 24.9 1.0
C A:PRO21 4.0 28.7 1.0
CG A:ARG23 4.2 27.8 1.0
CA A:PRO21 4.3 25.8 1.0
O A:THR7 4.3 29.8 1.0
CD A:ARG23 4.6 30.6 1.0
CA A:PRO6 4.7 30.7 1.0
CG A:GLU22 4.7 29.5 1.0
O A:HOH676 4.8 36.3 1.0
O A:PRO21 4.8 26.3 1.0
N A:THR7 4.9 26.7 1.0
CG A:PRO6 4.9 35.2 1.0
OE1 A:GLU22 4.9 25.2 1.0

Chlorine binding site 2 out of 5 in 5ra0

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Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13421A 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 N13421A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:43.0
occ:1.00
N A:ASP101 3.3 32.8 1.0
OG1 A:THR91 3.3 28.6 1.0
N A:ASN100 3.4 32.0 1.0
CB A:ALA93 3.5 28.9 1.0
N A:ALA93 3.7 32.4 1.0
CB A:ASP101 3.8 33.9 1.0
CG A:PRO92 3.9 31.8 1.0
CD A:PRO92 3.9 30.1 1.0
O A:GLU98 3.9 41.1 1.0
CA A:ALA93 4.1 32.7 1.0
CA A:ASP101 4.1 29.5 1.0
CA A:ASN100 4.1 33.7 1.0
O A:ASP101 4.1 29.0 1.0
C A:ASN100 4.2 31.1 1.0
CB A:ASN100 4.3 39.4 1.0
C A:PHE99 4.3 35.4 1.0
CA A:PHE99 4.3 34.8 1.0
OD2 A:ASP101 4.5 38.8 1.0
N A:PRO92 4.5 31.2 1.0
CG A:ASP101 4.5 38.4 1.0
C A:PRO92 4.6 34.6 1.0
C A:ASP101 4.6 30.4 1.0
C A:GLU98 4.7 40.5 1.0
CB A:THR91 4.8 27.8 1.0
CD1 A:PHE99 4.8 28.9 1.0
CB A:PRO92 4.9 32.0 1.0
N A:PHE99 4.9 38.7 1.0
CA A:PRO92 4.9 31.8 1.0

Chlorine binding site 3 out of 5 in 5ra0

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Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13421A 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 N13421A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:61.9
occ:1.00
O A:HOH567 2.9 37.1 1.0
O A:HOH523 3.0 43.3 1.0
CE A:LYS165 3.3 32.7 1.0
N A:GLY85 3.5 24.2 1.0
NZ A:LYS165 3.5 38.9 1.0
ND1 A:HIS107 3.5 44.1 1.0
CD A:LYS165 3.6 30.4 1.0
O A:VAL83 4.1 20.0 1.0
CA A:ILE84 4.3 25.3 1.0
C A:ILE84 4.3 23.7 1.0
CD1 A:ILE84 4.3 43.9 1.0
CA A:GLY85 4.3 24.0 1.0
O A:GLY85 4.4 20.4 1.0
CE1 A:HIS107 4.4 40.0 1.0
CE A:MET109 4.4 62.1 1.0
CG A:HIS107 4.5 37.2 1.0
CB A:HIS107 4.5 35.2 1.0
C A:GLY85 4.8 24.1 1.0
C A:VAL83 4.9 20.7 1.0
N A:HIS107 4.9 29.1 1.0

Chlorine binding site 4 out of 5 in 5ra0

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Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13421A 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 N13421A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:49.1
occ:1.00
N A:ASP324 3.0 29.2 1.0
CB A:ASP324 3.6 28.2 1.0
NH2 A:ARG73 3.6 24.6 1.0
O A:PRO322 3.7 23.4 1.0
CA A:TYR323 3.7 25.7 1.0
C A:TYR323 3.8 29.6 1.0
CA A:ASP324 3.9 25.0 1.0
O A:HOH702 4.2 35.2 1.0
O A:HOH716 4.3 30.3 1.0
C A:PRO322 4.4 24.9 1.0
N A:TYR323 4.4 23.8 1.0
CD1 A:TYR323 4.4 26.8 1.0
O A:HOH546 4.5 25.8 1.0
O A:ASP324 4.5 25.1 1.0
CD2 A:HIS77 4.7 25.4 1.0
C A:ASP324 4.7 21.4 1.0
CB A:TYR323 4.8 26.2 1.0
CZ A:ARG73 4.8 21.3 1.0
NE2 A:HIS77 4.8 31.9 1.0
CG A:ASP324 4.9 28.3 1.0
CG A:TYR323 5.0 27.0 1.0

Chlorine binding site 5 out of 5 in 5ra0

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Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13421A 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 N13421A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:34.2
occ:1.00
O A:HOH652 3.0 35.3 1.0
OG A:SER154 3.2 22.1 1.0
N A:SER154 3.3 20.6 1.0
CB A:SER154 3.5 23.2 1.0
CD A:PRO153 3.6 21.1 1.0
O A:HOH687 3.7 39.4 1.0
ND2 A:ASN114 3.7 46.9 0.5
CG A:LYS152 3.8 25.6 1.0
N A:PRO153 3.8 19.7 1.0
CB A:LYS152 3.8 22.4 1.0
CD A:LYS152 3.9 26.3 1.0
CA A:SER154 4.0 22.8 1.0
C A:PRO153 4.2 18.8 1.0
CB A:PRO153 4.2 22.2 1.0
CB A:ALA184 4.3 26.4 1.0
CA A:PRO153 4.3 20.1 1.0
C A:LYS152 4.4 21.1 1.0
CG A:PRO153 4.4 20.3 1.0
CE1 A:TYR188 4.5 18.4 1.0
CG A:ASN114 4.6 48.8 0.5
CE A:LYS152 4.7 31.4 1.0
OD1 A:ASN114 4.7 51.1 0.5
CA A:LYS152 4.7 21.9 1.0
OH A:TYR188 5.0 23.1 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 Dec 12 12:23:42 2020

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