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Chlorine in PDB 5r9n: 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: 5r9n 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 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.904, 86.682, 125.827, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 20.2

Other elements in 5r9n:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13421A 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 N13421A in Complex with Map Kinase P38-Alpha (pdb code 5r9n). 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 N13421A in Complex with Map Kinase P38-Alpha, PDB code: 5r9n:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5r9n

Go back to Chlorine Binding Sites List in 5r9n
Chlorine binding site 1 out of 6 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:34.0
occ:0.64
 O A:HOH760 2.8 35.1 1.0
O A:HOH626 3.0 34.3 1.0
N A:ARG23 3.2 23.1 1.0
O A:HOH726 3.2 38.1 1.0
N A:GLU22 3.5 25.8 1.0
CB A:PRO6 3.7 37.0 1.0
CB A:ARG23 3.7 31.9 1.0
CB A:PRO21 3.8 24.1 1.0
CB A:GLU22 3.9 25.3 1.0
C A:GLU22 4.0 24.5 1.0
CA A:GLU22 4.0 28.2 1.0
CA A:ARG23 4.0 25.4 1.0
C A:PRO21 4.1 26.1 1.0
CG A:ARG23 4.2 28.3 1.0
O A:THR7 4.3 31.2 1.0
CA A:PRO21 4.3 23.2 1.0
CD A:ARG23 4.6 26.5 1.0
CA A:PRO6 4.7 36.0 1.0
CG A:GLU22 4.7 31.9 1.0
N A:THR7 4.8 30.1 1.0
O A:PRO21 4.8 23.7 1.0
CG A:PRO6 4.9 39.0 1.0
OE1 A:GLU22 4.9 30.0 1.0
O A:HOH672 4.9 34.2 1.0

Chlorine binding site 2 out of 6 in 5r9n

Go back to Chlorine Binding Sites List in 5r9n
Chlorine binding site 2 out of 6 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:42.4
occ:1.00
 N A:ASP101 3.2 30.6 1.0
N A:ASN100 3.2 34.0 1.0
OG1 A:THR91 3.3 29.2 1.0
CB A:ALA93 3.5 32.8 1.0
O A:GLU98 3.6 40.1 1.0
N A:ALA93 3.7 32.3 1.0
CA A:ASN100 3.9 34.0 1.0
CB A:ASP101 3.9 30.7 1.0
CG A:PRO92 4.0 32.8 1.0
CA A:ALA93 4.0 33.3 1.0
C A:ASN100 4.1 35.1 1.0
CB A:ASN100 4.1 40.6 1.0
CA A:ASP101 4.1 30.4 1.0
CD A:PRO92 4.1 27.8 1.0
O A:ASP101 4.1 28.5 1.0
C A:PHE99 4.2 39.4 1.0
CA A:PHE99 4.3 35.8 1.0
CG A:ASP101 4.5 41.6 1.0
N A:PRO92 4.6 27.5 1.0
C A:PRO92 4.6 35.6 1.0
C A:ASP101 4.6 23.2 1.0
C A:GLU98 4.7 42.6 1.0
OD2 A:ASP101 4.7 39.7 1.0
CD1 A:PHE99 4.7 28.4 1.0
CB A:THR91 4.8 28.2 1.0
CB A:PRO92 4.9 30.5 1.0
N A:PHE99 4.9 36.5 1.0
CA A:PRO92 5.0 31.4 1.0

Chlorine binding site 3 out of 6 in 5r9n

Go back to Chlorine Binding Sites List in 5r9n
Chlorine binding site 3 out of 6 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:29.9
occ:0.53
 O A:HOH530 3.0 37.8 1.0
N A:ASP324 3.0 25.7 1.0
CB A:ASP324 3.6 25.5 1.0
NH2 A:ARG73 3.6 25.8 1.0
O A:PRO322 3.7 27.4 1.0
CA A:TYR323 3.8 27.0 1.0
CA A:ASP324 3.9 25.8 1.0
C A:TYR323 3.9 27.2 1.0
CD1 A:TYR323 4.3 25.8 1.0
O A:HOH727 4.4 47.2 1.0
O A:ASP324 4.4 27.9 1.0
O A:HOH749 4.5 29.4 1.0
C A:PRO322 4.5 27.5 1.0
N A:TYR323 4.5 24.7 1.0
O A:HOH545 4.5 30.1 1.0
C A:ASP324 4.6 26.5 1.0
CE1 A:HIS77 4.8 30.7 1.0
CZ A:ARG73 4.8 25.0 1.0
ND1 A:HIS77 4.8 31.0 1.0
CB A:TYR323 4.9 27.2 1.0
CG A:TYR323 4.9 25.8 1.0
CG A:ASP324 5.0 31.8 1.0

Chlorine binding site 4 out of 6 in 5r9n

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Chlorine binding site 4 out of 6 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:34.2
occ:0.88
 O A:HOH627 3.0 35.4 1.0
OG A:SER154 3.2 27.1 1.0
N A:SER154 3.2 23.7 1.0
CB A:SER154 3.6 25.4 1.0
O A:HOH698 3.6 44.4 1.0
CD A:PRO153 3.7 20.6 1.0
CG A:LYS152 3.8 24.0 1.0
N A:PRO153 3.8 19.9 1.0
ND2 A:ASN114 3.8 38.9 1.0
CB A:LYS152 3.9 23.0 1.0
CD A:LYS152 3.9 25.7 1.0
CA A:SER154 4.0 25.1 1.0
CB A:PRO153 4.1 24.6 1.0
C A:PRO153 4.1 22.0 1.0
CA A:PRO153 4.2 20.3 1.0
C A:LYS152 4.3 21.6 1.0
CG A:PRO153 4.4 22.7 1.0
CB A:ALA184 4.4 31.1 1.0
CE1 A:TYR188 4.4 20.7 1.0
CE A:LYS152 4.7 29.1 1.0
CA A:LYS152 4.7 20.3 1.0
CG A:ASN114 4.8 43.2 1.0
OD1 A:ASN114 4.8 49.8 1.0
OH A:TYR188 4.9 23.7 1.0
CZ A:TYR188 4.9 22.8 1.0

Chlorine binding site 5 out of 6 in 5r9n

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Chlorine binding site 5 out of 6 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:39.4
occ:0.62
 N A:GLN264 3.1 27.6 1.0
CA A:ALA263 3.6 28.4 1.0
C A:ALA263 3.8 29.3 1.0
CB A:ALA263 3.9 30.0 1.0
CB A:GLN264 4.0 31.7 1.0
CA A:GLN264 4.1 27.0 1.0
CG A:GLN264 4.1 38.6 1.0
NE2 A:GLN264 4.6 39.2 1.0
O A:GLN264 4.7 28.9 1.0
N A:ALA263 4.8 28.0 1.0
O A:LEU262 4.9 32.8 1.0
CD A:GLN264 4.9 42.8 1.0
C A:GLN264 5.0 28.9 1.0

Chlorine binding site 6 out of 6 in 5r9n

Go back to Chlorine Binding Sites List in 5r9n
Chlorine binding site 6 out of 6 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 6 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:Cl407

b:45.6
occ:0.91
 O A:ALA144 3.5 25.7 1.0
N A:TYR323 3.6 24.7 1.0
C A:ALA144 3.7 28.0 1.0
O A:HOH521 3.7 30.9 1.0
O A:TYR323 3.9 29.2 1.0
OD2 A:ASP145 3.9 46.4 1.0
CA A:ALA144 4.0 25.2 1.0
CA A:PRO322 4.1 25.2 1.0
CG A:ASP145 4.2 40.5 1.0
CB A:ASP145 4.3 31.4 1.0
O A:SER143 4.3 29.7 1.0
C A:PRO322 4.4 27.5 1.0
N A:ASP145 4.4 25.9 1.0
CA A:TYR323 4.5 27.0 1.0
CB A:PRO322 4.5 28.0 1.0
C A:TYR323 4.5 27.2 1.0
O A:HOH730 4.7 38.9 1.0
CB A:TYR323 4.7 27.2 1.0
CB A:ALA144 4.9 28.5 1.0
O A:HOH725 4.9 37.9 1.0
CA A:ASP145 5.0 28.7 1.0
OD1 A:ASP145 5.0 40.9 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 16:07:27 2024

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