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Chlorine in PDB 5r9s: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13470A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13470A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13470A 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 N13470A in Complex with Map Kinase P38-Alpha, PDB code: 5r9s 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 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.785, 86.041, 127.473, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 19.9

Other elements in 5r9s:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13470A 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 N13470A in Complex with Map Kinase P38-Alpha (pdb code 5r9s). 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 N13470A in Complex with Map Kinase P38-Alpha, PDB code: 5r9s:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5r9s

Go back to Chlorine Binding Sites List in 5r9s
Chlorine binding site 1 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13470A 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 N13470A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:32.2
occ:0.48
 CL1 A:A9B401 0.0 32.2 0.5
C3 A:A9B401 1.7 31.5 0.5
C2 A:A9B401 2.6 32.0 0.5
C4 A:A9B401 2.8 31.4 0.5
CD1 A:LEU232 3.8 18.9 1.0
CD1 A:ILE259 3.9 33.6 0.5
C1 A:A9B401 3.9 33.1 0.5
CD2 A:LEU236 4.0 20.4 1.0
C5 A:A9B401 4.1 32.2 0.5
CD2 A:LEU291 4.2 28.1 1.0
CZ3 A:TRP197 4.2 17.8 0.5
CD1 A:LEU291 4.3 25.1 1.0
CG A:LEU291 4.4 29.3 1.0
CB A:PRO191 4.4 22.1 0.5
C6 A:A9B401 4.5 32.4 0.5
CG1 A:ILE259 4.6 32.4 0.5
CG A:PRO242 4.6 20.5 0.5
CD1 A:LEU236 4.7 20.3 1.0
CE3 A:TRP197 4.7 17.8 0.5
CG A:LEU236 4.8 18.5 1.0
CD A:PRO242 4.8 19.9 0.5
CG A:PRO191 4.8 21.7 0.5
CG A:LEU232 4.9 18.8 1.0
CD2 A:LEU232 5.0 21.7 1.0

Chlorine binding site 2 out of 6 in 5r9s

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Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13470A 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 N13470A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:43.7
occ:1.00
 O A:HOH735 2.7 27.5 1.0
O A:HOH619 2.9 25.6 1.0
O A:HOH701 3.0 31.1 1.0
N A:ARG23 3.0 20.1 1.0
N A:GLU22 3.4 21.3 1.0
CB A:ARG23 3.6 26.7 1.0
CB A:PRO21 3.8 19.9 1.0
CB A:PRO6 3.8 29.6 1.0
CA A:ARG23 3.8 21.1 1.0
C A:GLU22 3.8 19.4 1.0
CA A:GLU22 3.9 20.4 1.0
CB A:GLU22 4.0 18.4 1.0
C A:PRO21 4.0 19.8 1.0
CG A:ARG23 4.0 27.1 1.0
CA A:PRO21 4.3 18.5 1.0
O A:THR7 4.4 23.1 1.0
CD A:ARG23 4.5 25.2 1.0
O A:PRO21 4.7 16.9 1.0
CG A:GLU22 4.8 20.8 1.0
CA A:PRO6 4.8 27.7 1.0
O A:HOH665 4.8 28.4 1.0
CG A:PRO6 4.9 29.8 1.0
OE1 A:GLU22 4.9 22.0 1.0

Chlorine binding site 3 out of 6 in 5r9s

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Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13470A 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 N13470A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:39.0
occ:1.00
 N A:ASP101 3.2 24.7 1.0
N A:ASN100 3.2 27.1 1.0
OG1 A:THR91 3.5 22.0 1.0
CB A:ALA93 3.7 24.5 1.0
O A:GLU98 3.7 36.1 1.0
CB A:ASP101 3.8 29.6 1.0
N A:ALA93 3.9 25.0 1.0
CA A:ASN100 4.0 29.1 1.0
C A:ASN100 4.0 27.7 1.0
CA A:ASP101 4.0 25.3 1.0
CD A:PRO92 4.1 22.0 1.0
CB A:ASN100 4.1 35.4 1.0
O A:ASP101 4.1 22.6 1.0
CG A:PRO92 4.1 24.7 1.0
C A:PHE99 4.2 27.3 1.0
CA A:ALA93 4.2 25.8 1.0
CA A:PHE99 4.3 27.0 1.0
OD2 A:ASP101 4.4 35.3 1.0
CG A:ASP101 4.4 36.2 1.0
C A:ASP101 4.6 21.0 1.0
N A:PRO92 4.6 20.6 1.0
C A:GLU98 4.7 35.8 1.0
C A:PRO92 4.7 28.8 1.0
CD1 A:PHE99 4.8 23.3 1.0
CB A:THR91 4.9 20.8 1.0
CB A:PRO92 4.9 23.5 1.0
ND2 A:ASN100 4.9 47.8 1.0
N A:PHE99 5.0 30.9 1.0

Chlorine binding site 4 out of 6 in 5r9s

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Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13470A 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 N13470A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:46.0
occ:1.00
 O A:HOH643 2.9 33.9 1.0
O A:HOH521 3.1 32.6 1.0
N A:GLY85 3.2 23.7 1.0
ND1 A:HIS107 3.7 40.9 1.0
CE A:LYS165 3.7 32.7 1.0
CD A:LYS165 3.8 29.1 1.0
CD1 A:ILE84 3.9 39.7 1.0
O A:VAL83 4.0 18.2 1.0
CA A:GLY85 4.0 25.0 1.0
C A:ILE84 4.0 23.2 1.0
CA A:ILE84 4.0 22.5 1.0
NZ A:LYS165 4.1 35.9 1.0
O A:GLY85 4.4 22.9 1.0
CE1 A:HIS107 4.5 39.4 1.0
C A:GLY85 4.6 22.6 1.0
CG A:HIS107 4.7 33.9 1.0
CG1 A:ILE84 4.8 31.1 1.0
CE A:MET109 4.8 63.2 1.0
CB A:HIS107 4.8 30.7 1.0
C A:VAL83 4.8 18.0 1.0
O A:HOH547 4.8 20.2 1.0
N A:ILE84 4.9 18.9 1.0

Chlorine binding site 5 out of 6 in 5r9s

Go back to Chlorine Binding Sites List in 5r9s
Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13470A 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 N13470A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:37.7
occ:1.00
 N A:ASP324 3.0 18.5 1.0
CB A:ASP324 3.6 18.6 1.0
NH2 A:ARG73 3.6 22.4 1.0
O A:PRO322 3.8 18.9 1.0
CA A:TYR323 3.8 18.5 1.0
C A:TYR323 3.9 20.7 1.0
CA A:ASP324 3.9 18.0 1.0
O A:HOH709 4.4 36.4 1.0
CD1 A:TYR323 4.4 21.5 1.0
O A:HOH721 4.4 25.1 1.0
O A:HOH533 4.5 23.5 1.0
C A:PRO322 4.5 19.4 1.0
O A:ASP324 4.5 20.6 1.0
N A:TYR323 4.5 19.6 1.0
C A:ASP324 4.7 18.7 1.0
CD2 A:HIS77 4.8 18.4 1.0
CZ A:ARG73 4.8 21.0 1.0
NE2 A:HIS77 4.8 23.9 1.0
CB A:TYR323 4.9 19.7 1.0
CG A:TYR323 5.0 19.5 1.0

Chlorine binding site 6 out of 6 in 5r9s

Go back to Chlorine Binding Sites List in 5r9s
Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13470A 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 N13470A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:33.5
occ:1.00
 O A:HOH592 3.0 28.1 1.0
O A:HOH697 3.2 46.0 1.0
OG A:SER154 3.2 21.2 1.0
ND2 A:ASN114 3.2 44.0 0.5
N A:SER154 3.3 19.0 1.0
CB A:SER154 3.5 22.6 1.0
CD A:PRO153 3.7 18.5 1.0
N A:PRO153 3.8 17.4 1.0
CG A:LYS152 3.9 20.9 1.0
CB A:LYS152 3.9 18.5 1.0
CD A:LYS152 3.9 21.8 1.0
CA A:SER154 4.0 21.4 1.0
CG A:ASN114 4.1 42.5 0.5
C A:PRO153 4.2 18.4 1.0
CB A:PRO153 4.2 19.1 1.0
OD1 A:ASN114 4.2 46.9 0.5
CA A:PRO153 4.3 16.1 1.0
C A:LYS152 4.3 18.5 1.0
CB A:ALA184 4.3 22.3 0.5
CE1 A:TYR188 4.4 15.1 0.5
CG A:PRO153 4.4 18.1 1.0
CA A:LYS152 4.7 17.4 1.0
OH A:TYR188 4.7 16.7 0.5
CE A:LYS152 4.7 25.7 1.0
CZ A:TYR188 4.9 15.2 0.5
O A:LYS152 5.0 17.9 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 16:08:07 2024

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