Atomistry » Chlorine » PDB 5qtj-5r9a » 5r8v
Atomistry »
  Chlorine »
    PDB 5qtj-5r9a »
      5r8v »

Chlorine in PDB 5r8v: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09139B in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09139B in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09139B 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 N09139B in Complex with Map Kinase P38-Alpha, PDB code: 5r8v 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) 29.34 / 1.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.871, 86.243, 127.662, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 19.5

Other elements in 5r8v:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09139B 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 N09139B in Complex with Map Kinase P38-Alpha (pdb code 5r8v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09139B in Complex with Map Kinase P38-Alpha, PDB code: 5r8v:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5r8v

Go back to Chlorine Binding Sites List in 5r8v
Chlorine binding site 1 out of 4 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09139B 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 N09139B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:41.5
occ:1.00
 O A:HOH882 2.7 30.1 1.0
O A:HOH824 2.9 33.1 1.0
O A:HOH659 3.0 26.6 1.0
N A:ARG23 3.0 18.5 1.0
N A:GLU22 3.5 19.1 1.0
CB A:ARG23 3.5 24.4 1.0
CA A:ARG23 3.8 19.0 1.0
C A:GLU22 3.9 18.3 1.0
CB A:PRO6 3.9 24.6 1.0
CB A:PRO21 3.9 18.3 1.0
CB A:GLU22 3.9 17.8 1.0
CA A:GLU22 3.9 19.6 1.0
CG A:ARG23 4.0 24.9 1.0
C A:PRO21 4.1 18.5 1.0
CA A:PRO21 4.4 16.5 1.0
CD A:ARG23 4.4 22.8 1.0
O A:THR7 4.5 21.5 1.0
O A:HOH540 4.8 40.2 1.0
O A:PRO21 4.8 18.2 1.0
O A:HOH716 4.8 31.2 1.0
CG A:GLU22 4.9 21.8 1.0
CA A:PRO6 4.9 25.9 1.0
O A:GLU22 5.0 18.2 1.0
OE1 A:GLU22 5.0 23.0 1.0
CG A:PRO6 5.0 27.0 1.0

Chlorine binding site 2 out of 4 in 5r8v

Go back to Chlorine Binding Sites List in 5r8v
Chlorine binding site 2 out of 4 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09139B 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 N09139B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:34.9
occ:1.00
 O A:HOH607 3.1 46.4 1.0
N A:ASN100 3.2 24.2 1.0
N A:ASP101 3.2 24.3 1.0
OG1 A:THR91 3.4 21.8 1.0
O A:GLU98 3.7 32.6 1.0
CB A:ALA93 3.7 26.0 1.0
N A:ALA93 3.8 24.5 1.0
CB A:ASP101 3.9 24.1 1.0
CA A:ASN100 3.9 24.1 1.0
CD A:PRO92 4.0 22.4 1.0
C A:ASN100 4.0 23.5 1.0
CA A:ASP101 4.1 22.7 1.0
CB A:ASN100 4.1 33.0 1.0
CA A:ALA93 4.2 24.9 1.0
C A:PHE99 4.2 29.8 1.0
CG A:PRO92 4.2 29.5 1.0
O A:ASP101 4.2 21.9 1.0
CA A:PHE99 4.3 24.7 1.0
OD2 A:ASP101 4.4 33.9 1.0
CG A:ASP101 4.5 31.0 1.0
N A:PRO92 4.6 20.5 1.0
C A:ASP101 4.6 21.2 1.0
C A:PRO92 4.7 25.5 1.0
C A:GLU98 4.7 34.7 1.0
CD1 A:PHE99 4.8 23.2 1.0
CB A:PRO92 4.9 23.2 1.0
CB A:THR91 4.9 19.3 1.0
CA A:PRO92 5.0 22.2 1.0
N A:PHE99 5.0 27.6 1.0

Chlorine binding site 3 out of 4 in 5r8v

Go back to Chlorine Binding Sites List in 5r8v
Chlorine binding site 3 out of 4 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09139B 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 N09139B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:34.7
occ:1.00
 O A:HOH589 2.8 34.6 1.0
N A:ASP324 3.0 19.0 1.0
CB A:ASP324 3.6 20.0 1.0
NH2 A:ARG73 3.6 20.1 1.0
O A:PRO322 3.7 20.4 1.0
CA A:TYR323 3.7 18.6 1.0
C A:TYR323 3.8 20.5 1.0
CA A:ASP324 3.9 19.0 1.0
CD1 A:TYR323 4.4 23.2 1.0
C A:PRO322 4.4 18.2 1.0
N A:TYR323 4.5 18.7 1.0
O A:ASP324 4.5 21.1 1.0
O A:HOH840 4.5 36.0 1.0
O A:HOH543 4.5 26.7 1.0
O A:HOH859 4.5 25.1 1.0
C A:ASP324 4.7 20.8 1.0
CE1 A:HIS77 4.7 22.4 1.0
CZ A:ARG73 4.8 19.6 1.0
ND1 A:HIS77 4.8 22.7 1.0
CB A:TYR323 4.8 18.7 1.0
CG A:TYR323 4.9 20.2 1.0
CG A:ASP324 5.0 23.3 1.0

Chlorine binding site 4 out of 4 in 5r8v

Go back to Chlorine Binding Sites List in 5r8v
Chlorine binding site 4 out of 4 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09139B 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 N09139B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:32.1
occ:1.00
 O A:HOH693 3.0 28.9 1.0
O A:HOH762 3.1 42.2 1.0
N A:SER154 3.2 19.0 1.0
OG A:SER154 3.2 20.9 1.0
ND2 A:ASN114 3.4 37.7 1.0
CB A:SER154 3.5 20.5 1.0
CD A:PRO153 3.7 17.1 1.0
N A:PRO153 3.7 16.4 1.0
CG A:LYS152 3.8 20.4 1.0
CB A:LYS152 3.9 18.0 1.0
CD A:LYS152 3.9 21.0 1.0
CA A:SER154 4.0 19.7 1.0
CB A:PRO153 4.1 18.6 1.0
C A:PRO153 4.1 20.7 1.0
CA A:PRO153 4.2 18.1 1.0
CG A:ASN114 4.2 40.5 1.0
C A:LYS152 4.3 16.8 1.0
OD1 A:ASN114 4.3 50.1 1.0
CG A:PRO153 4.3 18.3 1.0
CE1 A:TYR188 4.4 15.2 1.0
CB A:ALA184 4.4 20.5 1.0
CA A:LYS152 4.7 17.5 1.0
CE A:LYS152 4.7 23.0 1.0
OH A:TYR188 4.8 17.5 1.0
CZ A:TYR188 4.9 14.7 1.0
O A:LYS152 5.0 16.9 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: Sat Jul 12 07:47:57 2025

Last articles

F in 4ZT3
F in 4ZQD
F in 4ZOM
F in 4ZNL
F in 4ZPG
F in 4ZPF
F in 4ZPE
F in 4ZJR
F in 4ZNS
F in 4ZMS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy