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Chlorine in PDB 5r93: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL077 in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL077 in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL077 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 KCL077 in Complex with Map Kinase P38-Alpha, PDB code: 5r93 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) 29.89 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.826, 85.875, 127.515, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 19.5

Other elements in 5r93:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL077 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 KCL077 in Complex with Map Kinase P38-Alpha (pdb code 5r93). 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 KCL077 in Complex with Map Kinase P38-Alpha, PDB code: 5r93:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5r93

Go back to Chlorine Binding Sites List in 5r93
Chlorine binding site 1 out of 4 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL077 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 KCL077 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:33.0
occ:0.58
 O A:HOH829 2.7 33.2 1.0
O A:HOH645 3.0 29.0 1.0
N A:ARG23 3.1 19.8 1.0
N A:GLU22 3.4 21.3 1.0
CB A:ARG23 3.6 24.1 1.0
CB A:PRO21 3.8 21.1 1.0
CB A:PRO6 3.8 32.0 1.0
CA A:ARG23 3.9 19.7 1.0
C A:GLU22 3.9 20.9 1.0
CA A:GLU22 3.9 21.7 1.0
CB A:GLU22 4.0 21.0 1.0
CG A:ARG23 4.0 25.3 1.0
C A:PRO21 4.0 19.3 1.0
CA A:PRO21 4.3 18.8 1.0
CD A:ARG23 4.4 23.2 1.0
O A:THR7 4.4 25.1 1.0
O A:HOH726 4.8 31.8 1.0
O A:PRO21 4.8 20.5 1.0
CA A:PRO6 4.9 30.3 1.0
CG A:PRO6 4.9 32.6 1.0
CG A:GLU22 4.9 27.5 1.0
N A:THR7 4.9 26.5 1.0

Chlorine binding site 2 out of 4 in 5r93

Go back to Chlorine Binding Sites List in 5r93
Chlorine binding site 2 out of 4 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL077 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 KCL077 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:38.8
occ:1.00
 N A:ASP101 3.2 27.1 1.0
N A:ASN100 3.2 28.4 1.0
OG1 A:THR91 3.4 25.6 1.0
CB A:ALA93 3.7 27.5 1.0
O A:GLU98 3.7 38.0 1.0
CB A:ASP101 3.8 28.9 1.0
N A:ALA93 3.8 28.3 1.0
CA A:ASN100 3.9 30.8 1.0
C A:ASN100 4.0 32.6 1.0
CA A:ASP101 4.0 28.6 1.0
CG A:PRO92 4.0 32.8 1.0
CD A:PRO92 4.1 24.8 1.0
CB A:ASN100 4.1 37.2 1.0
O A:ASP101 4.1 24.3 1.0
CA A:ALA93 4.2 28.8 1.0
C A:PHE99 4.2 33.3 1.0
CA A:PHE99 4.3 30.0 1.0
CG A:ASP101 4.5 35.2 1.0
OD2 A:ASP101 4.5 34.5 1.0
C A:ASP101 4.6 22.4 1.0
N A:PRO92 4.6 23.3 1.0
C A:PRO92 4.7 29.3 1.0
C A:GLU98 4.7 37.6 1.0
CD1 A:PHE99 4.7 28.1 1.0
CB A:THR91 4.8 22.6 1.0
ND2 A:ASN100 4.9 50.9 1.0
CB A:PRO92 5.0 28.6 1.0
N A:PHE99 5.0 33.9 1.0

Chlorine binding site 3 out of 4 in 5r93

Go back to Chlorine Binding Sites List in 5r93
Chlorine binding site 3 out of 4 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL077 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 KCL077 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:38.8
occ:1.00
 O A:HOH591 2.9 34.3 1.0
N A:ASP324 3.0 21.1 1.0
NH2 A:ARG73 3.6 23.1 1.0
CB A:ASP324 3.6 22.4 1.0
O A:PRO322 3.7 22.0 1.0
CA A:TYR323 3.8 20.8 1.0
C A:TYR323 3.8 21.0 1.0
CA A:ASP324 3.9 20.8 1.0
CD1 A:TYR323 4.3 23.2 1.0
C A:PRO322 4.5 20.1 1.0
O A:HOH803 4.5 38.9 1.0
O A:ASP324 4.5 23.4 1.0
N A:TYR323 4.5 21.0 1.0
O A:HOH814 4.5 30.1 1.0
O A:HOH568 4.6 28.5 1.0
C A:ASP324 4.7 22.0 1.0
CE1 A:HIS77 4.7 24.9 1.0
CZ A:ARG73 4.7 22.1 1.0
ND1 A:HIS77 4.8 24.3 1.0
CB A:TYR323 4.8 21.0 1.0
CG A:TYR323 4.9 21.4 1.0

Chlorine binding site 4 out of 4 in 5r93

Go back to Chlorine Binding Sites List in 5r93
Chlorine binding site 4 out of 4 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment KCL077 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 KCL077 in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:31.6
occ:1.00
 O A:HOH659 3.0 31.0 1.0
O A:HOH735 3.0 42.3 1.0
OG A:SER154 3.2 22.5 1.0
N A:SER154 3.2 20.1 1.0
ND2 A:ASN114 3.3 43.5 1.0
CB A:SER154 3.6 21.1 1.0
CD A:PRO153 3.7 19.3 1.0
N A:PRO153 3.8 17.4 1.0
CG A:LYS152 3.9 20.3 1.0
CB A:LYS152 3.9 18.8 1.0
CD A:LYS152 4.0 22.2 1.0
CA A:SER154 4.0 20.0 1.0
C A:PRO153 4.2 20.4 1.0
O A:HOH784 4.2 46.2 1.0
CB A:PRO153 4.2 19.4 1.0
CG A:ASN114 4.2 42.3 1.0
CA A:PRO153 4.2 19.9 1.0
C A:LYS152 4.3 17.2 1.0
OD1 A:ASN114 4.4 48.5 1.0
CB A:ALA184 4.4 24.8 1.0
CG A:PRO153 4.4 19.6 1.0
CE1 A:TYR188 4.4 17.0 1.0
CE A:LYS152 4.7 23.2 1.0
CA A:LYS152 4.7 18.9 1.0
OH A:TYR188 4.9 19.2 1.0
CZ A:TYR188 4.9 18.0 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 07:50:21 2025

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