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Chlorine in PDB 5r9r: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13413A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13413A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13413A 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 N13413A in Complex with Map Kinase P38-Alpha, PDB code: 5r9r 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) 29.29 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.932, 86.144, 126.967, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.8

Other elements in 5r9r:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13413A 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 N13413A in Complex with Map Kinase P38-Alpha (pdb code 5r9r). 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 N13413A in Complex with Map Kinase P38-Alpha, PDB code: 5r9r:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5r9r

Go back to Chlorine Binding Sites List in 5r9r
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13413A 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 N13413A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:44.1
occ:1.00
 O A:HOH756 2.8 28.5 1.0
O A:HOH678 2.9 29.5 1.0
O A:HOH714 3.0 39.3 1.0
N A:ARG23 3.0 22.8 1.0
N A:GLU22 3.4 23.8 1.0
CB A:ARG23 3.6 30.0 1.0
CB A:PRO6 3.7 32.5 1.0
CB A:PRO21 3.8 20.4 1.0
CA A:ARG23 3.8 24.8 1.0
C A:GLU22 3.9 23.0 1.0
CB A:GLU22 3.9 22.4 1.0
CA A:GLU22 3.9 23.8 1.0
C A:PRO21 4.0 23.2 1.0
CG A:ARG23 4.0 27.2 1.0
CA A:PRO21 4.2 20.2 1.0
O A:THR7 4.4 26.4 1.0
CD A:ARG23 4.5 25.7 1.0
O A:PRO21 4.7 19.6 1.0
CG A:GLU22 4.7 24.4 1.0
CA A:PRO6 4.8 29.6 1.0
O A:HOH701 4.8 29.1 1.0
CG A:PRO6 4.8 33.8 1.0
N A:THR7 5.0 25.3 1.0
OE1 A:GLU22 5.0 24.5 1.0
O A:GLU22 5.0 22.4 1.0

Chlorine binding site 2 out of 5 in 5r9r

Go back to Chlorine Binding Sites List in 5r9r
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13413A 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 N13413A 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 27.0 1.0
N A:ASN100 3.3 30.4 1.0
OG1 A:THR91 3.4 25.9 1.0
CB A:ALA93 3.7 28.2 1.0
O A:GLU98 3.7 37.3 1.0
N A:ALA93 3.8 28.3 1.0
CB A:ASP101 3.9 29.9 1.0
CA A:ASN100 4.0 32.2 1.0
C A:ASN100 4.0 32.5 1.0
CA A:ASP101 4.0 28.3 1.0
CB A:ASN100 4.1 40.0 1.0
CD A:PRO92 4.1 23.6 1.0
O A:ASP101 4.2 26.3 1.0
CG A:PRO92 4.2 28.1 1.0
CA A:ALA93 4.2 30.5 1.0
C A:PHE99 4.2 33.6 1.0
CA A:PHE99 4.3 28.8 1.0
OD2 A:ASP101 4.4 35.7 1.0
CG A:ASP101 4.5 37.7 1.0
N A:PRO92 4.6 23.2 1.0
C A:ASP101 4.6 23.6 1.0
C A:PRO92 4.7 29.5 1.0
C A:GLU98 4.7 38.2 1.0
CB A:THR91 4.8 23.8 1.0
CD1 A:PHE99 4.8 25.1 1.0
ND2 A:ASN100 4.9 44.6 1.0
CB A:PRO92 4.9 26.5 1.0
N A:PHE99 5.0 33.5 1.0

Chlorine binding site 3 out of 5 in 5r9r

Go back to Chlorine Binding Sites List in 5r9r
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13413A 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 N13413A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:60.8
occ:1.00
 O A:HOH547 2.9 32.1 1.0
O A:HOH515 3.0 40.2 1.0
N A:GLY85 3.2 23.1 1.0
CE A:LYS165 3.6 36.4 1.0
CD A:LYS165 3.8 33.4 1.0
NZ A:LYS165 4.0 41.1 1.0
CA A:GLY85 4.0 24.0 1.0
O A:VAL83 4.0 20.9 1.0
C A:ILE84 4.1 21.8 1.0
CA A:ILE84 4.2 22.9 1.0
O A:GLY85 4.3 23.3 1.0
CB A:HIS107 4.4 33.8 0.4
ND1 A:HIS107 4.4 37.7 0.4
CD1 A:ILE84 4.5 41.1 1.0
C A:GLY85 4.6 24.6 1.0
O A:HOH600 4.7 21.6 1.0
CG A:HIS107 4.9 34.8 0.4
C A:VAL83 4.9 20.0 1.0
N A:ILE84 5.0 20.6 1.0

Chlorine binding site 4 out of 5 in 5r9r

Go back to Chlorine Binding Sites List in 5r9r
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13413A 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 N13413A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:40.3
occ:1.00
 N A:ASP324 2.9 21.8 1.0
CB A:ASP324 3.6 23.0 1.0
NH2 A:ARG73 3.7 23.5 1.0
O A:PRO322 3.7 22.7 1.0
CA A:TYR323 3.7 21.9 1.0
C A:TYR323 3.8 23.2 1.0
CA A:ASP324 3.8 21.5 1.0
CD1 A:TYR323 4.3 23.6 1.0
O A:ASP324 4.4 24.4 1.0
O A:HOH525 4.4 27.3 1.0
O A:HOH737 4.4 26.5 1.0
O A:HOH728 4.4 36.0 1.0
C A:PRO322 4.4 20.9 1.0
N A:TYR323 4.5 20.7 1.0
C A:ASP324 4.6 20.7 1.0
CD2 A:HIS77 4.7 19.9 1.0
NE2 A:HIS77 4.8 27.5 1.0
CZ A:ARG73 4.8 23.1 1.0
CB A:TYR323 4.9 21.9 1.0
CG A:TYR323 4.9 23.5 1.0
O A:TYR323 5.0 24.5 1.0
CE1 A:TYR323 5.0 25.1 1.0
CG A:ASP324 5.0 25.0 1.0

Chlorine binding site 5 out of 5 in 5r9r

Go back to Chlorine Binding Sites List in 5r9r
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13413A 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 N13413A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:34.6
occ:1.00
 O A:HOH655 2.9 30.2 1.0
OG A:SER154 3.2 23.0 1.0
N A:SER154 3.2 22.1 1.0
ND2 A:ASN114 3.3 47.4 0.4
CB A:SER154 3.5 22.6 1.0
CD A:PRO153 3.6 19.2 1.0
N A:PRO153 3.8 18.7 1.0
CG A:LYS152 3.9 21.0 1.0
CB A:LYS152 4.0 19.3 1.0
CA A:SER154 4.0 24.9 1.0
CD A:LYS152 4.0 23.4 1.0
O A:HOH692 4.1 47.7 1.0
CG A:ASN114 4.1 45.7 0.4
C A:PRO153 4.2 20.1 1.0
OD1 A:ASN114 4.2 48.5 0.4
CB A:PRO153 4.2 20.2 1.0
CA A:PRO153 4.2 18.2 1.0
CB A:ALA184 4.3 24.2 1.0
C A:LYS152 4.3 18.1 1.0
CG A:PRO153 4.4 18.6 1.0
CE1 A:TYR188 4.4 17.0 1.0
CA A:LYS152 4.8 18.6 1.0
CE A:LYS152 4.8 27.1 1.0
OH A:TYR188 4.9 19.7 1.0
CZ A:TYR188 5.0 18.6 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 16:08:02 2024

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