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Chlorine in PDB 5ra2: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09036B in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09036B in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09036B 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 N09036B in Complex with Map Kinase P38-Alpha, PDB code: 5ra2 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) 29.31 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.884, 86.282, 127.201, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 19.7

Other elements in 5ra2:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09036B 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 N09036B in Complex with Map Kinase P38-Alpha (pdb code 5ra2). 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 N09036B in Complex with Map Kinase P38-Alpha, PDB code: 5ra2:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5ra2

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Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09036B 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 N09036B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:43.4
occ:1.00
 O A:HOH753 2.8 31.7 1.0
O A:HOH651 2.9 28.7 1.0
O A:HOH715 2.9 34.2 1.0
N A:ARG23 3.0 21.0 1.0
N A:GLU22 3.5 20.9 1.0
CB A:ARG23 3.6 25.1 1.0
CB A:PRO21 3.8 20.0 1.0
CB A:PRO6 3.8 31.1 1.0
CA A:ARG23 3.8 21.8 1.0
C A:GLU22 3.8 20.8 1.0
CB A:GLU22 3.9 21.0 1.0
CA A:GLU22 3.9 21.7 1.0
C A:PRO21 4.0 20.9 1.0
CG A:ARG23 4.1 25.7 1.0
CA A:PRO21 4.3 19.9 1.0
O A:THR7 4.4 23.8 1.0
CD A:ARG23 4.5 24.2 1.0
O A:PRO21 4.7 20.2 1.0
CG A:GLU22 4.8 24.2 1.0
O A:HOH681 4.8 31.0 1.0
CA A:PRO6 4.8 28.6 1.0
CG A:PRO6 4.9 34.3 1.0
OE1 A:GLU22 4.9 25.2 1.0
O A:GLU22 5.0 21.0 1.0

Chlorine binding site 2 out of 5 in 5ra2

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Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09036B 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 N09036B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:39.2
occ:1.00
 N A:ASP101 3.1 28.6 1.0
N A:ASN100 3.2 28.4 1.0
OG1 A:THR91 3.4 25.2 1.0
O A:GLU98 3.7 37.5 1.0
CB A:ALA93 3.7 27.1 1.0
CB A:ASP101 3.7 28.2 1.0
N A:ALA93 3.8 26.3 1.0
CA A:ASN100 3.9 29.9 1.0
CA A:ASP101 4.0 29.2 1.0
C A:ASN100 4.0 30.8 1.0
CB A:ASN100 4.1 36.9 1.0
CD A:PRO92 4.1 24.7 1.0
O A:ASP101 4.1 25.4 1.0
C A:PHE99 4.2 31.8 1.0
CG A:PRO92 4.2 27.4 1.0
CA A:PHE99 4.2 27.9 1.0
CA A:ALA93 4.2 28.2 1.0
CG A:ASP101 4.4 37.0 1.0
OD2 A:ASP101 4.5 35.7 1.0
C A:ASP101 4.5 24.0 1.0
N A:PRO92 4.6 22.8 1.0
C A:GLU98 4.7 36.0 1.0
C A:PRO92 4.7 30.5 1.0
CD1 A:PHE99 4.7 25.1 1.0
CB A:THR91 4.8 23.9 1.0
ND2 A:ASN100 4.9 47.8 1.0
N A:PHE99 4.9 31.9 1.0
CB A:PRO92 5.0 27.1 1.0

Chlorine binding site 3 out of 5 in 5ra2

Go back to Chlorine Binding Sites List in 5ra2
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09036B 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 N09036B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:55.4
occ:1.00
 O A:HOH512 2.9 40.0 1.0
O A:HOH533 3.0 39.9 1.0
N A:GLY85 3.3 22.9 1.0
CE A:LYS165 3.6 37.0 1.0
CD A:LYS165 3.6 32.2 1.0
ND1 A:HIS107 3.6 41.7 1.0
NZ A:LYS165 3.8 42.5 1.0
O A:VAL83 4.0 19.9 1.0
CA A:GLY85 4.0 25.6 1.0
C A:ILE84 4.1 23.4 0.4
CA A:ILE84 4.2 23.4 0.4
O A:GLY85 4.3 24.5 1.0
CE1 A:HIS107 4.5 37.4 1.0
CE A:MET109 4.6 53.3 1.0
C A:GLY85 4.6 22.6 1.0
CG A:HIS107 4.6 33.3 1.0
CB A:HIS107 4.8 30.6 1.0
C A:VAL83 4.8 18.8 1.0
N A:ILE84 4.9 21.1 0.4
O A:HOH580 4.9 20.8 1.0

Chlorine binding site 4 out of 5 in 5ra2

Go back to Chlorine Binding Sites List in 5ra2
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09036B 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 N09036B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:37.6
occ:1.00
 N A:ASP324 3.0 19.8 1.0
CB A:ASP324 3.6 21.8 1.0
NH2 A:ARG73 3.6 23.1 1.0
O A:PRO322 3.8 21.0 1.0
CA A:TYR323 3.8 19.1 1.0
C A:TYR323 3.8 22.3 1.0
CA A:ASP324 3.9 19.7 1.0
CD1 A:TYR323 4.3 22.6 1.0
O A:ASP324 4.4 22.9 1.0
O A:HOH724 4.4 37.6 1.0
C A:PRO322 4.5 19.0 1.0
O A:HOH739 4.5 26.0 1.0
N A:TYR323 4.5 20.6 1.0
O A:HOH519 4.5 28.1 1.0
C A:ASP324 4.7 21.0 1.0
CD2 A:HIS77 4.7 24.0 0.4
CZ A:ARG73 4.7 22.1 1.0
NE2 A:HIS77 4.8 28.3 0.4
CB A:TYR323 4.9 20.5 1.0
CE1 A:TYR323 4.9 25.5 1.0
CG A:TYR323 5.0 20.2 1.0

Chlorine binding site 5 out of 5 in 5ra2

Go back to Chlorine Binding Sites List in 5ra2
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N09036B 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 N09036B 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:HOH631 2.9 33.5 1.0
OG A:SER154 3.2 21.3 1.0
N A:SER154 3.3 20.3 1.0
ND2 A:ASN114 3.5 46.5 0.5
CB A:SER154 3.5 21.2 1.0
CD A:PRO153 3.7 19.5 1.0
N A:PRO153 3.8 17.7 1.0
CG A:LYS152 3.9 19.8 1.0
CB A:LYS152 3.9 19.5 1.0
CD A:LYS152 4.0 22.5 1.0
CA A:SER154 4.0 22.2 1.0
C A:PRO153 4.2 19.0 1.0
CB A:PRO153 4.2 20.7 1.0
CA A:PRO153 4.2 18.0 1.0
C A:LYS152 4.3 19.3 1.0
CB A:ALA184 4.4 22.8 1.0
CG A:PRO153 4.4 19.6 1.0
CE1 A:TYR188 4.4 15.5 1.0
CG A:ASN114 4.4 47.3 0.5
OD1 A:ASN114 4.6 51.0 0.5
CA A:LYS152 4.7 18.4 1.0
CE A:LYS152 4.8 26.9 1.0
OH A:TYR188 4.9 19.1 1.0
CZ A:TYR188 4.9 15.6 1.0
O A:LYS152 5.0 18.8 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 16:12:34 2024

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