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Chlorine in PDB 5r9k: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14246A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14246A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14246A 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 N14246A in Complex with Map Kinase P38-Alpha, PDB code: 5r9k 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) 29.21 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.838, 86.228, 126.549, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 20.1

Other elements in 5r9k:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14246A 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 N14246A in Complex with Map Kinase P38-Alpha (pdb code 5r9k). 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 N14246A in Complex with Map Kinase P38-Alpha, PDB code: 5r9k:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5r9k

Go back to Chlorine Binding Sites List in 5r9k
Chlorine binding site 1 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14246A 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 N14246A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:36.7
occ:1.00
 O A:HOH786 2.7 28.2 1.0
O A:HOH649 3.0 26.0 1.0
O A:HOH746 3.1 32.7 1.0
N A:ARG23 3.1 20.8 1.0
N A:GLU22 3.5 19.3 1.0
CB A:ARG23 3.7 26.8 1.0
CB A:PRO6 3.7 26.7 1.0
CB A:PRO21 3.8 19.0 1.0
C A:GLU22 3.9 19.6 1.0
CA A:ARG23 3.9 20.4 1.0
CB A:GLU22 3.9 20.6 1.0
CA A:GLU22 3.9 20.4 1.0
C A:PRO21 4.1 18.6 1.0
CG A:ARG23 4.1 23.2 1.0
CA A:PRO21 4.3 18.8 1.0
O A:THR7 4.4 22.7 1.0
CD A:ARG23 4.5 22.5 1.0
O A:HOH709 4.7 29.1 1.0
CA A:PRO6 4.8 27.5 1.0
O A:PRO21 4.8 18.5 1.0
CG A:PRO6 4.8 29.9 1.0
CG A:GLU22 4.9 22.9 1.0
N A:THR7 4.9 24.0 1.0
O A:GLU22 5.0 20.9 1.0
OE1 A:GLU22 5.0 23.1 1.0

Chlorine binding site 2 out of 6 in 5r9k

Go back to Chlorine Binding Sites List in 5r9k
Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14246A 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 N14246A 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:ASN100 3.2 28.3 1.0
N A:ASP101 3.3 25.7 1.0
OG1 A:THR91 3.4 23.1 1.0
O A:GLU98 3.7 34.8 1.0
CB A:ALA93 3.7 24.3 1.0
N A:ALA93 3.9 23.2 1.0
CA A:ASN100 3.9 29.0 1.0
CB A:ASN100 4.0 36.8 1.0
CG A:PRO92 4.0 30.7 1.0
C A:ASN100 4.1 29.9 1.0
CD A:PRO92 4.1 23.9 1.0
CB A:ASP101 4.1 25.6 1.0
O A:ASP101 4.1 24.2 1.0
C A:PHE99 4.2 29.8 1.0
CA A:ASP101 4.2 25.3 1.0
CA A:PHE99 4.2 26.3 1.0
CA A:ALA93 4.2 24.3 1.0
OD2 A:ASP101 4.5 38.7 1.0
CG A:ASP101 4.6 35.0 1.0
N A:PRO92 4.6 23.1 1.0
C A:ASP101 4.6 20.6 1.0
C A:GLU98 4.7 33.1 1.0
C A:PRO92 4.7 26.2 1.0
CB A:THR91 4.8 21.1 1.0
CD1 A:PHE99 4.8 23.6 1.0
ND2 A:ASN100 4.9 42.9 1.0
N A:PHE99 4.9 30.1 1.0
CB A:PRO92 5.0 26.9 1.0

Chlorine binding site 3 out of 6 in 5r9k

Go back to Chlorine Binding Sites List in 5r9k
Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14246A 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 N14246A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:27.6
occ:0.58
 O A:HOH568 2.7 32.6 1.0
N A:ASP324 3.0 21.7 1.0
NH2 A:ARG73 3.6 20.9 1.0
CB A:ASP324 3.6 22.1 1.0
O A:PRO322 3.7 22.6 1.0
CA A:TYR323 3.8 18.7 1.0
C A:TYR323 3.9 20.8 1.0
CA A:ASP324 3.9 21.8 1.0
O A:HOH761 4.4 36.1 1.0
O A:ASP324 4.4 23.4 1.0
CD1 A:TYR323 4.4 21.3 1.0
C A:PRO322 4.5 20.6 1.0
O A:HOH536 4.5 27.5 1.0
N A:TYR323 4.5 19.9 1.0
O A:HOH775 4.5 25.0 1.0
C A:ASP324 4.6 20.9 1.0
ND1 A:HIS77 4.6 26.0 1.0
CE1 A:HIS77 4.7 24.2 1.0
CZ A:ARG73 4.8 19.1 1.0
CB A:TYR323 4.9 20.4 1.0

Chlorine binding site 4 out of 6 in 5r9k

Go back to Chlorine Binding Sites List in 5r9k
Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14246A 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 N14246A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:27.8
occ:1.00
 O A:HOH635 2.7 34.6 1.0
O A:HOH618 3.0 30.9 1.0
N A:SER154 3.2 18.3 1.0
OG A:SER154 3.3 21.9 1.0
OD1 A:ASN114 3.6 42.3 1.0
CB A:SER154 3.6 21.3 1.0
CD A:PRO153 3.7 18.1 1.0
N A:PRO153 3.8 16.9 1.0
CG A:LYS152 3.9 17.1 1.0
CB A:LYS152 3.9 17.8 1.0
CA A:SER154 4.0 18.6 1.0
CD A:LYS152 4.1 19.5 1.0
C A:PRO153 4.2 19.6 1.0
CB A:PRO153 4.2 19.9 1.0
CB A:ALA184 4.2 20.6 1.0
CA A:PRO153 4.2 17.6 1.0
C A:LYS152 4.3 15.7 1.0
CG A:PRO153 4.4 18.4 1.0
CG A:ASN114 4.4 41.3 1.0
CE1 A:TYR188 4.5 16.4 1.0
ND2 A:ASN114 4.5 41.2 1.0
CA A:LYS152 4.7 17.6 1.0
CE A:LYS152 4.8 18.4 1.0
OH A:TYR188 4.8 18.5 1.0
O A:HOH503 4.9 35.8 1.0
CZ A:TYR188 4.9 17.4 1.0

Chlorine binding site 5 out of 6 in 5r9k

Go back to Chlorine Binding Sites List in 5r9k
Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14246A 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 N14246A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:33.5
occ:0.90
 NH2 A:ARG189 3.2 32.2 1.0
N A:HIS174 3.4 32.0 1.0
CD2 A:HIS174 3.7 24.3 1.0
NH1 A:ARG189 3.8 33.1 1.0
CZ A:ARG189 4.0 27.8 1.0
CA A:ARG173 4.1 30.8 1.0
CB A:HIS174 4.1 28.7 1.0
CG A:HIS174 4.2 26.5 1.0
O A:HOH609 4.3 29.1 1.0
C A:ARG173 4.3 33.1 1.0
O A:HOH660 4.3 22.2 1.0
CB A:ARG173 4.4 33.6 1.0
CA A:HIS174 4.4 32.6 1.0
CB A:ARG149 4.6 22.5 1.0
CD A:ARG149 4.7 31.1 1.0
NE2 A:HIS174 4.9 24.8 1.0
O A:HIS174 5.0 36.1 1.0

Chlorine binding site 6 out of 6 in 5r9k

Go back to Chlorine Binding Sites List in 5r9k
Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N14246A 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 N14246A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:34.3
occ:0.60
 N A:GLN264 3.1 22.5 1.0
CA A:ALA263 3.7 23.3 1.0
C A:ALA263 3.9 23.4 1.0
CB A:GLN264 3.9 26.0 1.0
CG A:GLN264 3.9 27.8 1.0
CB A:ALA263 4.1 26.1 1.0
CA A:GLN264 4.1 20.6 1.0
NE2 A:GLN264 4.5 31.6 1.0
CD A:GLN264 4.7 34.0 1.0
O A:GLN264 4.8 23.5 1.0
C A:GLN264 4.9 22.9 1.0
N A:ALA263 4.9 23.3 1.0
O A:LEU262 5.0 27.0 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: Fri Jul 26 16:06:17 2024

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