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Chlorine in PDB 5ra9: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08051B in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08051B in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08051B 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 N08051B in Complex with Map Kinase P38-Alpha, PDB code: 5ra9 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) 29.76 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.919, 86.497, 126.673, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20.1

Other elements in 5ra9:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08051B 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 N08051B in Complex with Map Kinase P38-Alpha (pdb code 5ra9). 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 N08051B in Complex with Map Kinase P38-Alpha, PDB code: 5ra9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5ra9

Go back to Chlorine Binding Sites List in 5ra9
Chlorine binding site 1 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08051B 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 N08051B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:29.1
occ:0.30
 CL A:SWD401 0.0 29.1 0.3
C A:SWD401 1.6 24.4 0.3
C5 A:SWD401 2.5 24.0 0.3
N A:SWD401 2.6 22.1 0.3
N A:ASP168 2.8 17.2 0.3
S A:SWD401 3.2 23.9 0.3
CA A:LEU167 3.6 15.4 0.3
C A:LEU167 3.6 16.5 0.3
CB A:LEU167 3.6 16.1 0.3
CA A:ASP168 3.6 18.8 0.3
C1 A:SWD401 3.8 21.6 0.3
C2 A:SWD401 3.8 22.7 0.3
CG2 A:ILE84 3.9 28.5 1.0
CD1 A:TYR35 4.2 35.7 0.3
CE1 A:TYR35 4.2 35.7 0.3
N A:PHE169 4.3 18.9 0.3
N1 A:SWD401 4.3 21.8 0.3
CD2 A:LEU167 4.4 18.0 0.3
C A:ASP168 4.4 18.8 0.3
CG1 A:ILE84 4.5 32.4 1.0
CB A:ILE84 4.5 26.6 1.0
CG A:LEU167 4.6 17.3 0.3
C4 A:SWD401 4.6 23.6 0.3
CD2 A:PHE169 4.7 21.0 0.3
O A:LEU167 4.8 14.8 0.3
C3 A:SWD401 4.9 23.3 0.3
CB A:ASP168 4.9 18.8 0.3
CG A:TYR35 4.9 35.4 0.3

Chlorine binding site 2 out of 6 in 5ra9

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Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08051B 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 N08051B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:42.2
occ:1.00
 O A:HOH724 2.7 31.3 1.0
O A:HOH627 2.9 29.6 1.0
O A:HOH698 3.0 37.8 1.0
N A:ARG23 3.1 21.6 1.0
N A:GLU22 3.5 21.6 1.0
CB A:ARG23 3.6 28.1 1.0
CB A:PRO6 3.7 32.6 1.0
CB A:PRO21 3.8 20.2 1.0
CA A:ARG23 3.9 22.7 1.0
C A:GLU22 3.9 21.5 1.0
CB A:GLU22 3.9 21.2 1.0
CA A:GLU22 4.0 23.1 1.0
C A:PRO21 4.0 20.5 1.0
CG A:ARG23 4.1 26.0 1.0
CA A:PRO21 4.3 20.3 1.0
O A:THR7 4.4 26.1 1.0
CD A:ARG23 4.5 26.1 1.0
CA A:PRO6 4.7 30.4 1.0
CG A:GLU22 4.7 26.1 1.0
O A:HOH662 4.8 32.6 1.0
O A:PRO21 4.8 19.6 1.0
CG A:PRO6 4.8 35.1 1.0
N A:THR7 4.9 26.5 1.0
OE1 A:GLU22 4.9 24.9 1.0

Chlorine binding site 3 out of 6 in 5ra9

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Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08051B 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 N08051B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:42.3
occ:1.00
 N A:ASP101 3.2 27.5 1.0
N A:ASN100 3.3 30.1 1.0
OG1 A:THR91 3.3 25.4 1.0
CB A:ALA93 3.7 26.7 1.0
O A:GLU98 3.8 35.9 1.0
CB A:ASP101 3.8 27.9 1.0
N A:ALA93 3.9 27.9 1.0
CA A:ASN100 4.0 32.7 1.0
CA A:ASP101 4.0 25.5 1.0
C A:ASN100 4.0 32.7 1.0
CD A:PRO92 4.0 24.7 1.0
O A:ASP101 4.0 26.0 1.0
CB A:ASN100 4.1 39.5 1.0
C A:PHE99 4.2 33.8 1.0
CA A:ALA93 4.2 28.2 1.0
CA A:PHE99 4.2 27.9 1.0
CG A:PRO92 4.2 29.3 1.0
CG A:ASP101 4.4 37.1 1.0
C A:ASP101 4.5 22.7 1.0
OD2 A:ASP101 4.5 38.9 1.0
N A:PRO92 4.6 24.7 1.0
C A:GLU98 4.7 37.1 1.0
CB A:THR91 4.8 23.9 1.0
C A:PRO92 4.8 29.4 1.0
CD1 A:PHE99 4.8 23.2 1.0
ND2 A:ASN100 4.8 53.2 1.0
N A:PHE99 5.0 32.8 1.0
CB A:PRO92 5.0 25.3 1.0

Chlorine binding site 4 out of 6 in 5ra9

Go back to Chlorine Binding Sites List in 5ra9
Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08051B 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 N08051B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:62.5
occ:1.00
 O A:HOH512 2.8 41.1 1.0
O A:HOH510 2.9 38.7 1.0
N A:GLY85 3.3 24.0 1.0
ND1 A:HIS107 3.6 41.5 1.0
CE A:LYS165 3.6 39.6 1.0
CD A:LYS165 3.7 32.4 1.0
NZ A:LYS165 3.9 43.6 1.0
O A:VAL83 4.0 19.4 1.0
CA A:GLY85 4.1 25.2 1.0
C A:ILE84 4.2 21.1 1.0
CA A:ILE84 4.2 21.5 1.0
CD1 A:ILE84 4.4 39.7 1.0
O A:GLY85 4.4 23.0 1.0
CE1 A:HIS107 4.4 39.7 1.0
CG A:HIS107 4.6 36.6 1.0
C A:GLY85 4.7 23.7 1.0
CB A:HIS107 4.7 37.4 1.0
CE A:MET109 4.8 62.8 1.0
O A:HOH566 4.8 21.7 1.0
C A:VAL83 4.9 17.1 1.0

Chlorine binding site 5 out of 6 in 5ra9

Go back to Chlorine Binding Sites List in 5ra9
Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08051B 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 N08051B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:39.6
occ:1.00
 N A:ASP324 3.0 21.1 1.0
CB A:ASP324 3.6 22.8 1.0
NH2 A:ARG73 3.6 22.0 1.0
O A:PRO322 3.7 23.5 1.0
CA A:TYR323 3.8 20.6 1.0
C A:TYR323 3.8 22.6 1.0
CA A:ASP324 3.9 21.0 1.0
O A:ASP324 4.4 24.0 1.0
O A:HOH528 4.4 27.6 1.0
C A:PRO322 4.4 21.5 1.0
CD1 A:TYR323 4.4 24.1 1.0
O A:HOH707 4.4 36.8 1.0
O A:HOH717 4.5 27.9 1.0
N A:TYR323 4.5 20.0 1.0
C A:ASP324 4.7 21.5 1.0
CD2 A:HIS77 4.7 21.8 1.0
NE2 A:HIS77 4.8 29.7 1.0
CZ A:ARG73 4.8 21.0 1.0
CB A:TYR323 4.9 21.8 1.0

Chlorine binding site 6 out of 6 in 5ra9

Go back to Chlorine Binding Sites List in 5ra9
Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N08051B 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 N08051B in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:33.4
occ:1.00
 O A:HOH632 2.8 41.4 1.0
O A:HOH580 2.9 31.0 1.0
OG A:SER154 3.3 21.3 1.0
N A:SER154 3.3 19.6 1.0
ND2 A:ASN114 3.6 47.7 0.5
CB A:SER154 3.6 21.4 1.0
CD A:PRO153 3.7 18.2 1.0
N A:PRO153 3.8 17.1 1.0
CG A:LYS152 3.9 18.6 1.0
CB A:LYS152 4.0 18.3 1.0
CD A:LYS152 4.0 20.9 1.0
CA A:SER154 4.0 21.6 1.0
CB A:PRO153 4.2 21.2 1.0
OD1 A:ASN114 4.2 48.9 0.5
C A:PRO153 4.2 19.0 1.0
CA A:PRO153 4.2 17.1 1.0
CB A:ALA184 4.3 24.1 1.0
CG A:ASN114 4.3 46.1 0.5
C A:LYS152 4.3 18.6 1.0
CG A:PRO153 4.4 18.6 1.0
CE1 A:TYR188 4.4 17.1 1.0
CA A:LYS152 4.7 17.7 1.0
CE A:LYS152 4.8 23.2 1.0
OH A:TYR188 4.8 20.0 1.0
CZ A:TYR188 4.9 18.2 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 16:15:16 2024

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