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Chlorine in PDB 5ra4: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11337A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11337A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11337A 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 N11337A in Complex with Map Kinase P38-Alpha, PDB code: 5ra4 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 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.823, 85.946, 127.491, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 19.9

Other elements in 5ra4:

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11337A 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 N11337A in Complex with Map Kinase P38-Alpha (pdb code 5ra4). 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 N11337A in Complex with Map Kinase P38-Alpha, PDB code: 5ra4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5ra4

Go back to Chlorine Binding Sites List in 5ra4
Chlorine binding site 1 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11337A 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 N11337A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:43.1
occ:0.48
 CL A:SVG401 0.0 43.1 0.5
C A:SVG401 1.7 34.8 0.5
C1 A:SVG401 2.6 32.3 0.5
C5 A:SVG401 2.6 32.2 0.5
CD2 A:HIS126 3.0 43.0 1.0
N A:HIS126 3.5 26.5 1.0
CG A:HIS126 3.5 40.7 1.0
NE2 A:HIS126 3.5 42.2 1.0
CA A:HIS126 3.6 25.7 1.0
C A:ASP125 3.7 27.7 0.5
O A:ASP125 3.9 27.5 0.5
C4 A:SVG401 3.9 31.5 0.5
C2 A:SVG401 3.9 30.1 0.5
CB A:ASP125 4.0 34.1 0.5
CB A:HIS126 4.1 30.2 1.0
CE1 A:HIS126 4.2 44.3 1.0
ND1 A:HIS126 4.2 45.6 1.0
C3 A:SVG401 4.4 30.4 0.5
CA A:ASP125 4.5 30.8 0.5
OG1 A:THR123 4.7 40.5 0.5
OH A:TYR311 4.9 34.8 1.0
SG A:CYS162 4.9 42.4 1.0
C A:HIS126 4.9 23.7 1.0

Chlorine binding site 2 out of 6 in 5ra4

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Chlorine binding site 2 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11337A 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 N11337A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:45.2
occ:1.00
 O A:HOH754 2.6 31.3 1.0
O A:HOH715 2.8 35.3 1.0
O A:HOH639 3.0 27.7 1.0
N A:ARG23 3.1 21.4 1.0
N A:GLU22 3.5 23.4 1.0
CB A:ARG23 3.6 26.8 1.0
CB A:PRO6 3.8 33.4 1.0
CB A:PRO21 3.8 20.2 1.0
CA A:ARG23 3.9 22.5 1.0
C A:GLU22 3.9 21.7 1.0
CA A:GLU22 4.0 23.0 1.0
CB A:GLU22 4.0 21.5 1.0
CG A:ARG23 4.1 26.6 1.0
C A:PRO21 4.1 21.2 1.0
CA A:PRO21 4.4 20.4 1.0
O A:THR7 4.4 25.1 1.0
CD A:ARG23 4.5 25.4 1.0
O A:HOH677 4.8 31.5 1.0
CA A:PRO6 4.8 29.4 1.0
CG A:PRO6 4.8 34.4 1.0
O A:PRO21 4.8 19.5 1.0
CG A:GLU22 4.8 24.7 1.0
OE1 A:GLU22 5.0 25.0 1.0

Chlorine binding site 3 out of 6 in 5ra4

Go back to Chlorine Binding Sites List in 5ra4
Chlorine binding site 3 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11337A 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 N11337A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:39.0
occ:1.00
 N A:ASP101 3.2 27.2 1.0
N A:ASN100 3.3 28.8 1.0
OG1 A:THR91 3.4 24.0 1.0
O A:GLU98 3.8 37.2 1.0
CB A:ALA93 3.8 27.6 1.0
CB A:ASP101 3.8 28.6 1.0
N A:ALA93 3.8 27.1 1.0
CA A:ASN100 4.0 30.5 1.0
CA A:ASP101 4.0 28.7 1.0
C A:ASN100 4.0 30.1 1.0
CD A:PRO92 4.1 24.5 1.0
CB A:ASN100 4.1 36.4 1.0
CG A:PRO92 4.1 28.1 1.0
O A:ASP101 4.2 25.1 1.0
C A:PHE99 4.2 32.1 1.0
CA A:ALA93 4.2 28.8 1.0
CA A:PHE99 4.3 28.3 1.0
OD2 A:ASP101 4.4 34.6 1.0
CG A:ASP101 4.4 34.6 1.0
C A:ASP101 4.6 23.9 1.0
N A:PRO92 4.6 23.4 1.0
C A:PRO92 4.7 29.6 1.0
C A:GLU98 4.7 36.2 1.0
ND2 A:ASN100 4.8 49.5 1.0
CD1 A:PHE99 4.8 25.8 1.0
CB A:THR91 4.9 22.8 1.0
CB A:PRO92 5.0 26.6 1.0
N A:PHE99 5.0 31.2 1.0

Chlorine binding site 4 out of 6 in 5ra4

Go back to Chlorine Binding Sites List in 5ra4
Chlorine binding site 4 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11337A 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 N11337A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:47.8
occ:1.00
 O A:HOH571 2.9 34.9 1.0
O A:HOH531 3.1 38.5 1.0
N A:GLY85 3.2 24.4 1.0
ND1 A:HIS107 3.6 42.2 1.0
CD A:LYS165 3.9 30.9 1.0
CE A:LYS165 3.9 34.9 1.0
NZ A:LYS165 4.0 39.0 1.0
CA A:GLY85 4.0 26.9 1.0
O A:VAL83 4.0 19.6 1.0
CD1 A:ILE84 4.1 40.4 1.0
C A:ILE84 4.1 24.4 1.0
CA A:ILE84 4.1 23.0 1.0
O A:GLY85 4.4 25.2 1.0
CE1 A:HIS107 4.4 40.3 1.0
C A:GLY85 4.6 25.6 1.0
CG A:HIS107 4.7 36.7 1.0
CG1 A:ILE84 4.8 30.7 1.0
CB A:HIS107 4.8 32.6 1.0
CE A:MET109 4.8 56.5 1.0
O A:HOH535 4.9 22.1 1.0
C A:VAL83 4.9 19.3 1.0
N A:ILE84 4.9 20.2 1.0

Chlorine binding site 5 out of 6 in 5ra4

Go back to Chlorine Binding Sites List in 5ra4
Chlorine binding site 5 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11337A 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 N11337A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:38.7
occ:1.00
 N A:ASP324 3.0 20.2 1.0
CB A:ASP324 3.6 22.0 1.0
NH2 A:ARG73 3.6 24.6 1.0
O A:PRO322 3.7 21.6 1.0
CA A:TYR323 3.8 21.1 1.0
C A:TYR323 3.8 23.4 1.0
CA A:ASP324 3.9 20.2 1.0
CD1 A:TYR323 4.3 23.5 1.0
O A:HOH723 4.4 43.8 1.0
O A:ASP324 4.4 23.5 1.0
C A:PRO322 4.4 20.0 1.0
O A:HOH741 4.5 27.9 1.0
N A:TYR323 4.5 20.8 1.0
O A:HOH534 4.5 29.0 1.0
C A:ASP324 4.7 20.5 1.0
CZ A:ARG73 4.8 23.3 1.0
NE2 A:HIS77 4.8 27.6 1.0
CD2 A:HIS77 4.8 21.0 1.0
CB A:TYR323 4.9 22.2 1.0
CE1 A:TYR323 4.9 26.6 1.0
CG A:TYR323 5.0 21.1 1.0

Chlorine binding site 6 out of 6 in 5ra4

Go back to Chlorine Binding Sites List in 5ra4
Chlorine binding site 6 out of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N11337A 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 N11337A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:30.0
occ:1.00
 O A:HOH600 2.8 33.8 1.0
O A:HOH688 2.8 46.0 1.0
ND2 A:ASN114 3.2 46.5 0.5
OG A:SER154 3.3 23.2 1.0
N A:SER154 3.4 21.5 1.0
CB A:SER154 3.6 23.2 1.0
CD A:PRO153 3.7 20.6 1.0
N A:PRO153 3.9 19.7 1.0
CG A:LYS152 4.1 21.4 1.0
CB A:LYS152 4.1 21.5 1.0
CD A:LYS152 4.1 24.0 1.0
CA A:SER154 4.1 23.3 1.0
CB A:ALA184 4.2 24.6 1.0
CG A:ASN114 4.3 46.4 0.5
C A:PRO153 4.3 20.5 1.0
CB A:PRO153 4.3 22.8 1.0
CA A:PRO153 4.4 20.6 1.0
CE1 A:TYR188 4.4 16.7 1.0
CG A:PRO153 4.5 22.0 1.0
C A:LYS152 4.5 20.4 1.0
OD1 A:ASN114 4.5 51.1 0.5
OH A:TYR188 4.8 19.8 1.0
CA A:LYS152 4.8 20.0 1.0
CE A:LYS152 4.9 27.0 1.0
CZ A:TYR188 4.9 16.9 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 16:14:31 2024

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