Chlorine in PDB 4b8e: Pry-Spry Domain of TRIM25

All present enzymatic activity of Pry-Spry Domain of TRIM25:
6.3.2.19;

The structure of Pry-Spry Domain of TRIM25, PDB code: 4b8e was solved by N.J.Kershaw, A.A.D'cruz, N.A.Nicola, S.E.Nicholson, J.J.Babon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.505 / 1.78
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.149, 73.561, 91.009, 90.00, 90.00, 90.00
R / Rfree (%)	17.34 / 19.44

The binding sites of Chlorine atom in the Pry-Spry Domain of TRIM25 (pdb code 4b8e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Pry-Spry Domain of TRIM25, PDB code: 4b8e:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Pry-Spry Domain of TRIM25


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pry-Spry Domain of TRIM25 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1634 b:27.2 occ:1.00 O B:HOH2040 3.1 31.8 1.0 N A:LYS513 3.1 18.9 1.0 O A:HOH2067 3.2 30.5 1.0 NZ B:LYS513 3.2 43.1 1.0 N A:ASN514 3.4 21.7 1.0 O A:ASN514 3.6 21.1 1.0 CE B:LYS513 3.6 36.3 1.0 O A:HOH2066 3.7 26.9 1.0 CA A:TYR512 3.9 17.5 1.0 CB A:LYS513 4.0 22.7 1.0 CA A:LYS513 4.0 23.5 1.0 C A:TYR512 4.0 16.3 1.0 C A:LYS513 4.2 23.6 1.0 O B:HOH2070 4.2 42.4 1.0 CA A:ASN514 4.3 23.6 1.0 C A:ASN514 4.4 19.6 1.0 O A:CYS511 4.4 19.5 1.0 CE1 A:HIS517 4.4 25.9 1.0 NE2 A:HIS517 4.5 21.6 1.0 CB A:ASN514 4.6 27.0 1.0 CB A:TYR512 4.6 18.3 1.0 O A:HOH2062 4.6 32.6 1.0 O B:HOH2068 4.7 34.8 1.0 CD1 A:TYR512 4.8 20.3 1.0 N A:TYR512 4.9 15.1 1.0

Chlorine binding site 2 out of 6 in the Pry-Spry Domain of TRIM25


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pry-Spry Domain of TRIM25 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1635 b:26.0 occ:1.00 NE1 A:TRP621 3.2 20.5 1.0 OG A:SER504 3.2 21.6 0.6 N A:SER504 3.3 19.4 1.0 CA A:CYS503 3.6 17.6 1.0 CD1 A:PHE623 3.9 28.4 1.0 C A:CYS503 3.9 18.1 1.0 CB A:CYS503 4.1 19.1 1.0 CD1 A:TRP621 4.1 15.3 1.0 CB A:SER504 4.1 21.4 0.4 CE1 A:PHE623 4.1 35.8 1.0 CE2 A:TRP621 4.2 19.4 1.0 CB A:SER504 4.2 21.1 0.6 CA A:SER504 4.3 20.1 0.4 CA A:SER504 4.3 19.8 0.6 O A:TYR502 4.5 23.3 1.0 CZ2 A:TRP621 4.6 20.4 1.0 SG A:CYS503 4.7 26.9 1.0 N A:CYS503 4.8 17.7 1.0 NE A:ARG546 4.9 30.3 1.0 CG A:PHE623 4.9 28.4 1.0 CD A:ARG546 5.0 26.3 1.0

Chlorine binding site 3 out of 6 in the Pry-Spry Domain of TRIM25


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pry-Spry Domain of TRIM25 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1636 b:43.6 occ:1.00 N A:ARG454 3.1 27.1 1.0 CB A:LYS601 3.2 47.4 1.0 N A:VAL602 3.4 34.3 1.0 CA A:LYS601 3.5 43.7 1.0 CA A:SER453 3.7 32.6 1.0 CB A:ARG454 3.8 26.0 1.0 CB A:SER453 3.9 33.4 1.0 CG2 A:VAL602 3.9 26.6 1.0 C A:SER453 3.9 32.2 1.0 C A:LYS601 4.0 40.0 1.0 CA A:ARG454 4.0 24.1 1.0 O A:HOH2006 4.1 44.9 1.0 CA A:VAL602 4.5 26.3 1.0 CB A:VAL602 4.6 27.1 1.0 CG1 A:VAL602 4.8 30.2 1.0 N A:LYS601 4.9 47.6 1.0 O A:VAL602 4.9 27.3 1.0

Chlorine binding site 4 out of 6 in the Pry-Spry Domain of TRIM25


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pry-Spry Domain of TRIM25 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1637 b:48.4 occ:1.00 ND1 A:HIS590 2.6 40.0 1.0 O A:HOH2125 2.9 41.5 1.0 ND2 A:ASN587 3.0 23.6 1.0 CE1 A:HIS590 3.2 41.3 1.0 CD1 A:ILE516 3.5 30.8 1.0 OD1 A:ASN587 3.6 24.1 1.0 CG1 A:VAL445 3.7 32.9 1.0 CG A:ASN587 3.7 22.7 1.0 CG A:HIS590 3.8 39.3 1.0 CG1 A:ILE516 4.2 25.1 1.0 CB A:HIS590 4.2 27.4 1.0 CB A:ASP589 4.4 29.7 1.0 NE2 A:HIS590 4.5 44.1 1.0 N A:HIS590 4.6 26.2 1.0 CG2 A:VAL445 4.7 42.1 1.0 CE1 A:PHE449 4.7 28.4 1.0 CB A:VAL445 4.7 36.1 1.0 CD2 A:HIS590 4.7 44.5 1.0 OD2 A:ASP589 4.8 30.9 1.0 O A:HOH2015 5.0 38.1 1.0

Chlorine binding site 5 out of 6 in the Pry-Spry Domain of TRIM25


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pry-Spry Domain of TRIM25 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1638 b:50.9 occ:1.00 N A:ASN561 2.9 21.6 1.0 CE1 A:PHE528 3.0 37.8 1.0 O A:HOH2101 3.1 29.2 1.0 CD1 A:PHE528 3.2 37.7 1.0 N A:ASN560 3.4 20.5 1.0 CA A:ASN561 3.6 24.2 1.0 C A:PHE559 3.7 19.9 1.0 CA A:PHE559 3.9 19.1 1.0 N A:PHE559 3.9 18.2 1.0 C A:ASN560 4.0 22.1 1.0 OD1 A:ASN561 4.0 29.5 1.0 CA A:ASN560 4.1 21.8 1.0 CZ A:PHE528 4.3 38.0 1.0 O A:ASN527 4.3 36.3 1.0 C A:TRP558 4.3 20.1 1.0 O A:ASN526 4.3 51.1 1.0 O A:PHE559 4.4 20.2 1.0 O A:TRP558 4.5 17.4 1.0 C A:ASN561 4.6 28.2 1.0 CG A:PHE528 4.6 40.5 1.0 N A:LYS562 4.7 21.1 1.0 CG A:ASN561 4.7 28.3 1.0 CB A:ASN561 4.8 24.4 1.0 C A:ASN527 4.8 35.7 1.0 CB A:TRP558 4.9 18.8 1.0 CA A:PHE528 5.0 26.1 1.0 C A:ASN526 5.0 47.4 1.0 O A:LYS562 5.0 19.1 1.0

Chlorine binding site 6 out of 6 in the Pry-Spry Domain of TRIM25


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Pry-Spry Domain of TRIM25 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1633 b:45.5 occ:1.00 NE1 B:TRP621 3.1 39.5 1.0 N B:SER504 3.3 35.8 1.0 OG B:SER504 3.5 43.7 1.0 CA B:CYS503 3.6 37.8 1.0 C B:CYS503 3.9 35.8 1.0 CB B:CYS503 3.9 37.2 1.0 CD1 B:TRP621 4.0 37.3 1.0 CE2 B:TRP621 4.1 40.9 1.0 CB B:SER504 4.3 41.5 1.0 CA B:SER504 4.4 37.1 1.0 CD1 B:PHE623 4.4 52.7 1.0 CZ2 B:TRP621 4.5 41.0 1.0 O B:TYR502 4.5 37.6 1.0 SG B:CYS503 4.7 44.5 1.0 CE1 B:PHE623 4.7 55.7 1.0 N B:CYS503 4.8 38.2 1.0 NE B:ARG546 4.8 45.9 1.0 CD B:ARG546 4.9 41.0 1.0

A.A.D'cruz, N.J.Kershaw, J.J.Chiang, M.K.Wang, N.A.Nicola, J.J.Babon, M.U.Gack, S.E.Nicholson. Crystal Structure of the TRIM25 B30.2 (Pryspry) Domain: A Key Component of Antiviral Signaling. Biochem.J. V. 456 231 2013.
ISSN: ISSN 0264-6021
PubMed: 24015671
DOI: 10.1042/BJ20121425