Bromine in PDB 4nkt: Structure of CID1 in Complex with the Utp Analog Umpnpp

The structure of Structure of CID1 in Complex with the Utp Analog Umpnpp, PDB code: 4nkt was solved by P.Munoz-Tello, C.Gabus, S.Thore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.84 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.770, 77.320, 82.110, 90.00, 90.86, 90.00
R / Rfree (%)	17.9 / 21.2

The structure of Structure of CID1 in Complex with the Utp Analog Umpnpp also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Bromine atom in the Structure of CID1 in Complex with the Utp Analog Umpnpp (pdb code 4nkt). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Structure of CID1 in Complex with the Utp Analog Umpnpp, PDB code: 4nkt:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Structure of CID1 in Complex with the Utp Analog Umpnpp


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of CID1 in Complex with the Utp Analog Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Br402 b:27.9 occ:1.00 O A:HOH784 2.8 37.2 1.0 O A:HOH541 3.4 20.5 1.0 NH2 A:ARG277 3.7 24.6 1.0 CG A:LYS282 4.2 33.1 1.0 NE A:ARG277 4.3 18.7 1.0 O A:HOH775 4.3 28.5 1.0 CZ A:ARG277 4.4 24.1 1.0 CB A:TYR281 4.5 19.6 1.0 CB A:LYS282 4.6 21.2 1.0 O A:ARG277 4.6 13.9 1.0 CD2 A:TYR281 4.7 23.3 1.0 O A:HOH509 4.8 12.7 1.0 CB A:ARG277 4.9 13.5 1.0

Bromine binding site 2 out of 3 in the Structure of CID1 in Complex with the Utp Analog Umpnpp


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of CID1 in Complex with the Utp Analog Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Br403 b:20.7 occ:0.60 N3A A:2KH401 3.3 27.3 0.7 O A:HOH635 3.4 24.1 1.0 O3' A:2KH401 3.5 19.0 1.0 NZ A:LYS193 3.8 21.0 1.0 O2B A:2KH401 3.9 40.8 1.0 CG2 A:VAL215 3.9 8.4 1.0 CA A:TYR212 3.9 12.8 1.0 CE A:LYS193 4.0 21.9 1.0 N A:TYR212 4.1 10.1 1.0 CB A:TYR212 4.3 10.0 1.0 CB A:SER90 4.3 18.4 1.0 PB A:2KH401 4.3 32.5 0.5 C3' A:2KH401 4.4 18.2 1.0 C A:SER211 4.5 11.4 1.0 PA A:2KH401 4.5 24.3 1.0 CD1 A:TYR212 4.5 12.3 1.0 O5' A:2KH401 4.5 22.8 1.0 C5' A:2KH401 4.5 20.7 1.0 O A:SER211 4.6 9.9 1.0 N A:SER90 4.6 17.8 1.0 CD2 A:LEU175 4.7 15.1 1.0 CB A:VAL215 4.7 8.5 1.0 CA A:SER90 4.7 18.6 1.0 CB A:SER211 4.8 18.7 1.0 CG A:TYR212 4.9 12.9 1.0 O1A A:2KH401 5.0 18.3 1.0 O A:HOH562 5.0 21.4 1.0

Bromine binding site 3 out of 3 in the Structure of CID1 in Complex with the Utp Analog Umpnpp


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of CID1 in Complex with the Utp Analog Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Br402 b:18.8 occ:0.61 N3A B:2KH401 3.0 26.5 0.7 O2B B:2KH401 3.5 44.5 1.0 O B:HOH616 3.6 30.8 1.0 O3' B:2KH401 3.7 19.4 1.0 CG2 B:VAL215 3.9 12.4 1.0 PB B:2KH401 3.9 39.0 0.5 NZ B:LYS193 3.9 22.4 1.0 CA B:TYR212 4.0 14.4 1.0 N B:TYR212 4.1 12.5 1.0 PA B:2KH401 4.3 31.4 1.0 CB B:TYR212 4.4 14.3 1.0 C B:SER211 4.4 14.0 1.0 C3' B:2KH401 4.5 20.1 1.0 O B:SER211 4.5 12.7 1.0 CB B:SER90 4.5 26.0 1.0 CD2 B:LEU175 4.5 18.9 1.0 C5' B:2KH401 4.6 26.0 1.0 O5' B:2KH401 4.6 29.2 1.0 CD1 B:TYR212 4.6 14.3 1.0 O3B B:2KH401 4.6 42.9 0.9 N B:SER90 4.7 21.1 1.0 CB B:SER211 4.7 19.2 1.0 CB B:VAL215 4.7 10.5 1.0 O1A B:2KH401 4.8 20.4 1.0 O B:HOH693 4.8 30.9 1.0 CA B:SER90 4.8 18.9 1.0 CE B:LYS193 4.9 23.4 1.0

P.Munoz-Tello, C.Gabus, S.Thore. A Critical Switch in the Enzymatic Properties of the CID1 Protein Deciphered From Its Product-Bound Crystal Structure. Nucleic Acids Res. V. 42 3372 2014.
ISSN: ISSN 0305-1048
PubMed: 24322298
DOI: 10.1093/NAR/GKT1278