Atomistry » Chlorine » PDB 7k9w-7kil » 7kdx
Atomistry »
  Chlorine »
    PDB 7k9w-7kil »
      7kdx »

Chlorine in PDB 7kdx: Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine

Protein crystallography data

The structure of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine, PDB code: 7kdx was solved by H.L.Knox, S.J.Booker, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.35 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.644, 137.739, 77.914, 90, 90.47, 90
R / Rfree (%) 16.5 / 19.3

Other elements in 7kdx:

The structure of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Cobalt (Co) 2 atoms
Potassium (K) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine (pdb code 7kdx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine, PDB code: 7kdx:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7kdx

Go back to Chlorine Binding Sites List in 7kdx
Chlorine binding site 1 out of 2 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1919

b:66.2
occ:1.00
ND1 B:HIS264 3.1 30.3 1.0
CE1 B:HIS264 3.9 29.2 1.0
CG B:GLU268 4.1 41.8 1.0
CG B:HIS264 4.2 25.0 1.0
O B:HOH2250 4.3 23.9 1.0
O B:HIS264 4.4 18.2 1.0
OE2 B:GLU268 4.4 58.2 1.0
CB B:HIS264 4.4 18.2 1.0
CB B:ALA267 4.5 15.0 1.0
CA B:HIS264 4.7 20.6 1.0
CG2 B:THR297 4.7 20.6 1.0
CD B:GLU268 4.8 54.3 1.0
C B:HIS264 5.0 19.6 1.0
N B:GLU268 5.0 18.2 1.0

Chlorine binding site 2 out of 2 in 7kdx

Go back to Chlorine Binding Sites List in 7kdx
Chlorine binding site 2 out of 2 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1920

b:28.7
occ:1.00
NZ B:LYS225 3.3 49.3 1.0
N B:ARG258 3.3 20.0 1.0
CD B:PRO257 3.4 22.0 1.0
CG B:ARG258 3.6 21.7 1.0
CB B:ARG258 3.6 21.1 1.0
N B:PRO257 3.7 18.4 1.0
CB B:PRO257 3.9 20.1 1.0
CG B:PRO257 4.0 23.3 1.0
CB B:MET256 4.0 23.2 1.0
CE B:LYS225 4.0 45.7 1.0
CA B:ARG258 4.1 18.2 1.0
C B:PRO257 4.2 21.2 1.0
CA B:PRO257 4.2 21.0 1.0
CD B:ARG258 4.2 24.4 1.0
C B:MET256 4.3 18.1 1.0
O B:HOH2199 4.4 40.6 1.0
CA B:MET256 4.6 19.7 1.0
CG B:MET256 4.7 31.5 1.0
SD B:MET256 4.8 37.9 1.0
CD B:LYS225 4.8 42.0 1.0
NE B:ARG258 5.0 21.6 1.0

Reference:

H.L.Knox, E.K.Sinner, C.A.Townsend, A.K.Boal, S.J.Booker. Structure of A B 12 -Dependent Radical Sam Enzyme in Carbapenem Biosynthesis. Nature V. 602 343 2022.
ISSN: ESSN 1476-4687
PubMed: 35110734
DOI: 10.1038/S41586-021-04392-4
Page generated: Sun Jul 13 03:17:43 2025

Last articles

Na in 1T3M
Na in 1T3P
Na in 1T2X
Na in 1SUZ
Na in 1SVY
Na in 1SVE
Na in 1SUP
Na in 1SU3
Na in 1SU4
Na in 1SUE
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy