Chlorine in PDB 6m60: Plumbagin in Complex with CRM1#-Ran-RANBP1

The structure of Plumbagin in Complex with CRM1#-Ran-RANBP1, PDB code: 6m60 was solved by Q.Sun, Y.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.72 / 2.17
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.59, 105.59, 305.04, 90, 90, 90
R / Rfree (%)	18.1 / 21.3

The structure of Plumbagin in Complex with CRM1#-Ran-RANBP1 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Plumbagin in Complex with CRM1#-Ran-RANBP1 (pdb code 6m60). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Plumbagin in Complex with CRM1#-Ran-RANBP1, PDB code: 6m60:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Plumbagin in Complex with CRM1#-Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Plumbagin in Complex with CRM1#-Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1102 b:92.6 occ:1.00 NE2 C:HIS609 3.4 71.5 1.0 O C:HOH1364 3.7 68.9 1.0 NZ C:LYS567 3.8 75.6 1.0 CD2 C:HIS609 3.8 71.7 1.0 CD C:LYS567 4.0 70.0 1.0 CE C:LYS567 4.1 72.5 1.0 CD1 C:TYR608 4.3 81.2 1.0 CB C:TYR608 4.3 72.2 1.0 CE1 C:HIS609 4.5 72.2 1.0 CG C:TYR608 4.5 76.3 1.0 CG C:LYS567 4.6 67.7 1.0

Chlorine binding site 2 out of 3 in the Plumbagin in Complex with CRM1#-Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Plumbagin in Complex with CRM1#-Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1103 b:91.6 occ:1.00 O C:ARG325 3.6 47.4 1.0 O C:ALA324 3.6 54.8 1.0 N C:ALA328 3.8 53.1 1.0 N C:ARG327 3.8 48.3 1.0 CG C:ARG327 3.8 51.7 1.0 C C:ARG325 3.8 50.8 1.0 O C:LEU323 4.1 50.0 1.0 CB C:ALA328 4.1 56.2 1.0 N C:ASN326 4.1 48.8 1.0 O C:HOH1571 4.2 66.0 1.0 C C:ALA324 4.3 47.8 1.0 C C:ASN326 4.4 49.2 1.0 O C:HOH1457 4.5 73.5 1.0 NE C:ARG327 4.5 51.0 1.0 CA C:ALA328 4.6 55.2 1.0 CA C:ARG327 4.6 52.0 1.0 CA C:ASN326 4.6 48.9 1.0 CA C:ARG325 4.6 50.8 1.0 C C:ARG327 4.6 49.4 1.0 CZ C:ARG327 4.7 53.5 1.0 N C:ARG325 4.8 49.4 1.0 CB C:ARG327 4.8 50.9 1.0 CD C:ARG327 4.9 52.1 1.0 NH2 C:ARG327 4.9 56.8 1.0

Chlorine binding site 3 out of 3 in the Plumbagin in Complex with CRM1#-Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Plumbagin in Complex with CRM1#-Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1104 b:97.2 occ:1.00 O C:LYS183 3.8 52.5 1.0 CB C:SER187 4.0 61.5 1.0 CB C:LYS183 4.0 54.6 1.0 C C:LYS183 4.0 54.1 1.0 CE1 C:PHE167 4.2 50.3 1.0 OG C:SER187 4.3 66.8 1.0 OD1 C:ASN184 4.3 59.3 1.0 CZ C:PHE167 4.4 49.4 1.0 N C:ASN184 4.5 52.5 1.0 CA C:LYS183 4.6 54.0 1.0 CA C:ASN184 4.8 55.1 1.0 CG C:LYS183 4.9 55.0 1.0

Y.Lei, Y.Li, Y.Tan, Z.Qian, Q.Zhou, D.Jia, Q.Sun. Novel Mechanistic Observations and Nes-Binding Groove Features Revealed By the CRM1 Inhibitors Plumbagin and Oridonin. J.Nat.Prod. V. 84 1478 2021.
ISSN: ESSN 1520-6025
PubMed: 33890470
DOI: 10.1021/ACS.JNATPROD.0C01231