Chlorine in PDB 7dbg: Yeast CRM1E (Apo) in Complex with Ran-RANBP1

The structure of Yeast CRM1E (Apo) in Complex with Ran-RANBP1, PDB code: 7dbg 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)	30.12 / 2.06
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.9, 105.9, 304.29, 90, 90, 90
R / Rfree (%)	20.1 / 22.8

The structure of Yeast CRM1E (Apo) in Complex with Ran-RANBP1 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1 (pdb code 7dbg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1, PDB code: 7dbg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Yeast CRM1E (Apo) in Complex with Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:72.7 occ:1.00 N A:VAL51 3.2 44.5 1.0 O A:HOH471 3.5 59.6 1.0 CA A:LEU50 3.7 42.0 1.0 O A:PRO49 3.9 46.7 1.0 C A:LEU50 4.0 43.5 1.0 CB A:VAL51 4.1 47.5 1.0 CD1 A:LEU50 4.1 44.8 1.0 O A:VAL51 4.1 42.9 1.0 CA A:VAL51 4.2 43.9 1.0 CG2 A:VAL51 4.4 48.0 1.0 N A:LEU50 4.5 44.3 1.0 C A:PRO49 4.5 45.9 1.0 C A:VAL51 4.7 40.6 1.0 NZ B:LYS133 4.7 50.1 1.0 CB A:LEU50 4.8 42.3 1.0 CD2 A:LEU31 4.8 51.0 1.0 CG A:LEU50 4.9 44.3 1.0

Chlorine binding site 2 out of 12 in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Yeast CRM1E (Apo) in Complex with Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1101 b:74.6 occ:1.00 NE2 C:HIS609 3.4 51.0 1.0 O C:HOH1529 3.7 50.8 1.0 CD C:LYS567 3.7 51.4 1.0 CE C:LYS567 3.8 53.3 1.0 CD2 C:HIS609 3.8 52.2 1.0 NZ C:LYS567 4.1 54.0 1.0 CB C:TYR608 4.3 57.0 1.0 CG C:LYS567 4.4 49.8 1.0 CD1 C:TYR608 4.4 65.1 1.0 CE1 C:HIS609 4.6 53.8 1.0 CG C:TYR608 4.6 60.9 1.0 CB C:LYS567 4.9 46.8 1.0

Chlorine binding site 3 out of 12 in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Yeast CRM1E (Apo) in Complex with Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1102 b:76.9 occ:1.00 O C:ARG325 3.3 40.3 1.0 N C:ALA328 3.6 42.0 1.0 N C:ARG327 3.6 36.4 1.0 C C:ARG325 3.6 40.6 1.0 CB C:ALA328 3.8 40.8 1.0 O C:ALA324 3.9 43.5 1.0 CG C:ARG327 3.9 37.9 1.0 N C:ASN326 3.9 37.4 1.0 O C:HOH1611 4.1 46.1 1.0 C C:ASN326 4.2 36.8 1.0 O C:LEU323 4.2 35.7 1.0 CA C:ALA328 4.3 41.4 1.0 CA C:ASN326 4.4 37.2 1.0 CA C:ARG327 4.4 39.1 1.0 C C:ARG327 4.5 37.7 1.0 C C:ALA324 4.5 39.8 1.0 CA C:ARG325 4.5 43.6 1.0 NE C:ARG327 4.6 38.4 1.0 CB C:ARG327 4.7 38.0 1.0 N C:ARG325 4.7 41.6 1.0 O C:HOH1530 4.8 65.6 1.0 CD C:ARG327 4.9 38.1 1.0 O C:HOH1436 4.9 56.3 1.0 CZ C:ARG327 5.0 39.0 1.0

Chlorine binding site 4 out of 12 in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Yeast CRM1E (Apo) in Complex with Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1103 b:81.5 occ:1.00 NH1 C:ARG77 3.5 86.1 1.0 NE2 C:HIS1005 4.0 43.2 1.0 O C:LYS1040 4.0 41.8 1.0 CD2 C:HIS1005 4.2 41.9 1.0 O C:ILE1039 4.2 40.2 1.0 C C:LYS1040 4.2 43.6 1.0 CE1 C:HIS1005 4.3 43.9 1.0 N C:GLU1041 4.3 43.0 1.0 CG C:HIS1005 4.5 40.1 1.0 CA C:GLU1041 4.5 44.4 1.0 ND1 C:HIS1005 4.5 40.9 1.0 C C:GLU1041 4.6 42.4 1.0 CZ C:ARG77 4.7 84.0 1.0 CG2 C:VAL1042 4.7 42.3 1.0 O C:GLU1041 4.7 39.5 1.0 O C:HOH1589 4.7 60.9 1.0 CA C:LYS1040 4.8 45.5 1.0 O C:ARG77 4.9 51.4 1.0

Chlorine binding site 5 out of 12 in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Yeast CRM1E (Apo) in Complex with Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1104 b:81.6 occ:1.00 O C:LYS183 3.8 36.5 1.0 CB C:SER187 3.8 47.1 1.0 CE1 C:PHE167 4.0 38.9 1.0 CB C:LYS183 4.1 41.2 1.0 C C:LYS183 4.1 41.8 1.0 OG C:SER187 4.2 50.5 1.0 CZ C:PHE167 4.2 38.6 1.0 OD1 C:ASN184 4.4 44.9 1.0 N C:ASN184 4.6 41.6 1.0 CA C:LYS183 4.6 42.6 1.0 CE3 C:TRP223 4.9 40.6 1.0 CA C:ASN184 4.9 42.3 1.0

Chlorine binding site 6 out of 12 in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Yeast CRM1E (Apo) in Complex with Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1107 b:76.8 occ:1.00 O C:HOH1333 3.3 53.5 1.0 CE3 C:TRP891 4.0 44.1 1.0 O C:HOH1235 4.1 55.2 1.0 CB C:TRP891 4.1 42.3 1.0 CD2 C:TRP891 4.1 42.8 1.0 CG C:TRP891 4.2 41.1 1.0 CB C:ASN846 4.3 42.6 1.0 O C:ASP887 4.3 46.4 1.0 CB C:ASP887 4.5 50.6 1.0 C C:ASP887 4.7 46.2 1.0 ND2 C:ASN846 4.7 42.9 1.0 CZ3 C:TRP891 4.8 45.1 1.0 O C:ASN846 4.9 44.2 1.0 CE2 C:TRP891 4.9 42.0 1.0 CD1 C:TRP891 5.0 41.6 1.0 CG C:ASN846 5.0 43.6 1.0

Chlorine binding site 7 out of 12 in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Yeast CRM1E (Apo) in Complex with Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1108 b:81.0 occ:1.00 CD C:PRO878 4.0 62.1 1.0 OE1 C:GLU839 4.0 58.8 1.0 CD2 C:LEU877 4.2 58.7 1.0 CB C:ALA881 4.3 51.7 1.0 CG C:GLN835 4.4 51.1 1.0 CG C:PRO878 4.4 64.4 1.0 O C:HOH1537 4.8 43.9 1.0 CA C:GLN835 5.0 45.8 1.0

Chlorine binding site 8 out of 12 in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Yeast CRM1E (Apo) in Complex with Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1110 b:81.3 occ:0.50 OE1 C:GLN630 4.0 58.3 1.0 O C:HOH1296 4.6 56.7 1.0 CD C:GLN630 4.8 58.0 1.0 NE2 C:GLN670 4.8 55.0 1.0

Chlorine binding site 9 out of 12 in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Yeast CRM1E (Apo) in Complex with Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1111 b:83.9 occ:1.00 CB C:ALA1002 3.8 41.1 1.0 OG1 C:THR944 3.9 42.5 1.0 CA C:PHE941 4.2 48.0 1.0 CE2 C:PHE1003 4.2 40.8 1.0 N C:PHE941 4.3 44.0 1.0 C C:PHE940 4.4 43.3 1.0 O C:PHE940 4.4 43.1 1.0 CZ C:PHE1003 4.6 40.3 1.0 CB C:PHE940 4.6 43.9 1.0 CE C:MET998 4.7 48.5 1.0 CB C:PHE941 4.9 50.8 1.0 CG C:MET998 4.9 46.3 1.0 CD1 C:PHE941 4.9 59.5 1.0

Chlorine binding site 10 out of 12 in the Yeast CRM1E (Apo) in Complex with Ran-RANBP1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Yeast CRM1E (Apo) in Complex with Ran-RANBP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1112 b:66.4 occ:1.00 O C:HOH1504 3.3 43.4 1.0 CB C:GLU357 4.0 37.1 1.0 O A:LEU144 4.0 35.5 1.0 CD C:GLN313 4.0 39.1 1.0 CG C:GLN313 4.1 37.2 1.0 NE2 C:GLN313 4.2 35.6 1.0 N C:LEU358 4.3 36.0 1.0 CD2 A:HIS139 4.3 38.7 1.0 OE1 C:GLN313 4.4 39.4 1.0 C C:GLU357 4.4 37.7 1.0 CA A:ARG140 4.5 37.4 1.0 O C:GLU357 4.7 39.7 1.0 CA C:LEU358 4.7 36.6 1.0 O A:HIS139 4.8 37.4 1.0 CA C:GLU357 4.8 38.1 1.0 O A:ARG140 4.8 34.8 1.0 CB C:LEU358 5.0 36.8 1.0 CB C:GLN313 5.0 36.7 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