Chlorine in PDB 2vfx: Structure of the Symmetric MAD2 Dimer

The structure of Structure of the Symmetric MAD2 Dimer, PDB code: 2vfx was solved by M.Yang, B.Li, C.-J.Liu, D.R.Tomchick, M.Machius, J.Rizo, H.Yu, X.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.337, 191.407, 154.307, 90.00, 90.02, 90.00
R / Rfree (%)	20.8 / 24.7

The structure of Structure of the Symmetric MAD2 Dimer also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Chlorine atom in the Structure of the Symmetric MAD2 Dimer (pdb code 2vfx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 37 binding sites of Chlorine where determined in the Structure of the Symmetric MAD2 Dimer, PDB code: 2vfx:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 37 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Symmetric MAD2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1207 b:18.2 occ:1.00 O A:HOH2028 3.2 26.7 1.0 N A:ILE175 3.3 15.8 1.0 NE A:ARG99 3.5 22.3 1.0 CD A:ARG99 3.6 19.4 1.0 CG2 A:ILE175 3.7 16.4 1.0 CA A:PHE174 3.7 16.6 1.0 CD1 A:PHE174 3.9 14.3 1.0 CZ A:ARG99 3.9 22.6 1.0 O A:ILE175 4.0 18.0 1.0 C A:PHE174 4.1 16.4 1.0 NH1 A:ARG99 4.3 24.4 1.0 CB A:PHE174 4.3 15.6 1.0 CA A:ILE175 4.3 16.6 1.0 CB A:ILE175 4.4 16.1 1.0 NH2 A:ARG99 4.4 24.8 1.0 CG A:PHE174 4.6 15.7 1.0 C A:ILE175 4.6 17.7 1.0 O A:GLN173 4.6 19.3 1.0 O A:HOH2071 4.7 26.3 1.0 O A:HOH2072 4.7 37.5 1.0 N A:PHE174 4.7 17.5 1.0 CE1 A:PHE174 4.8 14.8 1.0

Chlorine binding site 2 out of 37 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Symmetric MAD2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1208 b:69.0 occ:1.00 OD1 A:ASP103 3.9 29.1 1.0 CG A:ASN194 3.9 19.4 1.0 CB A:ASN194 4.0 18.4 1.0 NH1 A:ARG182 4.0 39.4 1.0 ND2 A:ASN194 4.0 19.6 1.0 CB A:ASP103 4.1 19.9 1.0 CG A:ASP103 4.2 23.7 1.0 NH2 A:ARG182 4.2 35.9 1.0 CZ A:ARG182 4.4 38.6 1.0 OD1 A:ASN194 4.4 19.6 1.0 O A:HOH2125 4.6 17.7 1.0

Chlorine binding site 3 out of 37 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Symmetric MAD2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1209 b:27.8 occ:0.50 O A:HOH2094 3.2 24.7 1.0 CA A:ALA137 3.7 16.9 1.0 CG2 A:THR136 3.9 20.5 1.0 N A:ALA137 3.9 17.3 1.0 CB A:ALA137 4.0 16.3 1.0 O A:HOH2096 4.1 38.6 1.0 C A:THR136 4.3 18.5 1.0 O A:THR136 4.4 18.8 1.0 CB A:THR136 4.7 19.1 1.0 CG2 A:THR140 4.7 16.6 1.0 O A:ARG133 4.8 17.1 1.0

Chlorine binding site 4 out of 37 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the Symmetric MAD2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1207 b:24.8 occ:1.00 OG B:SER185 3.0 24.5 1.0 NZ B:LYS192 3.1 16.4 1.0 CE B:LYS192 3.6 17.5 1.0 NH2 B:ARG182 3.7 44.2 1.0 CB B:SER185 3.9 20.5 1.0 OD1 B:ASN194 4.7 23.7 1.0 CZ B:ARG182 4.8 44.3 1.0

Chlorine binding site 5 out of 37 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the Symmetric MAD2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1208 b:25.0 occ:1.00 OG B:SER178 2.9 25.2 1.0 N B:SER178 3.8 22.8 1.0 CB B:SER178 3.8 24.6 1.0 CA B:THR176 3.8 21.5 1.0 O B:ILE175 3.9 21.2 1.0 N B:ASN177 3.9 21.7 1.0 C B:THR176 4.0 21.5 1.0 CA B:SER178 4.3 24.0 1.0 CG2 B:ILE175 4.3 22.6 1.0 C B:ILE175 4.4 21.6 1.0 N B:THR176 4.4 21.4 1.0 C B:ASN177 4.7 22.4 1.0 O B:SER178 4.8 24.8 1.0 O B:THR176 4.8 20.5 1.0 CA B:ASN177 4.8 21.9 1.0 C B:SER178 4.9 24.8 1.0 CB B:THR176 5.0 21.0 1.0

Chlorine binding site 6 out of 37 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the Symmetric MAD2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1209 b:26.9 occ:1.00 O E:HOH2090 3.1 21.5 1.0 O B:HOH2089 3.2 26.5 1.0 CA E:ALA137 3.7 21.1 1.0 CA B:ALA137 3.7 21.1 1.0 N E:ALA137 3.9 21.2 1.0 CG2 E:THR136 3.9 23.8 1.0 O B:HOH2090 3.9 42.8 1.0 N B:ALA137 4.0 21.6 1.0 CG2 B:THR136 4.0 22.9 1.0 CB E:ALA137 4.0 20.6 1.0 CB B:ALA137 4.0 20.6 1.0 C E:THR136 4.3 22.4 1.0 C B:THR136 4.3 22.2 1.0 O B:THR136 4.5 22.7 1.0 O E:THR136 4.5 22.0 1.0 CB E:THR136 4.6 23.3 1.0 O E:HOH2093 4.6 37.0 1.0 CG2 E:THR140 4.7 18.6 1.0 CG2 B:THR140 4.7 20.2 1.0 CB B:THR136 4.7 23.0 1.0 O B:ARG133 4.8 20.3 1.0 O E:ARG133 4.8 23.7 1.0

Chlorine binding site 7 out of 37 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the Symmetric MAD2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl3111 b:19.6 occ:1.00 O B:HOH2074 3.1 23.8 1.0 NZ B:LYS192 3.3 16.4 1.0 O B:HOH2075 4.0 24.0 1.0 CD B:LYS192 4.0 18.3 1.0 CE B:LYS192 4.3 17.5 1.0 OE2 B:GLU105 5.0 26.9 1.0

Chlorine binding site 8 out of 37 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of the Symmetric MAD2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1207 b:20.1 occ:0.50 O C:HOH2027 3.3 23.5 0.5 O C:HOH2079 3.4 22.8 1.0 CA C:ALA137 3.7 20.0 1.0 CG2 C:THR136 3.8 21.9 1.0 N C:ALA137 3.9 20.6 1.0 CB C:ALA137 4.1 19.4 1.0 C C:THR136 4.2 21.7 1.0 O C:THR136 4.3 21.8 1.0 CG2 C:THR140 4.4 19.6 1.0 CB C:THR136 4.7 22.4 1.0 O C:HOH2080 4.8 38.6 1.0 C C:ALA137 4.9 19.8 1.0 O C:HOH2019 4.9 20.0 1.0

Chlorine binding site 9 out of 37 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of the Symmetric MAD2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1208 b:24.4 occ:1.00 OG C:SER178 3.2 23.2 1.0 O C:ILE175 3.8 20.6 1.0 CA C:THR176 3.9 21.3 1.0 N C:SER178 3.9 23.1 1.0 N C:ASN177 4.0 22.5 1.0 CB C:SER178 4.0 23.4 1.0 C C:THR176 4.1 21.8 1.0 CG2 C:ILE175 4.4 21.0 1.0 C C:ILE175 4.4 20.7 1.0 N C:THR176 4.5 20.8 1.0 CA C:SER178 4.5 23.4 1.0 O C:HOH2102 4.6 34.0 1.0 O C:SER178 4.8 23.0 1.0 O C:THR176 4.9 21.6 1.0 C C:ASN177 4.9 23.4 1.0 CA C:ASN177 4.9 23.1 1.0 CB C:THR176 5.0 21.6 1.0

Chlorine binding site 10 out of 37 in the Structure of the Symmetric MAD2 Dimer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of the Symmetric MAD2 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1209 b:52.4 occ:1.00 O C:HOH2059 2.5 29.8 1.0 NE C:ARG99 2.9 26.1 1.0 OE1 C:GLN101 3.0 34.1 1.0 CB C:ARG99 3.4 22.4 1.0 CD C:ARG99 3.6 23.0 1.0 O C:HOH2060 3.7 33.2 1.0 CD C:GLN101 3.8 28.3 1.0 CB C:GLN101 3.8 24.3 1.0 CZ C:ARG99 3.9 25.6 1.0 CB C:ALA198 3.9 19.7 1.0 NH2 C:ARG99 4.0 29.6 1.0 CG C:ARG99 4.1 23.1 1.0 O C:ARG99 4.2 22.9 1.0 CG C:GLN101 4.4 27.4 1.0 CE C:MET196 4.5 23.4 0.5 CA C:ARG99 4.6 22.3 1.0 C C:ARG99 4.6 22.6 1.0 NE2 C:GLN101 4.7 30.1 1.0 SD C:MET196 4.7 24.0 0.5 CG1 C:VAL85 4.9 21.6 1.0

M.Yang, B.Li, C.-J.Liu, D.R.Tomchick, M.Machius, J.Rizo, H.Yu, X.Luo. Insights Into MAD2 Regulation in the Spindle Checkpoint Revealed By the Crystal Structure of the Symmetric MAD2 Dimer. Plos Biol. V. 6 E50 2008.
ISSN: ISSN 1544-9173
PubMed: 18318601
DOI: 10.1371/JOURNAL.PBIO.0060050