Chlorine in PDB 6yex: VCAM4I Restriction Endonuclease in the Absence of Dna

The structure of VCAM4I Restriction Endonuclease in the Absence of Dna, PDB code: 6yex was solved by M.Pastor, H.Czapinska, T.Lutz, I.Helbrecht, S.Xu, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.48 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.970, 93.532, 126.261, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.3

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the VCAM4I Restriction Endonuclease in the Absence of Dna (pdb code 6yex). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the VCAM4I Restriction Endonuclease in the Absence of Dna, PDB code: 6yex:
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 VCAM4I Restriction Endonuclease in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of VCAM4I Restriction Endonuclease in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:56.8 occ:1.00 N A:HIS34 3.0 27.4 1.0 O A:HOH809 3.3 43.0 1.0 CB A:HIS34 3.5 27.7 1.0 O A:HOH984 3.5 43.9 1.0 CB A:SER33 3.8 28.4 1.0 CA A:SER33 3.8 28.1 1.0 CA A:HIS34 3.8 26.7 1.0 C A:SER33 3.9 27.4 1.0 O A:HOH797 4.4 37.3 1.0 O A:HOH775 4.4 58.1 1.0 CE2 A:TYR35 4.5 30.9 1.0 CD2 A:TYR35 4.5 29.9 1.0 OG A:SER33 4.6 28.7 1.0 N A:TYR35 4.8 26.0 1.0 CE1 A:TYR117 4.9 42.0 1.0 CG A:HIS34 4.9 28.1 1.0 C A:HIS34 4.9 26.0 1.0

Chlorine binding site 2 out of 12 in the VCAM4I Restriction Endonuclease in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of VCAM4I Restriction Endonuclease in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:75.3 occ:1.00 N A:ASP122 3.3 52.7 1.0 O A:HOH892 3.5 55.7 1.0 CA A:GLN121 3.7 48.8 1.0 CB A:GLN121 3.8 50.2 1.0 O A:HOH790 3.8 51.5 1.0 C A:GLN121 4.0 50.5 1.0 O A:HOH642 4.1 42.7 1.0 CB A:ASP122 4.1 56.2 1.0 CG A:GLN121 4.2 50.1 1.0 CA A:ASP122 4.3 54.6 1.0 OD1 A:ASP122 4.4 56.2 1.0 CG A:ASP122 4.4 56.7 1.0 O A:HOH647 4.7 52.8 1.0 OE1 A:GLN121 4.8 53.2 1.0

Chlorine binding site 3 out of 12 in the VCAM4I Restriction Endonuclease in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of VCAM4I Restriction Endonuclease in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:74.6 occ:1.00 N A:TYR117 3.4 39.9 1.0 O A:HOH769 3.8 41.5 1.0 O A:HOH775 3.8 58.1 1.0 CA A:LYS116 3.9 44.2 1.0 CB A:LYS116 4.1 45.7 1.0 C A:LYS116 4.1 41.4 1.0 CE A:LYS116 4.1 48.8 1.0 CA A:TYR117 4.3 38.8 1.0 CG A:LYS116 4.4 47.9 1.0 CD1 A:TYR117 4.6 41.0 1.0 OH A:TYR35 4.7 32.8 1.0 O A:GLN115 4.8 47.2 1.0 CG A:TYR117 4.9 40.4 1.0 CD A:LYS116 4.9 48.8 1.0 CE1 A:TYR117 4.9 42.0 1.0

Chlorine binding site 4 out of 12 in the VCAM4I Restriction Endonuclease in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of VCAM4I Restriction Endonuclease in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:56.4 occ:1.00 N A:SER68 3.2 23.0 1.0 OG A:SER68 3.5 26.9 1.0 O B:HOH866 3.7 45.2 1.0 CA A:TYR67 3.8 21.5 1.0 CB A:SER68 3.8 25.3 1.0 C A:TYR67 4.0 22.1 1.0 CB A:TYR67 4.1 21.5 1.0 CA A:SER68 4.1 24.1 1.0 O A:HOH545 4.4 51.2 1.0 CZ3 A:TRP87 4.4 22.9 1.0 O A:ALA66 4.8 21.7 1.0 O A:HOH544 4.8 40.2 1.0

Chlorine binding site 5 out of 12 in the VCAM4I Restriction Endonuclease in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of VCAM4I Restriction Endonuclease in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:68.4 occ:1.00 N A:GLY126 3.0 44.0 1.0 O A:HOH506 3.3 50.4 1.0 O A:HOH943 3.5 45.7 1.0 CA A:GLY126 3.8 41.9 1.0 CA A:ASN125 3.9 48.0 1.0 C A:ASN125 3.9 45.6 1.0 CZ A:PHE51 4.3 33.6 1.0 OD1 A:ASN125 4.4 50.0 1.0 CB A:ASN125 4.4 48.9 1.0 CE2 A:PHE51 4.6 33.1 1.0 O A:GLY126 4.6 41.6 1.0 O A:HOH763 4.6 48.6 1.0 O A:GLY124 4.7 50.4 1.0 C A:GLY126 4.7 41.4 1.0 CG A:ASN125 4.8 50.2 1.0

Chlorine binding site 6 out of 12 in the VCAM4I Restriction Endonuclease in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of VCAM4I Restriction Endonuclease in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:42.2 occ:1.00 O B:HOH876 2.7 41.3 1.0 N B:ASP262 3.0 26.5 1.0 O B:HOH843 3.0 47.8 1.0 CZ B:ARG302 3.5 26.6 1.0 CA B:GLU261 3.6 25.7 1.0 CG B:ASP262 3.6 28.9 1.0 NH1 B:ARG302 3.6 26.1 1.0 NH2 B:ARG302 3.6 27.2 1.0 CB B:ASP262 3.7 28.4 1.0 C B:GLU261 3.8 25.7 1.0 CB B:GLU261 3.8 26.9 1.0 OD2 B:ASP262 3.8 30.2 1.0 OD1 B:ASP262 3.9 29.6 1.0 CA B:ASP262 3.9 27.0 1.0 NE B:ARG302 4.0 26.5 1.0 CG B:GLU261 4.4 27.8 1.0 CD B:ARG302 4.6 26.2 1.0 O B:HOH809 4.8 54.8 1.0 N B:GLU261 4.9 24.3 1.0 O B:HOH907 5.0 52.3 1.0 O B:GLU261 5.0 24.9 1.0

Chlorine binding site 7 out of 12 in the VCAM4I Restriction Endonuclease in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of VCAM4I Restriction Endonuclease in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:44.3 occ:1.00 O B:HOH900 2.7 42.5 1.0 N B:GLY239 3.1 23.6 1.0 OD1 B:ASP238 3.5 24.8 1.0 O B:HOH684 3.6 31.2 1.0 CA B:GLY239 3.8 23.5 1.0 O B:HOH812 3.8 41.3 1.0 CD B:ARG201 3.8 22.7 1.0 O B:HOH594 3.9 51.7 1.0 CB B:ARG201 4.0 21.7 1.0 C B:ASP238 4.0 23.4 1.0 CA B:ASP238 4.1 23.7 1.0 CG B:ARG201 4.1 22.2 1.0 ND1 B:HIS240 4.1 28.9 1.0 CE1 B:HIS240 4.4 29.2 1.0 O B:HOH954 4.4 45.6 1.0 O B:LEU237 4.5 23.4 1.0 N B:HIS240 4.5 24.2 1.0 NE B:ARG201 4.5 23.6 1.0 CG B:ASP238 4.5 24.6 1.0 C B:GLY239 4.6 23.6 1.0 O B:HOH916 4.8 55.5 1.0 NH1 B:ARG201 4.8 24.6 1.0 CB B:ASP238 4.9 24.0 1.0 CZ B:ARG201 5.0 24.1 1.0

Chlorine binding site 8 out of 12 in the VCAM4I Restriction Endonuclease in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of VCAM4I Restriction Endonuclease in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl408 b:59.9 occ:0.80 NE B:ARG101 2.9 70.8 1.0 NH2 B:ARG101 3.0 72.4 1.0 O B:HOH659 3.4 65.5 1.0 CZ B:ARG101 3.4 71.8 1.0 CD B:ARG101 4.1 69.8 1.0 CD2 B:LEU55 4.5 50.1 1.0 CB B:ARG101 4.6 64.7 1.0 NH1 B:ARG101 4.8 72.1 1.0 CG B:ARG101 4.9 66.5 1.0

Chlorine binding site 9 out of 12 in the VCAM4I Restriction Endonuclease in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of VCAM4I Restriction Endonuclease in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl409 b:82.6 occ:1.00 O B:HOH825 2.8 70.9 1.0 N B:ARG101 3.1 59.6 1.0 NE2 B:HIS105 3.6 64.2 1.0 CA B:ILE100 3.6 54.9 1.0 CB B:ILE100 3.8 54.2 1.0 O B:ARG101 3.8 63.0 1.0 C B:ILE100 3.9 56.4 1.0 O B:HOH659 4.0 65.5 1.0 CA B:ARG101 4.0 61.8 1.0 CB B:ARG101 4.0 64.7 1.0 C B:ARG101 4.3 62.3 1.0 CG2 B:ILE100 4.3 54.2 1.0 CE1 B:HIS105 4.5 64.6 1.0 CD2 B:HIS105 4.5 63.8 1.0 O B:LYS99 4.9 53.8 1.0 N B:ILE100 4.9 52.5 1.0 CB B:ALA104 5.0 73.2 1.0

Chlorine binding site 10 out of 12 in the VCAM4I Restriction Endonuclease in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of VCAM4I Restriction Endonuclease in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl410 b:51.1 occ:1.00 N B:GLN32 3.0 37.7 1.0 CA B:THR31 3.5 39.8 1.0 CG B:GLN32 3.7 37.6 1.0 CB B:THR31 3.7 40.1 1.0 C B:THR31 3.7 38.5 1.0 CB B:GLN32 3.8 37.1 1.0 O B:HOH846 3.9 53.0 1.0 CA B:GLN32 4.0 37.0 1.0 O B:HOH848 4.0 56.4 1.0 CG2 B:THR31 4.1 41.3 1.0 O B:GLN32 4.8 37.5 1.0 N B:THR31 4.8 40.8 1.0 O B:GLY30 4.9 42.5 1.0 C B:GLN32 4.9 36.9 1.0 O B:THR31 4.9 38.5 1.0 OG1 B:THR31 5.0 40.1 1.0

M.Pastor, H.Czapinska, T.Lutz, I.Helbrecht, S.Xu, M.Bochtler. Crystal Structures of the Eve-Hnh Endonuclease VCAM4I in the Presence and Absence of Dna To Be Published.