Chlorine in PDB 2vxa: H. Halophila Dodecin in Complex with Riboflavin

The structure of H. Halophila Dodecin in Complex with Riboflavin, PDB code: 2vxa was solved by M.Grininger, H.Staudt, P.Johansson, J.Wachtveitl, D.Oesterhelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.760, 100.510, 100.470, 90.00, 90.00, 90.00
R / Rfree (%)	25.1 / 28.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Chlorine atom in the H. Halophila Dodecin in Complex with Riboflavin (pdb code 2vxa). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 24 binding sites of Chlorine where determined in the H. Halophila Dodecin in Complex with Riboflavin, PDB code: 2vxa:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 24 in the H. Halophila Dodecin in Complex with Riboflavin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of H. Halophila Dodecin in Complex with Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1069 b:53.2 occ:1.00 NZ B:LYS7 3.3 39.5 1.0 NZ A:LYS7 3.4 39.2 1.0 NZ C:LYS7 3.5 39.3 1.0 CG1 A:VAL9 3.9 30.5 1.0 CG1 B:VAL9 4.0 30.7 1.0 CG1 C:VAL9 4.1 30.5 1.0 CE B:LYS7 4.4 38.9 1.0 CE C:LYS7 4.4 38.7 1.0 CE A:LYS7 4.6 39.1 1.0 CB A:VAL9 4.7 30.2 1.0 CB B:VAL9 4.9 30.1 1.0 CB C:VAL9 4.9 30.2 1.0

Chlorine binding site 2 out of 24 in the H. Halophila Dodecin in Complex with Riboflavin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of H. Halophila Dodecin in Complex with Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1070 b:45.5 occ:1.00 NZ C:LYS62 2.9 30.5 1.0 NZ A:LYS62 3.0 30.5 1.0 NZ B:LYS62 3.3 30.6 1.0 OE1 C:GLU10 3.3 36.4 1.0 CE C:LYS62 3.4 28.9 1.0 OE1 B:GLU10 3.4 36.8 1.0 OE1 A:GLU10 3.6 36.6 1.0 CE A:LYS62 3.7 28.9 1.0 CE B:LYS62 3.8 28.9 1.0 CD C:GLU10 4.3 33.5 1.0 CD B:GLU10 4.3 33.6 1.0 CD A:GLU10 4.5 33.6 1.0 OE2 B:GLU10 4.7 39.0 1.0 CD C:LYS62 4.8 28.6 1.0 OE2 C:GLU10 4.8 39.0 1.0

Chlorine binding site 3 out of 24 in the H. Halophila Dodecin in Complex with Riboflavin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of H. Halophila Dodecin in Complex with Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1069 b:36.7 occ:1.00 NH2 B:ARG46 3.1 30.2 1.0 NE1 H:TRP39 3.3 28.8 1.0 NH1 B:ARG46 3.6 29.2 1.0 CZ B:ARG46 3.8 29.6 1.0 C6 H:RBF200 4.0 36.8 1.0 CE2 H:TRP39 4.0 29.4 1.0 CZ2 H:TRP39 4.1 30.0 1.0 C7M H:RBF200 4.3 36.5 1.0 CD1 H:TRP39 4.3 29.9 1.0 CD G:ARG46 4.5 29.7 1.0 C7 H:RBF200 4.6 36.7 1.0 NE G:ARG46 4.6 30.2 1.0 OE1 H:GLU41 4.7 40.6 1.0 OD2 G:ASP44 4.7 43.7 1.0 CD1 H:ILE8 4.8 30.3 1.0 C5A H:RBF200 4.9 36.5 1.0 N5 H:RBF200 5.0 36.9 1.0

Chlorine binding site 4 out of 24 in the H. Halophila Dodecin in Complex with Riboflavin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of H. Halophila Dodecin in Complex with Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1070 b:54.4 occ:1.00 OG B:SER14 3.0 38.8 1.0 OH C:TYR6 3.1 35.3 1.0 CE1 C:HIS4 3.2 52.9 1.0 NE2 B:GLN58 3.6 30.1 1.0 ND1 C:HIS4 3.7 53.1 1.0 CG B:HIS56 3.7 42.6 1.0 CD2 B:HIS56 3.9 43.8 1.0 CB B:HIS56 4.0 40.4 1.0 ND1 B:HIS56 4.0 44.1 1.0 CZ C:TYR6 4.1 34.4 1.0 CB B:SER14 4.1 36.1 1.0 NE2 C:HIS4 4.2 51.2 1.0 CE1 C:TYR6 4.2 32.8 1.0 NE2 B:HIS56 4.2 44.3 1.0 CE1 B:HIS56 4.3 43.9 1.0 CG B:GLN58 4.6 30.9 1.0 CD B:GLN58 4.6 32.1 1.0 CG C:HIS4 4.8 48.0 1.0 O5' C:RBF200 4.9 53.0 1.0

Chlorine binding site 5 out of 24 in the H. Halophila Dodecin in Complex with Riboflavin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of H. Halophila Dodecin in Complex with Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1069 b:38.4 occ:1.00 NH2 C:ARG46 3.1 30.2 1.0 NH1 C:ARG46 3.4 29.2 1.0 NE1 F:TRP39 3.4 29.1 1.0 CZ C:ARG46 3.7 29.6 1.0 C6 F:RBF200 4.0 36.8 1.0 CE2 F:TRP39 4.2 29.3 1.0 C7M F:RBF200 4.3 36.5 1.0 CD E:ARG46 4.3 29.9 1.0 CZ2 F:TRP39 4.3 30.1 1.0 NE E:ARG46 4.4 30.0 1.0 CD1 F:TRP39 4.4 30.1 1.0 OD2 E:ASP44 4.4 43.7 1.0 OE1 F:GLU41 4.5 40.5 1.0 C7 F:RBF200 4.6 36.8 1.0 CZ E:ARG46 4.7 29.6 1.0 N5 F:RBF200 4.9 36.7 1.0 C5A F:RBF200 4.9 36.6 1.0 CD F:GLU41 4.9 39.3 1.0 NH1 E:ARG46 4.9 29.6 1.0 NE C:ARG46 5.0 30.2 1.0

Chlorine binding site 6 out of 24 in the H. Halophila Dodecin in Complex with Riboflavin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of H. Halophila Dodecin in Complex with Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1070 b:45.8 occ:1.00 OG C:SER14 2.7 38.5 1.0 OH A:TYR6 3.1 35.2 1.0 CB C:SER14 3.6 35.8 1.0 NE2 C:GLN58 3.7 29.8 1.0 ND1 A:HIS4 3.7 43.1 1.0 CE1 A:TYR6 3.8 32.8 1.0 CG C:HIS56 3.9 42.7 1.0 CZ A:TYR6 3.9 34.2 1.0 CD2 C:HIS56 4.0 43.9 1.0 CB C:HIS56 4.1 40.4 1.0 ND1 C:HIS56 4.3 44.0 1.0 CG C:GLN58 4.4 31.0 1.0 NE2 C:HIS56 4.5 44.1 1.0 CG A:HIS4 4.5 40.3 1.0 CE1 A:HIS4 4.5 41.9 1.0 CD C:GLN58 4.5 32.2 1.0 CB A:HIS4 4.6 38.0 1.0 CE1 C:HIS56 4.7 43.7 1.0 CA C:SER14 4.9 36.0 1.0

Chlorine binding site 7 out of 24 in the H. Halophila Dodecin in Complex with Riboflavin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of H. Halophila Dodecin in Complex with Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl1069 b:50.4 occ:1.00 OH D:TYR6 2.7 35.8 1.0 OG F:SER14 3.1 38.6 1.0 ND1 D:HIS4 3.5 48.7 1.0 NE2 F:GLN58 3.5 30.2 1.0 CZ D:TYR6 3.6 34.3 1.0 CE1 D:TYR6 3.7 32.8 1.0 CB F:SER14 4.0 36.2 1.0 CE1 D:HIS4 4.1 49.5 1.0 CG F:HIS56 4.1 42.8 1.0 CB F:HIS56 4.3 40.4 1.0 CD2 F:HIS56 4.3 43.9 1.0 ND1 F:HIS56 4.4 44.1 1.0 CG F:GLN58 4.4 30.9 1.0 CG D:HIS4 4.4 45.0 1.0 CD F:GLN58 4.5 32.1 1.0 C8M D:RBF200 4.7 36.8 1.0 NE2 F:HIS56 4.7 44.2 1.0 CE1 F:HIS56 4.8 43.8 1.0 CB D:HIS4 4.8 40.5 1.0 O5' D:RBF200 4.9 53.2 1.0 CE2 D:TYR6 4.9 33.4 1.0

Chlorine binding site 8 out of 24 in the H. Halophila Dodecin in Complex with Riboflavin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of H. Halophila Dodecin in Complex with Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl1070 b:54.7 occ:1.00 OG D:SER14 2.7 38.8 1.0 OH E:TYR6 3.1 35.5 1.0 NE2 D:GLN58 3.4 30.4 1.0 CB D:SER14 3.7 36.3 1.0 CE1 E:TYR6 3.8 33.1 1.0 CG D:HIS56 3.8 43.0 1.0 CZ E:TYR6 4.0 34.2 1.0 CB D:HIS56 4.0 40.5 1.0 CD2 D:HIS56 4.0 43.8 1.0 CG D:GLN58 4.2 31.0 1.0 ND1 D:HIS56 4.3 44.3 1.0 CD D:GLN58 4.3 32.2 1.0 NE2 D:HIS56 4.5 44.1 1.0 ND1 E:HIS4 4.6 52.0 1.0 CE1 D:HIS56 4.7 44.0 1.0 O E:HIS4 4.8 41.5 1.0 CB E:HIS4 4.9 43.9 1.0 C8M E:RBF200 4.9 36.9 1.0 CA D:SER14 4.9 36.2 1.0

Chlorine binding site 9 out of 24 in the H. Halophila Dodecin in Complex with Riboflavin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of H. Halophila Dodecin in Complex with Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl1071 b:56.6 occ:1.00 NZ F:LYS62 3.0 30.4 1.0 OE1 E:GLU10 3.2 36.8 1.0 OE1 F:GLU10 3.2 36.5 1.0 NZ D:LYS62 3.3 30.6 1.0 NZ E:LYS62 3.4 30.8 1.0 CE F:LYS62 3.5 28.9 1.0 OE1 D:GLU10 3.6 36.6 1.0 CE D:LYS62 3.8 29.0 1.0 CE E:LYS62 3.8 29.0 1.0 CD E:GLU10 4.2 33.5 1.0 CD F:GLU10 4.2 33.8 1.0 CD D:GLU10 4.6 33.5 1.0 CD F:LYS62 4.8 28.6 1.0 OE2 E:GLU10 4.8 39.0 1.0 OE2 F:GLU10 4.9 39.1 1.0 CB F:GLU10 5.0 30.2 1.0

Chlorine binding site 10 out of 24 in the H. Halophila Dodecin in Complex with Riboflavin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of H. Halophila Dodecin in Complex with Riboflavin within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl1069 b:36.6 occ:1.00 NH2 E:ARG46 3.2 30.3 1.0 NE1 A:TRP39 3.4 29.3 1.0 NH1 E:ARG46 3.6 29.6 1.0 CZ E:ARG46 3.8 29.6 1.0 CE2 A:TRP39 4.1 29.3 1.0 C6 A:RBF200 4.1 36.7 1.0 CZ2 A:TRP39 4.2 29.9 1.0 C7M A:RBF200 4.4 36.4 1.0 CD1 A:TRP39 4.4 29.9 1.0 CD C:ARG46 4.5 29.8 1.0 NE C:ARG46 4.6 30.2 1.0 OE1 A:GLU41 4.6 40.3 1.0 OD2 C:ASP44 4.6 44.0 1.0 C7 A:RBF200 4.7 36.6 1.0 CD1 A:ILE8 4.9 30.2 1.0 CZ C:ARG46 5.0 29.6 1.0

M.Grininger, H.Staudtb, P.Johansson, J.Wachtveitl, D.Oesterhelt. Dodecin Is the Key Player in Flavin Homeostasis of Archaea. J.Biol.Chem. V. 284 13068 2009.
ISSN: ISSN 0021-9258
PubMed: 19224924
DOI: 10.1074/JBC.M808063200