Chlorine in PDB 3cfi: Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus

The structure of Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus, PDB code: 3cfi was solved by A.Y.Lam, E.Pardon, K.V.Korotkov, J.Steyaert, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.58
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.720, 67.243, 128.255, 96.54, 91.62, 90.20
R / Rfree (%)	22.9 / 27.9

The binding sites of Chlorine atom in the Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus (pdb code 3cfi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus, PDB code: 3cfi:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl1 b:48.6 occ:1.00 O H:HIS97 3.2 73.8 1.0 N H:HIS97 3.4 68.7 1.0 N H:TRP96 3.5 65.7 1.0 NH2 H:ARG93 3.6 67.1 1.0 NE2 H:GLN57 3.9 60.4 1.0 C H:HIS97 4.0 72.1 1.0 CA H:HIS97 4.1 70.1 1.0 ND1 H:HIS97 4.1 64.7 1.0 CA H:GLY95 4.1 64.2 1.0 CB H:HIS97 4.2 69.4 1.0 NH1 H:ARG93 4.3 67.9 1.0 C H:GLY95 4.3 64.2 1.0 C H:TRP96 4.4 67.0 1.0 CA H:TRP96 4.4 66.5 1.0 CZ H:ARG93 4.4 66.0 1.0 NH1 E:ARG46 4.4 72.7 1.0 NH2 E:ARG46 4.6 72.4 1.0 OE1 H:GLN57 4.6 55.8 1.0 CG H:HIS97 4.6 67.7 1.0 CB H:TRP96 4.7 66.8 1.0 CD H:GLN57 4.7 60.6 1.0 CB E:ALA39 4.9 62.8 1.0 CZ E:ARG46 5.0 72.3 1.0

Chlorine binding site 2 out of 4 in the Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl1 b:43.6 occ:1.00 N E:TRP96 3.6 62.8 1.0 N E:HIS97 3.7 66.3 1.0 NH2 H:ARG46 3.7 66.9 1.0 ND1 E:HIS97 3.7 64.5 1.0 NE2 E:GLN57 4.1 54.0 1.0 CA E:GLY95 4.2 64.2 1.0 NH2 E:ARG93 4.2 62.4 1.0 CB E:HIS97 4.3 66.5 1.0 CG E:HIS97 4.4 66.2 1.0 CA E:HIS97 4.4 66.7 1.0 C E:GLY95 4.4 64.2 1.0 CB H:ALA39 4.5 61.6 1.0 CA E:TRP96 4.5 63.4 1.0 C E:TRP96 4.6 64.5 1.0 NH1 E:ARG93 4.7 66.2 1.0 C E:HIS97 4.7 69.0 1.0 O H:ALA39 4.7 64.6 1.0 OE1 E:GLN57 4.7 50.6 1.0 CE1 E:HIS97 4.7 65.8 1.0 O E:HIS97 4.7 68.3 1.0 CB E:TRP96 4.8 61.9 1.0 CD E:GLN57 4.9 57.9 1.0 CZ E:ARG93 5.0 64.5 1.0 CZ H:ARG46 5.0 67.3 1.0

Chlorine binding site 3 out of 4 in the Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus within 5.0Å range: probe atom residue distance (Å) B Occ K:Cl1 b:45.1 occ:1.00 N K:TRP96 3.6 61.8 1.0 N K:HIS97 3.6 63.6 1.0 ND1 K:HIS97 3.7 61.6 1.0 NH2 K:ARG93 3.9 67.5 1.0 NH2 B:ARG46 4.0 65.5 1.0 CB K:HIS97 4.2 63.1 1.0 CA K:GLY95 4.2 64.2 1.0 NE2 K:GLN57 4.2 60.6 1.0 CA K:HIS97 4.3 64.3 1.0 CG K:HIS97 4.3 63.2 1.0 C K:GLY95 4.4 64.1 1.0 NH1 B:ARG46 4.4 67.5 1.0 CB B:ALA39 4.5 62.1 1.0 CA K:TRP96 4.5 62.4 1.0 C K:TRP96 4.5 62.6 1.0 OE1 K:GLN57 4.6 58.8 1.0 C K:HIS97 4.7 65.5 1.0 CZ B:ARG46 4.7 66.0 1.0 CE1 K:HIS97 4.7 62.5 1.0 O B:ALA39 4.7 64.6 1.0 NH1 K:ARG93 4.7 65.7 1.0 CZ K:ARG93 4.8 64.5 1.0 O K:HIS97 4.8 66.3 1.0 CB K:TRP96 4.9 61.0 1.0 CD K:GLN57 4.9 61.1 1.0

Chlorine binding site 4 out of 4 in the Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterdimer From Vibrio Vulnificus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1 b:50.7 occ:1.00 N B:TRP96 3.6 66.0 1.0 N B:HIS97 3.7 70.9 1.0 NE2 B:GLN57 3.7 62.6 1.0 NH1 B:ARG93 4.0 66.9 1.0 CA B:GLY95 4.1 64.3 1.0 CD2 B:HIS97 4.1 66.5 1.0 CB B:HIS97 4.2 70.4 1.0 C B:GLY95 4.3 64.2 1.0 NH2 B:ARG93 4.3 71.1 1.0 CA B:HIS97 4.4 72.1 1.0 NH1 K:ARG46 4.5 70.4 1.0 CG B:HIS97 4.5 67.7 1.0 CA B:TRP96 4.6 67.8 1.0 C B:HIS97 4.6 74.4 1.0 NH2 K:ARG46 4.6 70.3 1.0 C B:TRP96 4.6 68.6 1.0 CD B:GLN57 4.6 61.5 1.0 OE1 B:GLN57 4.6 58.9 1.0 CZ B:ARG93 4.7 69.8 1.0 O B:HIS97 4.8 74.9 1.0 CB K:ALA39 4.9 63.0 1.0 CB B:TRP96 4.9 68.7 1.0

A.Y.Lam, E.Pardon, K.V.Korotkov, W.G.Hol, J.Steyaert. Nanobody-Aided Structure Determination of the Epsi:Epsj Pseudopilin Heterodimer From Vibrio Vulnificus. J.Struct.Biol. V. 166 8 2009.
ISSN: ISSN 1047-8477
PubMed: 19118632
DOI: 10.1016/J.JSB.2008.11.008