Chlorine in PDB 3dp8: Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)

The structure of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form), PDB code: 3dp8 was solved by M.V.Cherrier, C.Cavazza, C.Bochot, D.Lemaire, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	158.570, 158.570, 134.940, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 27

The structure of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) also contains other interesting chemical elements:

Nickel

(Ni)

3 atoms

The binding sites of Chlorine atom in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) (pdb code 3dp8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form), PDB code: 3dp8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl509 b:62.0 occ:1.00 NE A:ARG95 3.9 55.4 1.0 NH2 A:ARG95 4.2 46.6 1.0 CZ A:ARG95 4.2 52.7 1.0 CD A:ARG95 4.6 57.8 1.0 NH1 A:ARG95 4.9 57.1 1.0

Chlorine binding site 2 out of 7 in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl510 b:90.1 occ:1.00 ND1 A:HIS416 2.9 68.3 1.0 CE1 A:HIS416 3.3 69.0 1.0 O A:HOH603 3.5 53.8 1.0 NE1 A:TRP398 3.8 38.5 1.0 CZ2 A:TRP398 3.8 36.8 1.0 CE1 A:HIS395 4.1 46.5 1.0 CE2 A:TRP398 4.2 38.4 1.0 CG A:HIS416 4.2 64.6 1.0 NI A:NI503 4.4 78.8 1.0 NE2 A:HIS416 4.6 70.5 1.0 O A:HOH584 4.7 35.6 1.0 O A:HOH590 4.8 52.6 1.0 ND1 A:HIS395 4.9 45.5 1.0 CB A:HIS416 4.9 60.7 1.0 C2 A:HCT511 4.9 53.9 1.0

Chlorine binding site 3 out of 7 in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl508 b:44.6 occ:0.50 N B:HIS442 3.7 48.0 1.0 OG1 B:THR441 3.7 50.0 1.0 N B:ASP443 4.1 48.1 1.0 CA B:THR441 4.3 46.3 1.0 CA B:HIS442 4.4 48.5 1.0 CB B:HIS442 4.4 48.2 1.0 CB B:THR441 4.5 46.9 1.0 C B:THR441 4.5 47.2 1.0 C B:HIS442 4.6 48.8 1.0 CB B:ASP443 4.6 48.3 1.0 CD2 B:HIS442 4.9 50.5 1.0 CA B:ASP443 5.0 48.2 1.0

Chlorine binding site 4 out of 7 in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl509 b:40.5 occ:1.00 N B:LEU293 3.0 35.3 1.0 O B:HOH522 3.2 31.1 1.0 O B:HOH555 3.4 45.5 1.0 ND1 B:HIS459 3.4 37.9 1.0 CB B:LEU293 3.7 32.9 1.0 CA B:THR292 3.8 35.6 1.0 CA B:LEU293 3.8 33.6 1.0 CA B:HIS459 3.8 36.3 1.0 C B:THR292 3.8 35.7 1.0 CB B:HIS459 3.9 36.1 1.0 CG B:HIS459 4.1 36.7 1.0 N B:HIS459 4.3 36.3 1.0 CB B:THR292 4.4 35.8 1.0 CD2 B:TYR464 4.4 29.6 1.0 CE1 B:HIS459 4.5 34.9 1.0 CG B:PRO466 4.5 32.5 1.0 CB B:TYR464 4.6 31.8 1.0 O B:HOH546 4.6 26.9 1.0 O B:ASP291 4.7 39.9 1.0 CG2 B:THR292 4.7 32.9 1.0 C B:LEU458 4.8 35.9 1.0 O B:LEU458 4.9 36.6 1.0

Chlorine binding site 5 out of 7 in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl510 b:50.2 occ:0.50 O B:LYS148 2.6 64.2 1.0 NZ B:LYS157 3.9 64.1 1.0 C B:LYS148 3.9 63.0 1.0 CE B:LYS157 4.6 62.0 1.0 OD1 B:ASN149 4.6 72.0 1.0 CA B:LYS148 4.7 60.4 1.0 CA B:ASN149 4.7 66.0 1.0 O B:PHE147 4.7 54.2 1.0 N B:ASN149 4.8 65.0 1.0 CG B:ASN149 4.9 69.5 1.0

Chlorine binding site 6 out of 7 in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl507 b:57.9 occ:1.00 N C:LEU373 3.6 44.3 1.0 NE2 C:GLN361 3.8 35.3 1.0 CA C:SER372 4.2 41.6 1.0 C C:SER372 4.4 43.1 1.0 CB C:LEU373 4.4 46.2 1.0 CA C:LEU373 4.5 45.9 1.0 O C:LEU373 4.6 47.8 1.0 O C:VAL371 4.8 41.4 1.0 CD C:GLN361 4.9 41.8 1.0 CB C:SER372 4.9 42.1 1.0

Chlorine binding site 7 out of 7 in the Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika (Nickel Butane-1,2,4- Tricarboxylate Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl508 b:58.9 occ:1.00 CG B:PRO429 3.9 37.5 1.0 CB C:ARG341 3.9 39.6 1.0 CB B:PRO429 4.0 35.0 1.0 CG C:ARG341 4.2 40.4 1.0 NE C:ARG341 4.3 43.2 1.0 OE1 C:GLN338 4.4 35.2 1.0 CD C:ARG341 4.8 42.6 1.0 O C:ARG341 5.0 39.7 1.0

M.V.Cherrier, C.Cavazza, C.Bochot, D.Lemaire, J.C.Fontecilla-Camps. Structural Characterization of A Putative Endogenous Metal Chelator in the Periplasmic Nickel Transporter Nika Biochemistry V. 47 9937 2008.
ISSN: ISSN 0006-2960
PubMed: 18759453
DOI: 10.1021/BI801051Y