Chlorine in PDB 7dxn: Plant Growth-Promoting Factor Yxal From Bacillus Velezensis

The structure of Plant Growth-Promoting Factor Yxal From Bacillus Velezensis, PDB code: 7dxn was solved by Y.Baek, N.-C.Ha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.76 / 1.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.524, 81.524, 195.905, 90, 90, 120
R / Rfree (%)	15.3 / 18.6

The binding sites of Chlorine atom in the Plant Growth-Promoting Factor Yxal From Bacillus Velezensis (pdb code 7dxn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Plant Growth-Promoting Factor Yxal From Bacillus Velezensis, PDB code: 7dxn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Plant Growth-Promoting Factor Yxal From Bacillus Velezensis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Plant Growth-Promoting Factor Yxal From Bacillus Velezensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:40.0 occ:1.00 O A:HOH877 2.8 31.5 1.0 O A:HOH643 3.0 24.3 1.0 CD A:LYS262 3.6 27.6 1.0 N A:THR263 3.6 13.1 1.0 OG1 A:THR263 3.9 14.7 1.0 CA A:LYS262 4.0 15.7 1.0 CB A:LYS262 4.1 16.0 1.0 O A:THR263 4.1 17.2 1.0 C A:LYS262 4.3 14.4 1.0 CG A:LYS262 4.4 18.3 1.0 O A:HOH723 4.5 27.4 1.0 O A:HOH626 4.5 18.9 1.0 CA A:THR263 4.6 14.5 1.0 C A:THR263 4.8 12.1 1.0 CE A:LYS262 4.8 33.0 1.0 CB A:THR263 4.8 15.4 1.0 NZ A:LYS262 4.9 30.9 1.0

Chlorine binding site 2 out of 6 in the Plant Growth-Promoting Factor Yxal From Bacillus Velezensis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Plant Growth-Promoting Factor Yxal From Bacillus Velezensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:39.0 occ:1.00 O A:HOH886 2.3 51.4 1.0 OE1 A:GLN66 3.4 30.1 1.0 CD A:GLN66 4.0 38.5 1.0 CG A:GLN66 4.5 24.6 1.0 O A:ALA45 4.6 33.5 1.0 NE2 A:GLN66 4.9 32.5 1.0

Chlorine binding site 3 out of 6 in the Plant Growth-Promoting Factor Yxal From Bacillus Velezensis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Plant Growth-Promoting Factor Yxal From Bacillus Velezensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl501 b:21.4 occ:0.50 N B:ASN94 3.1 15.9 1.0 CE B:LYS93 3.4 22.5 1.0 NZ B:LYS93 3.4 18.6 1.0 CA B:LYS93 3.5 23.1 1.0 C B:LYS93 3.8 23.0 1.0 ND2 B:ASN94 3.8 21.6 1.0 CG B:ASN94 3.9 24.0 1.0 CD B:LYS93 4.0 22.2 1.0 O B:GLU92 4.0 23.6 1.0 CB B:LYS93 4.1 18.2 1.0 CB B:ASN94 4.1 20.7 1.0 CA B:ASN94 4.2 22.0 1.0 O B:HOH670 4.3 23.5 1.0 OD1 B:ASN94 4.5 20.2 1.0 N B:LYS93 4.6 19.3 1.0 O B:HOH812 4.6 25.8 0.5 CG B:LYS93 4.7 23.1 1.0 C B:GLU92 4.7 21.9 1.0 O B:ASN94 5.0 20.6 1.0

Chlorine binding site 4 out of 6 in the Plant Growth-Promoting Factor Yxal From Bacillus Velezensis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Plant Growth-Promoting Factor Yxal From Bacillus Velezensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:36.4 occ:1.00 N B:ALA182 3.5 16.5 1.0 CA B:GLY181 3.8 17.4 1.0 CE B:LYS161 3.9 29.4 1.0 NZ B:LYS161 4.1 37.4 1.0 C B:GLY181 4.1 17.9 1.0 CB B:LEU200 4.2 17.2 1.0 CB B:ALA182 4.3 17.9 1.0 CA B:ALA182 4.5 18.0 1.0 N B:ASP201 4.6 17.1 1.0 C B:LEU200 4.7 21.6 1.0 CB B:ASP201 4.9 17.0 1.0 CD B:LYS161 4.9 21.2 1.0 CA B:LEU200 4.9 18.1 1.0

Chlorine binding site 5 out of 6 in the Plant Growth-Promoting Factor Yxal From Bacillus Velezensis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Plant Growth-Promoting Factor Yxal From Bacillus Velezensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:39.4 occ:1.00 O B:HOH657 2.9 28.3 1.0 N B:ASN387 3.4 16.4 1.0 CG B:ASN387 3.6 18.6 1.0 OD1 B:ASN387 3.6 18.7 1.0 OG B:SER386 3.8 20.4 1.0 ND2 B:ASN387 3.9 13.3 1.0 CA B:SER386 4.0 15.5 1.0 CD2 B:TYR405 4.0 16.9 1.0 CB B:ASN387 4.1 15.4 1.0 CE B:LYS367 4.1 21.6 1.0 NZ B:LYS367 4.2 20.9 1.0 C B:SER386 4.2 13.9 1.0 CB B:SER386 4.3 18.5 1.0 CA B:ASN387 4.4 15.4 1.0 CE2 B:TYR405 4.4 18.5 1.0

Chlorine binding site 6 out of 6 in the Plant Growth-Promoting Factor Yxal From Bacillus Velezensis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Plant Growth-Promoting Factor Yxal From Bacillus Velezensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl504 b:37.2 occ:1.00 NH2 B:ARG349 3.4 18.3 1.0 NH1 B:ARG349 3.5 17.1 1.0 O A:HOH798 3.6 29.1 1.0 CE1 A:HIS159 3.9 27.7 1.0 CZ B:ARG349 3.9 19.2 1.0 CZ B:PHE307 4.2 17.9 1.0 CD1 A:LEU200 4.2 20.3 1.0 CE2 B:PHE307 4.2 16.9 1.0 CE2 A:TYR142 4.3 32.8 1.0 NE2 A:HIS159 4.3 25.5 1.0 OH A:TYR142 4.9 36.8 1.0 CE1 B:PHE307 4.9 18.5 1.0

J.Kim, H.Pham, Y.Baek, I.Jo, Y.H.Kim, N.C.Ha. Structure of the Plant Growth-Promoting Factor Yxal From the Rhizobacterium Bacillus Velezensis and Its Application to Protein Engineering. Acta Crystallogr D Struct V. 78 104 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 34981766
DOI: 10.1107/S2059798321011724