Chlorine in PDB 6qp7: Drosophila Semaphorin 2A

The structure of Drosophila Semaphorin 2A, PDB code: 6qp7 was solved by R.A.Robinson, D.Rozbesky, K.Harlos, C.Siebold, E.Y.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.46 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.804, 109.977, 134.793, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.8

The binding sites of Chlorine atom in the Drosophila Semaphorin 2A (pdb code 6qp7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Drosophila Semaphorin 2A, PDB code: 6qp7:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Drosophila Semaphorin 2A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Drosophila Semaphorin 2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl729 b:52.6 occ:1.00 ND1 A:HIS132 2.6 18.2 1.0 O A:TYR67 2.9 23.3 1.0 NH1 A:ARG134 2.9 26.0 1.0 NH2 A:ARG134 3.1 21.1 1.0 CG A:HIS132 3.4 21.5 1.0 CB A:TYR67 3.4 21.7 1.0 CB A:HIS132 3.4 17.9 1.0 CZ A:ARG134 3.5 23.7 1.0 C A:ALA84 3.6 21.3 1.0 N A:MET85 3.6 22.1 1.0 CE1 A:HIS132 3.7 19.6 1.0 CA A:ALA84 3.8 19.3 1.0 C A:TYR67 3.9 22.9 1.0 O A:LEU66 3.9 23.4 1.0 O A:ALA84 4.0 22.2 1.0 CA A:HIS132 4.0 25.4 1.0 CA A:MET85 4.1 21.9 1.0 CA A:TYR67 4.2 24.6 1.0 CB A:MET85 4.5 25.3 1.0 CG A:TYR67 4.6 22.4 1.0 CD2 A:HIS132 4.6 19.4 1.0 C A:HIS132 4.6 28.5 1.0 N A:VAL133 4.7 20.2 1.0 N A:ALA84 4.7 21.6 1.0 NE2 A:HIS132 4.7 19.3 1.0 O A:VAL133 4.8 20.9 1.0 NE A:ARG134 4.8 21.2 1.0 O A:GLY83 4.8 20.8 1.0 C A:LEU66 4.8 22.7 1.0 CG A:ARG69 4.9 25.5 1.0 CB A:ALA84 4.9 20.5 1.0 CB A:ARG69 5.0 23.6 1.0 CD A:ARG69 5.0 26.6 1.0

Chlorine binding site 2 out of 4 in the Drosophila Semaphorin 2A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Drosophila Semaphorin 2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl730 b:43.5 occ:1.00 O A:HOH1056 3.2 30.2 1.0 N A:ASN388 3.3 33.4 1.0 CD A:LYS372 3.7 34.2 1.0 CG A:LYS372 3.8 24.3 1.0 CB A:ASN388 3.8 34.8 1.0 CA A:LEU387 4.1 36.7 1.0 CD2 A:LEU387 4.1 34.4 1.0 CA A:ASN388 4.2 34.5 1.0 C A:LEU387 4.2 36.5 1.0 CG A:ASN388 4.5 35.9 1.0 CB A:LEU387 4.6 32.0 1.0 ND2 A:ASN388 4.6 34.3 1.0 O A:HOH1088 4.8 47.0 1.0 CE A:LYS372 4.8 35.5 1.0 NZ A:LYS372 4.8 34.9 1.0 N A:SER389 4.9 40.2 1.0

Chlorine binding site 3 out of 4 in the Drosophila Semaphorin 2A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Drosophila Semaphorin 2A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl731 b:78.8 occ:1.00 O B:HOH896 2.6 47.3 1.0 NH1 B:ARG534 2.9 45.4 1.0 CD B:ARG534 3.4 40.9 1.0 ND2 B:ASN531 3.4 35.0 1.0 O B:ARG528 3.6 38.7 1.0 CZ B:ARG534 3.8 43.6 1.0 NE B:ARG534 4.0 41.4 1.0 CE1 B:PHE591 4.0 38.9 1.0 CB B:GLU36 4.1 75.9 1.0 CA B:GLU36 4.3 66.4 1.0 CG B:PRO595 4.3 36.7 1.0 CG B:GLU36 4.3 86.4 1.0 CG B:ARG534 4.4 39.5 1.0 CD1 B:TYR529 4.4 32.5 1.0 CA B:TYR529 4.4 30.7 1.0 OD1 B:ASP530 4.5 42.1 1.0 CB B:ARG534 4.6 33.3 1.0 CZ B:PHE591 4.6 39.2 1.0 CG B:ASN531 4.6 34.9 1.0 O B:TYR35 4.7 55.6 1.0 C B:ARG528 4.7 37.4 1.0 N B:ASP530 4.7 35.3 1.0 N B:GLU36 4.8 61.4 1.0 OD1 B:ASN531 4.9 35.4 1.0 NH2 B:ARG534 4.9 42.0 1.0 C B:TYR35 4.9 62.7 1.0 CD1 B:PHE591 5.0 37.6 1.0

Chlorine binding site 4 out of 4 in the Drosophila Semaphorin 2A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Drosophila Semaphorin 2A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl732 b:89.5 occ:1.00 NH1 B:ARG134 2.7 35.9 1.0 O B:TYR67 2.9 37.2 1.0 NH2 B:ARG134 3.1 31.8 1.0 ND1 B:HIS132 3.2 40.5 1.0 CZ B:ARG134 3.3 35.9 1.0 CB B:HIS132 3.4 34.4 1.0 C B:ALA84 3.6 44.6 1.0 CG B:HIS132 3.7 38.8 1.0 N B:MET85 3.7 41.9 1.0 CB B:TYR67 3.7 38.9 1.0 CA B:ALA84 3.8 36.1 1.0 O B:ALA84 4.0 41.4 1.0 CA B:HIS132 4.0 37.9 1.0 C B:TYR67 4.0 42.6 1.0 O B:LEU66 4.2 46.7 1.0 CA B:MET85 4.3 41.4 1.0 CE1 B:HIS132 4.3 40.3 1.0 O B:VAL133 4.3 34.5 1.0 N B:VAL133 4.4 34.1 1.0 C B:HIS132 4.4 39.3 1.0 CA B:TYR67 4.5 41.3 1.0 N B:ALA84 4.6 39.0 1.0 O B:GLY83 4.6 36.5 1.0 CG B:ARG69 4.6 35.8 1.0 NE B:ARG134 4.6 37.5 1.0 CB B:ARG69 4.7 39.0 1.0 CB B:MET85 4.8 41.1 1.0 N B:ARG69 4.9 33.8 1.0 CG B:TYR67 4.9 42.2 1.0 CB B:ALA84 4.9 37.5 1.0 C B:GLY83 4.9 34.3 1.0 CD B:ARG69 5.0 36.4 1.0

D.Rozbesky, R.A.Robinson, V.Jain, M.Renner, T.Malinauskas, K.Harlos, C.Siebold, E.Y.Jones. Diversity of Oligomerization in Drosophila Semaphorins Suggests A Mechanism of Functional Fine-Tuning. Nat Commun V. 10 3691 2019.
ISSN: ESSN 2041-1723
PubMed: 31417095
DOI: 10.1038/S41467-019-11683-Y