Chlorine in PDB 6z3j: Repulsive Guidance Molecule B (Rgmb) in Complex with Growth Differentiation Factor 5 (GDF5) (Crystal Form 1)

The structure of Repulsive Guidance Molecule B (Rgmb) in Complex with Growth Differentiation Factor 5 (GDF5) (Crystal Form 1), PDB code: 6z3j was solved by T.Malinauskas, T.V.Peer, B.Bishop, T.D.Muller, C.Siebold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.38 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.480, 127.750, 39.910, 90.00, 99.32, 90.00
R / Rfree (%)	19.1 / 21.9

The binding sites of Chlorine atom in the Repulsive Guidance Molecule B (Rgmb) in Complex with Growth Differentiation Factor 5 (GDF5) (Crystal Form 1) (pdb code 6z3j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Repulsive Guidance Molecule B (Rgmb) in Complex with Growth Differentiation Factor 5 (GDF5) (Crystal Form 1), PDB code: 6z3j:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Repulsive Guidance Molecule B (Rgmb) in Complex with Growth Differentiation Factor 5 (GDF5) (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Repulsive Guidance Molecule B (Rgmb) in Complex with Growth Differentiation Factor 5 (GDF5) (Crystal Form 1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl603 b:80.9 occ:1.00 O B:SER475 3.5 35.2 1.0 OG B:SER475 3.9 41.1 1.0 O B:HOH728 4.0 42.9 1.0 C B:SER475 4.2 35.1 1.0 CB B:SER475 4.2 38.6 1.0 O B:ALA420 4.4 32.0 1.0 CE B:LYS487 4.6 51.4 1.0 N B:LEU477 4.6 32.2 1.0 C B:ALA420 4.6 32.9 1.0 CD B:PRO421 4.6 31.0 1.0 CB B:LEU477 4.7 32.5 1.0 N B:PRO421 4.8 31.2 1.0 CB B:ALA420 4.8 35.2 1.0 CA B:SER475 4.9 35.9 1.0 N B:ILE476 4.9 31.0 1.0 CA B:ILE476 5.0 33.0 1.0

Chlorine binding site 2 out of 3 in the Repulsive Guidance Molecule B (Rgmb) in Complex with Growth Differentiation Factor 5 (GDF5) (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Repulsive Guidance Molecule B (Rgmb) in Complex with Growth Differentiation Factor 5 (GDF5) (Crystal Form 1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl203 b:86.8 occ:1.00 O C:GLY125 3.2 86.0 1.0 N C:GLY125 3.8 90.3 1.0 CD C:ARG86 3.9 55.9 1.0 CG2 C:THR127 4.0 58.7 1.0 CA C:ASP124 4.2 92.9 1.0 O C:LYS123 4.2 85.1 1.0 C C:GLY125 4.2 87.3 1.0 CB C:ARG86 4.3 43.2 1.0 C C:ASP124 4.4 91.9 1.0 CG C:ARG86 4.5 49.8 1.0 CA C:GLY125 4.6 90.0 1.0 NE C:ARG86 4.7 57.6 1.0 OD1 C:ASP124 4.8 96.9 1.0 CB C:ASP124 4.9 98.6 1.0 O C:ARG86 5.0 34.8 1.0

Chlorine binding site 3 out of 3 in the Repulsive Guidance Molecule B (Rgmb) in Complex with Growth Differentiation Factor 5 (GDF5) (Crystal Form 1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Repulsive Guidance Molecule B (Rgmb) in Complex with Growth Differentiation Factor 5 (GDF5) (Crystal Form 1) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl203 b:82.4 occ:1.00 NH1 D:ARG86 3.1 50.7 1.0 OG D:SER122 3.4 66.4 1.0 N D:SER122 3.4 54.4 1.0 NH2 D:ARG86 3.8 52.7 1.0 CA D:CYS121 3.8 44.1 1.0 CZ D:ARG86 3.9 52.3 1.0 CB D:CYS82 4.0 41.6 1.0 C D:CYS121 4.1 49.4 1.0 O D:ASN120 4.2 43.5 1.0 CB D:SER122 4.2 64.7 1.0 SG D:CYS82 4.3 45.0 1.0 CA D:SER122 4.4 61.5 1.0 CB D:CYS121 4.4 45.7 1.0 O D:SER122 4.9 59.0 1.0 N D:CYS121 4.9 41.9 1.0

T.Malinauskas, T.V.Peer, B.Bishop, T.D.Mueller, C.Siebold. Repulsive Guidance Molecules Lock Growth Differentiation Factor 5 in An Inhibitory Complex. Proc.Natl.Acad.Sci.Usa V. 117 15620 2020.
ISSN: ESSN 1091-6490
PubMed: 32576689
DOI: 10.1073/PNAS.2000561117