Chlorine in PDB 4mzg: Crystal Structure of Human SPINDLIN1 Bound to Histone H3K4ME3 Peptide

The structure of Crystal Structure of Human SPINDLIN1 Bound to Histone H3K4ME3 Peptide, PDB code: 4mzg was solved by X.Su, X.Ding, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.14 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.168, 122.037, 49.837, 90.00, 91.71, 90.00
R / Rfree (%)	18.3 / 20.7

The structure of Crystal Structure of Human SPINDLIN1 Bound to Histone H3K4ME3 Peptide also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Human SPINDLIN1 Bound to Histone H3K4ME3 Peptide (pdb code 4mzg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Human SPINDLIN1 Bound to Histone H3K4ME3 Peptide, PDB code: 4mzg:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Human SPINDLIN1 Bound to Histone H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human SPINDLIN1 Bound to Histone H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl304 b:27.8 occ:1.00 O D:HOH421 3.2 24.4 1.0 O B:HOH410 3.2 21.4 1.0 N B:ARG152 3.2 18.3 1.0 CE B:LYS172 3.5 40.4 1.0 CD B:LYS172 3.5 34.8 1.0 NZ B:LYS172 3.6 37.0 1.0 O B:HOH414 3.8 19.7 1.0 CA B:TRP151 3.9 20.9 1.0 CB B:ARG152 3.9 23.7 1.0 CG B:ARG152 4.0 30.6 1.0 O B:GLU150 4.0 22.1 1.0 C B:TRP151 4.0 19.2 1.0 CG B:LYS172 4.1 33.6 1.0 CA B:ARG152 4.2 17.7 1.0 NH2 D:ARG152 4.2 46.0 1.0 O D:HOH428 4.4 28.2 1.0 MG B:MG303 4.5 21.7 1.0 CD B:ARG152 4.7 34.0 1.0 CB B:TRP151 4.7 19.0 1.0 O B:ARG152 4.7 18.5 1.0 OE1 D:GLU138 4.8 33.9 1.0 CB B:LYS172 4.8 28.1 1.0 C B:GLU150 4.8 20.9 1.0 N B:TRP151 4.8 20.6 1.0 C B:ARG152 5.0 20.6 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Human SPINDLIN1 Bound to Histone H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human SPINDLIN1 Bound to Histone H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl303 b:24.7 occ:1.00 O D:HOH409 3.1 21.9 1.0 O B:HOH431 3.1 25.1 1.0 N D:ARG152 3.2 17.6 1.0 NH2 B:ARG152 3.6 39.4 1.0 O D:HOH422 3.6 19.4 1.0 CE D:LYS172 3.6 41.2 1.0 CD D:LYS172 3.7 33.4 1.0 CB D:ARG152 3.9 23.6 1.0 CA D:TRP151 3.9 23.2 1.0 NZ D:LYS172 4.0 41.4 1.0 C D:TRP151 4.0 21.6 1.0 O D:GLU150 4.0 21.6 1.0 CA D:ARG152 4.1 17.9 1.0 CG D:LYS172 4.1 25.6 1.0 O D:HOH465 4.2 37.1 1.0 O B:HOH428 4.3 25.4 1.0 MG B:MG303 4.4 21.7 1.0 CZ B:ARG152 4.6 41.8 1.0 O D:ARG152 4.6 18.8 1.0 OE1 B:GLU138 4.7 29.6 1.0 CB D:TRP151 4.7 21.0 1.0 NE B:ARG152 4.8 38.5 1.0 CB D:LYS172 4.8 26.3 1.0 N D:TRP151 4.9 18.6 1.0 C D:GLU150 4.9 23.4 1.0 C D:ARG152 4.9 20.8 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Human SPINDLIN1 Bound to Histone H3K4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human SPINDLIN1 Bound to Histone H3K4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl304 b:30.6 occ:1.00 NE1 D:TRP165 3.1 20.5 1.0 O D:HOH445 3.2 33.5 1.0 O D:HOH441 3.6 26.2 1.0 OE1 D:GLN180 4.0 31.5 1.0 CD1 D:TRP165 4.0 17.5 1.0 CE2 D:TRP165 4.1 19.6 1.0 OG1 D:THR164 4.1 29.9 1.0 CZ2 D:TRP165 4.4 22.2 1.0 CD D:GLN180 4.8 24.9 1.0

X.Su, G.Zhu, X.Ding, S.Y.Lee, Y.Dou, B.Zhu, W.Wu, H.Li. Molecular Basis Underlying Histone H3 Lysine-Arginine Methylation Pattern Readout By Spin/Ssty Repeats of SPINDLIN1 Genes Dev. V. 28 622 2014.
ISSN: ISSN 0890-9369
PubMed: 24589551
DOI: 10.1101/GAD.233239.113