Zinc in PDB 5c13: Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide

The structure of Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide, PDB code: 5c13 was solved by H.Li, J.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.62 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	30.212, 50.105, 85.949, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 28

The binding sites of Zinc atom in the Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide (pdb code 5c13). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide, PDB code: 5c13:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:28.6 occ:1.00 SG A:CYS888 2.2 25.5 1.0 SG A:CYS885 2.4 20.6 1.0 SG A:CYS914 2.4 32.6 1.0 SG A:CYS911 2.4 29.3 1.0 H A:CYS888 2.9 35.3 1.0 HB2 A:CYS914 3.1 51.5 1.0 HB3 A:CYS888 3.2 33.2 1.0 HB2 A:CYS885 3.2 27.9 1.0 CB A:CYS885 3.2 23.2 1.0 HB3 A:CYS885 3.3 27.9 1.0 HB3 A:CYS911 3.3 39.8 1.0 CB A:CYS888 3.3 27.6 1.0 O A:PHE910 3.4 49.0 1.0 CB A:CYS914 3.4 42.9 1.0 CB A:CYS911 3.6 33.2 1.0 HB3 A:ASP887 3.6 42.2 1.0 N A:CYS888 3.7 29.4 1.0 H A:CYS914 3.7 44.1 1.0 HB3 A:CYS914 4.0 51.5 1.0 HB2 A:LYS913 4.0 49.1 1.0 CA A:CYS888 4.1 25.3 1.0 HB2 A:CYS888 4.1 33.2 1.0 HB2 A:ASP890 4.1 22.5 1.0 HB2 A:CYS911 4.1 39.8 1.0 N A:CYS914 4.2 36.8 1.0 H A:ASP889 4.3 32.4 1.0 H A:ASP890 4.3 29.9 1.0 O A:HOH1104 4.4 26.7 1.0 C A:PHE910 4.4 38.1 1.0 CA A:CYS914 4.4 32.9 1.0 H A:ASP887 4.4 33.7 1.0 CB A:ASP887 4.5 35.2 1.0 CA A:CYS885 4.7 22.7 1.0 N A:ASP889 4.7 27.0 1.0 CA A:CYS911 4.7 32.0 1.0 C A:CYS888 4.7 31.0 1.0 C A:ASP887 4.8 29.6 1.0 O A:CYS911 4.9 31.5 1.0 HA A:CYS888 4.9 30.3 1.0 HA A:CYS914 4.9 39.4 1.0 HA A:PHE910 4.9 47.5 1.0 HE1 A:TYR892 4.9 26.4 1.0 HA A:CYS885 5.0 27.2 1.0 CB A:LYS913 5.0 41.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:23.6 occ:1.00 ND1 A:HIS893 2.0 22.3 1.0 SG A:CYS870 2.2 20.1 1.0 SG A:CYS896 2.3 25.8 1.0 SG A:CYS873 2.4 23.0 1.0 HB3 A:CYS870 2.8 21.3 1.0 HB3 A:CYS873 2.9 29.7 1.0 H A:CYS873 2.9 28.9 1.0 CE1 A:HIS893 2.9 27.1 1.0 HB2 A:HIS893 3.0 35.9 1.0 HE1 A:HIS893 3.0 32.5 1.0 CB A:CYS870 3.0 17.7 1.0 CG A:HIS893 3.1 23.7 1.0 CB A:CYS873 3.2 24.8 1.0 HB2 A:CYS870 3.3 21.3 1.0 HB2 A:CYS896 3.3 29.9 1.0 CB A:CYS896 3.3 24.9 1.0 H A:HIS893 3.3 21.5 1.0 N A:CYS873 3.5 24.1 1.0 HB3 A:CYS896 3.5 29.9 1.0 CB A:HIS893 3.6 29.9 1.0 CA A:CYS873 4.0 25.1 1.0 HB2 A:CYS873 4.0 29.7 1.0 NE2 A:HIS893 4.0 29.8 1.0 N A:HIS893 4.1 17.9 1.0 HA3 A:GLY872 4.1 30.6 1.0 CD2 A:HIS893 4.2 29.8 1.0 H A:GLY872 4.2 24.6 1.0 HB3 A:HIS893 4.3 35.9 1.0 H A:ASN874 4.3 29.9 1.0 C A:GLY872 4.4 26.3 1.0 CA A:CYS870 4.4 17.7 1.0 CA A:HIS893 4.5 22.1 1.0 CA A:GLY872 4.6 25.5 1.0 H A:CYS896 4.7 32.7 1.0 N A:GLY872 4.7 20.5 1.0 HA A:CYS873 4.7 30.1 1.0 H A:LYS875 4.7 27.4 1.0 O A:CYS870 4.7 18.7 1.0 CA A:CYS896 4.7 33.5 1.0 C A:CYS870 4.8 20.0 1.0 HE2 A:HIS893 4.8 35.7 1.0 N A:ASN874 4.8 24.9 1.0 HA A:TYR892 4.9 22.5 1.0 C A:CYS873 4.9 23.9 1.0 HA A:CYS870 4.9 21.3 1.0 HA A:CYS896 5.0 40.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:27.9 occ:1.00 SG C:CYS888 2.1 24.4 1.0 SG C:CYS885 2.3 25.2 1.0 SG C:CYS914 2.4 34.1 1.0 SG C:CYS911 2.4 28.9 1.0 H C:CYS888 2.9 40.6 1.0 HB3 C:CYS911 2.9 35.6 1.0 CB C:CYS885 3.1 27.1 1.0 HB2 C:CYS885 3.1 32.6 1.0 HB3 C:CYS885 3.1 32.6 1.0 HB3 C:CYS888 3.2 39.6 1.0 HB2 C:CYS914 3.3 45.2 1.0 CB C:CYS888 3.3 33.0 1.0 CB C:CYS911 3.3 29.7 1.0 HB3 C:ASP887 3.5 42.2 1.0 CB C:CYS914 3.5 37.7 1.0 O C:PHE910 3.6 55.5 1.0 N C:CYS888 3.7 33.8 1.0 HB2 C:CYS911 3.8 35.6 1.0 H C:CYS914 4.0 46.5 1.0 HB2 C:LYS913 4.0 48.5 1.0 HB2 C:ASP890 4.0 29.2 1.0 HB2 C:CYS888 4.1 39.6 1.0 CA C:CYS888 4.1 29.8 1.0 HB3 C:CYS914 4.2 45.2 1.0 N C:CYS914 4.3 38.8 1.0 H C:ASP887 4.4 34.9 1.0 H C:ASP889 4.4 29.3 1.0 H C:ASP890 4.4 31.2 1.0 C C:PHE910 4.4 39.0 1.0 CB C:ASP887 4.5 35.2 1.0 O C:HOH1102 4.5 35.7 1.0 CA C:CYS911 4.5 32.1 1.0 CA C:CYS914 4.6 34.1 1.0 CA C:CYS885 4.6 21.8 1.0 C C:ASP887 4.8 33.6 1.0 O C:CYS911 4.8 31.5 1.0 C C:CYS888 4.8 27.3 1.0 N C:ASP889 4.8 24.4 1.0 HA C:CYS888 4.8 35.7 1.0 HA C:CYS885 4.9 26.2 1.0 HB2 C:ASP887 4.9 42.2 1.0 C C:CYS911 4.9 30.5 1.0 N C:CYS911 4.9 36.5 1.0 HA C:PHE910 4.9 39.3 1.0 CB C:LYS913 5.0 40.4 1.0 HE1 C:TYR892 5.0 19.5 1.0 CB C:ASP890 5.0 24.3 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1002 b:22.0 occ:1.00 ND1 C:HIS893 2.0 25.7 1.0 SG C:CYS896 2.3 21.4 1.0 SG C:CYS870 2.3 17.6 1.0 SG C:CYS873 2.3 22.2 1.0 HB3 C:CYS870 2.8 21.1 1.0 CE1 C:HIS893 2.9 26.6 1.0 H C:CYS873 2.9 27.8 1.0 HB3 C:CYS873 2.9 25.4 1.0 HB2 C:HIS893 2.9 34.3 1.0 CB C:CYS870 3.0 17.6 1.0 HE1 C:HIS893 3.0 31.9 1.0 CG C:HIS893 3.1 20.3 1.0 CB C:CYS873 3.2 21.1 1.0 HB2 C:CYS896 3.2 26.2 1.0 CB C:CYS896 3.3 21.9 1.0 H C:HIS893 3.3 23.3 1.0 HB2 C:CYS870 3.3 21.1 1.0 HB3 C:CYS896 3.4 26.2 1.0 CB C:HIS893 3.5 28.6 1.0 N C:CYS873 3.5 23.2 1.0 HB2 C:CYS873 4.0 25.4 1.0 CA C:CYS873 4.0 22.0 1.0 NE2 C:HIS893 4.0 31.9 1.0 N C:HIS893 4.0 19.4 1.0 H C:GLY872 4.1 22.7 1.0 CD2 C:HIS893 4.2 32.5 1.0 HB3 C:HIS893 4.2 34.3 1.0 HA3 C:GLY872 4.3 26.7 1.0 CA C:HIS893 4.4 23.9 1.0 H C:ASN874 4.4 33.5 1.0 CA C:CYS870 4.4 18.6 1.0 C C:GLY872 4.5 25.3 1.0 H C:CYS896 4.6 26.0 1.0 O C:CYS870 4.6 18.4 1.0 HA C:CYS873 4.7 26.4 1.0 CA C:CYS896 4.7 26.0 1.0 CA C:GLY872 4.7 22.3 1.0 N C:GLY872 4.7 18.9 1.0 H C:LYS875 4.7 29.3 1.0 C C:CYS870 4.7 17.7 1.0 HE2 C:HIS893 4.8 38.3 1.0 O C:HOH1121 4.8 44.5 1.0 N C:ASN874 4.9 27.9 1.0 HA C:CYS870 4.9 22.3 1.0 HA C:TYR892 4.9 22.4 1.0 C C:CYS873 4.9 24.3 1.0 HA C:CYS896 4.9 31.2 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:29.0 occ:1.00 SG E:CYS888 2.2 25.8 1.0 SG E:CYS885 2.4 23.6 1.0 SG E:CYS914 2.5 31.3 1.0 SG E:CYS911 2.5 29.9 1.0 HB3 E:CYS911 2.9 43.7 1.0 H E:CYS888 3.0 33.5 1.0 HB3 E:CYS888 3.1 36.3 1.0 HB2 E:CYS914 3.2 52.4 1.0 HB2 E:CYS885 3.2 31.2 1.0 CB E:CYS885 3.2 26.0 1.0 HB3 E:CYS885 3.2 31.2 1.0 CB E:CYS888 3.3 30.3 1.0 CB E:CYS911 3.3 36.4 1.0 O E:PHE910 3.4 52.9 1.0 CB E:CYS914 3.5 43.6 1.0 HB3 E:ASP887 3.7 45.5 1.0 H E:CYS914 3.7 51.6 1.0 N E:CYS888 3.7 27.9 1.0 HB2 E:CYS911 3.9 43.7 1.0 HB2 E:CYS888 4.0 36.3 1.0 CA E:CYS888 4.1 31.4 1.0 HB3 E:CYS914 4.1 52.4 1.0 HB2 E:LYS913 4.1 68.9 1.0 HB2 E:ASP890 4.2 30.7 1.0 N E:CYS914 4.2 43.0 1.0 H E:ASP887 4.4 36.8 1.0 H E:ASP890 4.4 32.0 1.0 O E:HOH1102 4.4 35.5 1.0 C E:PHE910 4.4 40.1 1.0 H E:ASP889 4.5 30.5 1.0 CA E:CYS914 4.5 45.5 1.0 CA E:CYS911 4.5 36.1 1.0 CB E:ASP887 4.6 37.9 1.0 CA E:CYS885 4.7 21.8 1.0 O E:CYS911 4.7 35.2 1.0 C E:CYS888 4.8 33.5 1.0 N E:ASP889 4.8 25.4 1.0 C E:CYS911 4.8 41.1 1.0 C E:ASP887 4.9 33.6 1.0 H E:LYS913 4.9 60.8 1.0 HA E:CYS888 4.9 37.7 1.0 HE1 E:TYR892 4.9 22.6 1.0 N E:CYS911 4.9 39.5 1.0 HA E:PHE910 4.9 38.6 1.0 HA E:CYS885 5.0 26.2 1.0 HB2 E:ASP887 5.0 45.5 1.0 HD3 E:LYS913 5.0 76.8 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1002 b:23.1 occ:1.00 ND1 E:HIS893 2.1 33.9 1.0 SG E:CYS870 2.3 18.5 1.0 SG E:CYS873 2.3 24.3 1.0 SG E:CYS896 2.3 22.6 1.0 HB3 E:CYS870 2.8 23.6 1.0 H E:CYS873 2.9 24.0 1.0 CE1 E:HIS893 2.9 28.0 1.0 HE1 E:HIS893 3.0 33.6 1.0 HB3 E:CYS873 3.0 28.5 1.0 CB E:CYS870 3.0 19.6 1.0 HB2 E:HIS893 3.1 27.8 1.0 CG E:HIS893 3.2 28.2 1.0 CB E:CYS873 3.2 23.8 1.0 HB2 E:CYS896 3.3 27.2 1.0 HB2 E:CYS870 3.3 23.6 1.0 H E:HIS893 3.3 24.0 1.0 CB E:CYS896 3.4 22.7 1.0 N E:CYS873 3.4 20.0 1.0 HB3 E:CYS896 3.6 27.2 1.0 CB E:HIS893 3.6 23.1 1.0 CA E:CYS873 3.9 23.1 1.0 HB2 E:CYS873 4.0 28.5 1.0 NE2 E:HIS893 4.0 28.4 1.0 N E:HIS893 4.1 20.0 1.0 CD2 E:HIS893 4.2 29.6 1.0 HA3 E:GLY872 4.2 23.4 1.0 H E:ASN874 4.3 30.6 1.0 H E:GLY872 4.3 23.7 1.0 HB3 E:HIS893 4.4 27.8 1.0 C E:GLY872 4.4 24.2 1.0 CA E:HIS893 4.5 26.5 1.0 CA E:CYS870 4.5 19.7 1.0 CA E:GLY872 4.6 19.5 1.0 H E:CYS896 4.6 27.2 1.0 HA E:CYS873 4.7 27.8 1.0 H E:LYS875 4.7 31.3 1.0 N E:GLY872 4.8 19.8 1.0 N E:ASN874 4.8 25.5 1.0 HE2 E:HIS893 4.8 34.1 1.0 CA E:CYS896 4.8 26.3 1.0 C E:CYS873 4.8 24.7 1.0 C E:CYS870 4.8 21.2 1.0 O E:CYS870 4.8 18.2 1.0 HA E:CYS870 4.9 23.6 1.0 HA E:TYR892 5.0 17.1 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1001 b:28.9 occ:1.00 SG G:CYS888 2.2 28.6 1.0 SG G:CYS911 2.4 28.6 1.0 SG G:CYS885 2.4 26.0 1.0 SG G:CYS914 2.5 38.3 1.0 H G:CYS888 2.9 40.5 1.0 HB2 G:CYS914 3.1 54.6 1.0 HB3 G:CYS888 3.1 35.0 1.0 HB3 G:CYS885 3.2 32.5 1.0 HB3 G:CYS911 3.2 46.2 1.0 CB G:CYS885 3.2 27.1 1.0 HB2 G:CYS885 3.3 32.5 1.0 CB G:CYS888 3.3 29.2 1.0 O G:PHE910 3.3 50.4 1.0 CB G:CYS914 3.4 45.5 1.0 CB G:CYS911 3.5 38.5 1.0 HB3 G:ASP887 3.6 47.9 1.0 N G:CYS888 3.7 33.8 1.0 H G:CYS914 3.9 54.9 1.0 HB3 G:CYS914 4.0 54.6 1.0 CA G:CYS888 4.0 32.2 1.0 HB2 G:CYS888 4.0 35.0 1.0 HB2 G:CYS911 4.1 46.2 1.0 HB2 G:ASP890 4.1 28.4 1.0 HB2 G:LYS913 4.2 58.2 1.0 N G:CYS914 4.3 45.7 1.0 H G:ASP889 4.3 31.5 1.0 C G:PHE910 4.4 41.2 1.0 H G:ASP887 4.4 36.7 1.0 H G:ASP890 4.4 32.8 1.0 CA G:CYS914 4.5 46.1 1.0 O G:HOH1105 4.5 30.1 1.0 CB G:ASP887 4.5 39.9 1.0 CA G:CYS911 4.7 32.2 1.0 CA G:CYS885 4.7 27.8 1.0 O G:CYS911 4.7 41.5 1.0 N G:ASP889 4.7 26.2 1.0 C G:CYS888 4.8 32.9 1.0 C G:ASP887 4.8 33.2 1.0 HB2 G:ASP887 4.8 47.9 1.0 HA G:CYS888 4.9 38.7 1.0 HE1 G:TYR892 4.9 24.0 1.0 N G:CYS911 5.0 38.4 1.0 HA G:CYS914 5.0 55.3 1.0 C G:CYS911 5.0 39.4 1.0 HA G:PHE910 5.0 49.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of TAF3 Phd Finger Bound to Histone H3C4ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1002 b:23.5 occ:1.00 ND1 G:HIS893 1.9 29.1 1.0 SG G:CYS870 2.3 17.5 1.0 SG G:CYS896 2.3 23.4 1.0 SG G:CYS873 2.3 27.6 1.0 HB2 G:HIS893 2.8 36.8 1.0 HB3 G:CYS870 2.8 27.6 1.0 HB3 G:CYS873 2.8 21.8 1.0 CE1 G:HIS893 2.8 30.0 1.0 CG G:HIS893 3.0 25.2 1.0 HE1 G:HIS893 3.0 36.0 1.0 H G:CYS873 3.0 31.6 1.0 CB G:CYS870 3.0 23.0 1.0 CB G:CYS873 3.1 18.2 1.0 HB2 G:CYS870 3.3 27.6 1.0 HB2 G:CYS896 3.3 29.3 1.0 H G:HIS893 3.4 25.5 1.0 CB G:CYS896 3.4 24.4 1.0 CB G:HIS893 3.4 30.7 1.0 N G:CYS873 3.5 26.4 1.0 HB3 G:CYS896 3.6 29.3 1.0 HB2 G:CYS873 3.9 21.8 1.0 CA G:CYS873 3.9 29.4 1.0 NE2 G:HIS893 4.0 31.8 1.0 CD2 G:HIS893 4.0 31.2 1.0 HB3 G:HIS893 4.1 36.8 1.0 N G:HIS893 4.1 21.3 1.0 H G:GLY872 4.2 24.2 1.0 HA3 G:GLY872 4.2 34.9 1.0 H G:ASN874 4.3 31.5 1.0 CA G:HIS893 4.3 22.2 1.0 C G:GLY872 4.4 32.3 1.0 CA G:CYS870 4.5 17.9 1.0 H G:CYS896 4.7 30.2 1.0 CA G:GLY872 4.7 29.1 1.0 HA G:CYS873 4.7 35.3 1.0 N G:GLY872 4.7 20.1 1.0 HE2 G:HIS893 4.7 38.2 1.0 O G:CYS870 4.8 22.1 1.0 CA G:CYS896 4.8 28.4 1.0 N G:ASN874 4.8 26.2 1.0 C G:CYS870 4.8 18.9 1.0 C G:CYS873 4.8 30.1 1.0 H G:LYS875 4.9 27.6 1.0 HD2 G:HIS893 4.9 37.4 1.0 HA G:CYS870 4.9 21.5 1.0

J.Huang, H.Li. Crystal Structure of JARID1A Phd Finger Bound to Histone H3C4ME3 Peptide Nat Commun 2015.
ISSN: ESSN 2041-1723