Zinc in PDB 3u5o: Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide

The structure of Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide, PDB code: 3u5o was solved by Z.Wang, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.47 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	63.639, 63.650, 125.195, 90.05, 89.98, 89.93
R / Rfree (%)	20.5 / 28

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide (pdb code 3u5o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide, PDB code: 3u5o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone 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 the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:86.2 occ:1.00 SG A:CYS890 1.9 80.1 1.0 SG A:CYS893 2.1 68.6 1.0 SG A:CYS913 2.2 79.4 1.0 ND1 A:HIS910 2.5 72.4 1.0 CB A:CYS890 3.0 72.9 1.0 CB A:CYS913 3.3 75.2 1.0 CG A:HIS910 3.3 76.3 1.0 CB A:CYS893 3.3 66.2 1.0 CB A:HIS910 3.4 73.4 1.0 CE1 A:HIS910 3.6 73.7 1.0 N A:CYS893 3.6 68.6 1.0 CA A:CYS893 4.0 65.5 1.0 N A:HIS910 4.1 74.4 1.0 CA A:HIS910 4.3 77.0 1.0 CA A:CYS890 4.4 72.3 1.0 CD2 A:HIS910 4.5 81.5 1.0 NE2 A:HIS910 4.6 84.0 1.0 CB A:VAL892 4.6 58.0 1.0 CA A:CYS913 4.7 71.7 1.0 C A:VAL892 4.8 62.5 1.0 C A:CYS893 4.9 66.4 1.0 N A:GLN894 5.0 68.8 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone 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 the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:96.4 occ:1.00 SG A:CYS905 2.2 94.1 1.0 SG A:CYS928 2.2 87.1 1.0 SG A:CYS931 2.4 95.8 1.0 SG A:CYS902 2.5 97.1 1.0 CB A:CYS931 3.2 93.7 1.0 CB A:CYS905 3.4 93.0 1.0 CB A:CYS928 3.6 86.1 1.0 N A:CYS905 3.6 99.4 1.0 CB A:CYS902 3.7 99.8 1.0 CA A:CYS905 4.0 0.6 1.0 N A:CYS928 4.0 91.9 1.0 CA A:CYS928 4.3 90.3 1.0 N A:CYS931 4.3 92.7 1.0 CA A:CYS931 4.3 96.0 1.0 O A:CYS905 4.4 0.5 1.0 C A:CYS905 4.5 0.3 1.0 C A:LYS904 4.6 0.3 1.0 CB A:LYS904 4.7 0.2 1.0 CB A:PHE930 4.7 82.3 1.0 C A:CYS928 4.7 90.8 1.0 O A:CYS928 4.7 87.8 1.0 CA A:LYS904 5.0 0.4 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone 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 the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:83.2 occ:1.00 SG B:CYS890 2.0 86.0 1.0 SG B:CYS893 2.1 69.1 1.0 SG B:CYS913 2.1 76.6 1.0 ND1 B:HIS910 2.3 77.5 1.0 CB B:CYS890 3.1 72.9 1.0 CB B:CYS893 3.2 68.3 1.0 CG B:HIS910 3.2 76.3 1.0 CB B:CYS913 3.2 72.8 1.0 CE1 B:HIS910 3.3 75.7 1.0 CB B:HIS910 3.5 74.5 1.0 N B:CYS893 3.7 65.0 1.0 CA B:CYS893 4.1 64.9 1.0 N B:HIS910 4.3 76.0 1.0 NE2 B:HIS910 4.4 78.6 1.0 CD2 B:HIS910 4.4 77.6 1.0 CA B:CYS890 4.5 70.8 1.0 CA B:HIS910 4.5 76.0 1.0 CB B:VAL892 4.7 57.5 1.0 CA B:CYS913 4.7 70.1 1.0 C B:CYS893 4.8 64.6 1.0 C B:VAL892 4.8 58.0 1.0 N B:GLN894 5.0 67.2 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone 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 the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:0.5 occ:1.00 SG B:CYS905 2.0 88.3 1.0 SG B:CYS928 2.3 90.0 1.0 SG B:CYS931 2.3 92.5 1.0 SG B:CYS902 2.5 91.7 1.0 CB B:CYS905 3.2 86.4 1.0 N B:CYS905 3.5 0.8 1.0 CB B:CYS931 3.5 91.1 1.0 CB B:CYS928 3.5 87.8 1.0 CB B:CYS902 3.8 94.2 1.0 CA B:CYS905 3.8 96.7 1.0 N B:CYS928 4.0 96.3 1.0 N B:CYS931 4.2 93.0 1.0 CA B:CYS928 4.3 92.2 1.0 CB B:LYS904 4.4 0.5 1.0 O B:CYS905 4.4 93.9 1.0 C B:CYS905 4.4 91.6 1.0 C B:LYS904 4.5 0.5 1.0 CA B:CYS931 4.5 95.1 1.0 CB B:PHE930 4.6 85.0 1.0 C B:CYS928 4.7 91.2 1.0 O B:CYS928 4.7 89.2 1.0 CA B:LYS904 4.9 0.1 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone 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 the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1 b:84.7 occ:1.00 SG C:CYS890 1.9 77.6 1.0 SG C:CYS913 2.1 74.4 1.0 SG C:CYS893 2.1 65.9 1.0 ND1 C:HIS910 2.4 80.3 1.0 CB C:CYS890 3.0 72.3 1.0 CB C:CYS913 3.2 73.4 1.0 CG C:HIS910 3.2 79.1 1.0 CB C:CYS893 3.3 60.6 1.0 CB C:HIS910 3.4 76.0 1.0 CE1 C:HIS910 3.4 80.7 1.0 N C:CYS893 3.7 68.2 1.0 CA C:CYS893 4.0 63.6 1.0 N C:HIS910 4.1 77.3 1.0 CA C:HIS910 4.4 79.0 1.0 CD2 C:HIS910 4.4 83.7 1.0 CA C:CYS890 4.4 70.4 1.0 NE2 C:HIS910 4.5 90.0 1.0 CA C:CYS913 4.6 73.1 1.0 CB C:VAL892 4.7 57.4 1.0 C C:CYS893 4.8 63.0 1.0 C C:VAL892 4.9 60.9 1.0 O C:ASN895 4.9 78.7 1.0 N C:GLN894 4.9 66.8 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone 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 the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2 b:99.5 occ:1.00 SG C:CYS931 2.2 99.3 1.0 SG C:CYS905 2.2 87.2 1.0 SG C:CYS902 2.4 92.8 1.0 SG C:CYS928 2.6 90.7 1.0 CB C:CYS905 3.5 92.5 1.0 CB C:CYS902 3.5 94.8 1.0 CB C:CYS931 3.5 92.0 1.0 CB C:CYS928 3.7 88.3 1.0 N C:CYS905 3.8 0.3 1.0 CA C:CYS905 4.1 0.2 1.0 N C:CYS928 4.2 93.5 1.0 N C:CYS931 4.3 91.6 1.0 CA C:CYS928 4.4 91.5 1.0 CA C:CYS931 4.5 94.6 1.0 CB C:LYS904 4.6 0.1 1.0 CB C:PHE930 4.6 82.3 1.0 C C:CYS905 4.6 98.9 1.0 O C:CYS905 4.6 0.4 1.0 C C:LYS904 4.8 0.5 1.0 C C:CYS928 4.8 90.9 1.0 CA C:CYS902 4.9 0.9 1.0 O C:CYS928 4.9 91.4 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone 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 the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1 b:85.7 occ:1.00 SG D:CYS890 1.9 81.1 1.0 SG D:CYS893 2.1 64.4 1.0 SG D:CYS913 2.2 73.8 1.0 ND1 D:HIS910 2.6 73.7 1.0 CB D:CYS890 3.0 70.9 1.0 CB D:CYS913 3.2 73.5 1.0 CG D:HIS910 3.3 75.5 1.0 CB D:HIS910 3.3 72.1 1.0 CB D:CYS893 3.4 63.1 1.0 CE1 D:HIS910 3.7 73.4 1.0 N D:CYS893 3.9 63.9 1.0 N D:HIS910 4.1 71.2 1.0 CA D:CYS893 4.2 61.6 1.0 CA D:HIS910 4.3 75.4 1.0 CA D:CYS890 4.4 69.6 1.0 CD2 D:HIS910 4.5 79.4 1.0 NE2 D:HIS910 4.7 81.5 1.0 CA D:CYS913 4.7 72.2 1.0 CB D:VAL892 4.7 55.9 1.0 C D:CYS893 5.0 62.3 1.0 C D:VAL892 5.0 57.5 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone 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 the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2 b:93.5 occ:1.00 SG D:CYS905 2.0 90.9 1.0 SG D:CYS902 2.3 94.5 1.0 SG D:CYS931 2.5 92.1 1.0 SG D:CYS928 2.5 92.4 1.0 CB D:CYS905 3.3 86.2 1.0 CB D:CYS931 3.4 91.4 1.0 CB D:CYS902 3.5 94.5 1.0 N D:CYS905 3.6 0.2 1.0 CB D:CYS928 3.8 86.8 1.0 CA D:CYS905 3.9 97.0 1.0 N D:CYS928 4.1 93.1 1.0 O D:CYS905 4.3 0.5 1.0 N D:CYS931 4.3 90.1 1.0 CA D:CYS928 4.4 90.4 1.0 C D:CYS905 4.4 93.5 1.0 CB D:LYS904 4.5 0.9 1.0 CA D:CYS931 4.5 93.1 1.0 C D:LYS904 4.5 0.8 1.0 CB D:PHE930 4.7 80.5 1.0 O D:CYS928 4.7 85.5 1.0 C D:CYS928 4.8 88.6 1.0 CA D:CYS902 4.9 0.8 1.0 CA D:LYS904 4.9 0.9 1.0 N D:LYS904 5.0 0.1 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1 b:88.2 occ:1.00 SG E:CYS890 1.9 85.7 1.0 SG E:CYS913 2.0 75.8 1.0 SG E:CYS893 2.0 68.9 1.0 ND1 E:HIS910 2.5 72.8 1.0 CB E:CYS890 3.0 70.4 1.0 CB E:CYS913 3.1 77.8 1.0 CG E:HIS910 3.3 71.8 1.0 CB E:HIS910 3.3 68.7 1.0 CB E:CYS893 3.4 66.3 1.0 CE1 E:HIS910 3.6 73.6 1.0 N E:CYS893 3.7 68.3 1.0 N E:HIS910 4.0 69.3 1.0 CA E:CYS893 4.1 66.3 1.0 CA E:HIS910 4.3 71.6 1.0 CA E:CYS890 4.4 68.1 1.0 CD2 E:HIS910 4.5 76.8 1.0 CA E:CYS913 4.6 74.4 1.0 NE2 E:HIS910 4.6 81.0 1.0 CB E:VAL892 4.7 55.4 1.0 O E:ASN895 4.8 70.5 1.0 C E:VAL892 4.8 57.7 1.0 N E:VAL892 5.0 58.2 1.0 C E:CYS893 5.0 67.5 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Complex of TRIM33 Phd-Bromo and H3(1-22) K9ME3K14ACK18AC Histone Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn2 b:99.1 occ:1.00 SG E:CYS905 2.2 91.6 1.0 SG E:CYS928 2.2 85.3 1.0 SG E:CYS931 2.4 0.9 1.0 SG E:CYS902 2.5 93.9 1.0 CB E:CYS931 3.0 96.4 1.0 CB E:CYS905 3.3 86.8 1.0 N E:CYS905 3.6 0.5 1.0 CB E:CYS902 3.7 94.9 1.0 CB E:CYS928 3.8 85.8 1.0 CA E:CYS905 4.0 97.8 1.0 N E:CYS928 4.1 92.4 1.0 CA E:CYS931 4.1 95.3 1.0 N E:CYS931 4.2 89.1 1.0 CA E:CYS928 4.4 90.2 1.0 CB E:LYS904 4.5 0.6 1.0 CB E:PHE930 4.6 76.9 1.0 C E:LYS904 4.6 0.7 1.0 C E:CYS905 4.6 94.0 1.0 O E:CYS905 4.7 98.7 1.0 O E:CYS928 4.8 89.6 1.0 C E:CYS928 4.8 89.5 1.0 CA E:LYS904 4.9 0.3 1.0 C E:PHE930 5.0 86.5 1.0

Q.Xi, Z.Wang, A.I.Zaromytidou, X.H.Zhang, L.F.Chow-Tsang, J.X.Liu, H.Kim, A.Barlas, K.Manova-Todorova, V.Kaartinen, L.Studer, W.Mark, D.J.Patel, J.Massague. A Poised Chromatin Platform For Tgf-Beta Access to Master Regulators Cell(Cambridge,Mass.) V. 147 1511 2011.
ISSN: ISSN 0092-8674
PubMed: 22196728
DOI: 10.1016/J.CELL.2011.11.032