Zinc in PDB 5tdw: SET3 Phd Finger in Complex with Histone H3K4ME3

The structure of SET3 Phd Finger in Complex with Histone H3K4ME3, PDB code: 5tdw was solved by F.H.Andrews, M.Ali, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.53 / 1.70
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.870, 43.680, 85.060, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.9

The structure of SET3 Phd Finger in Complex with Histone H3K4ME3 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the SET3 Phd Finger in Complex with Histone H3K4ME3 (pdb code 5tdw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the SET3 Phd Finger in Complex with Histone H3K4ME3, PDB code: 5tdw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the SET3 Phd Finger in Complex with Histone H3K4ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SET3 Phd Finger in Complex with Histone H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:4.9 occ:1.00 ND1 A:HIS27 2.2 4.0 1.0 SG A:CYS30 2.3 3.2 1.0 SG A:CYS7 2.3 5.2 1.0 SG A:CYS5 2.3 4.2 1.0 CE1 A:HIS27 3.1 4.5 1.0 CG A:HIS27 3.2 4.8 1.0 CB A:CYS5 3.2 5.3 1.0 CB A:CYS30 3.2 4.0 1.0 CB A:CYS7 3.3 5.5 1.0 CB A:HIS27 3.5 3.6 1.0 CG A:GLN62 3.7 3.5 1.0 N A:CYS7 3.9 5.9 1.0 NE2 A:GLN62 4.0 6.0 1.0 CD A:GLN62 4.2 7.1 1.0 N A:HIS27 4.2 4.2 1.0 NE2 A:HIS27 4.2 6.3 1.0 CA A:CYS7 4.3 5.9 1.0 CD2 A:HIS27 4.3 5.8 1.0 N A:ILE6 4.4 4.6 1.0 CA A:HIS27 4.4 4.1 1.0 CA A:CYS5 4.5 4.7 1.0 C A:CYS5 4.6 5.3 1.0 CA A:CYS30 4.6 4.0 1.0 O A:HIS27 4.8 4.3 1.0 CG1 A:ILE6 4.9 9.5 1.0 CB A:GLN62 4.9 7.0 1.0 CB A:ALA58 5.0 4.3 1.0

Zinc binding site 2 out of 2 in the SET3 Phd Finger in Complex with Histone H3K4ME3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SET3 Phd Finger in Complex with Histone H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:9.3 occ:1.00 SG A:CYS19 2.3 7.8 1.0 SG A:CYS22 2.3 10.4 1.0 SG A:CYS48 2.3 11.0 1.0 SG A:CYS45 2.3 7.0 1.0 CB A:CYS19 3.1 10.8 1.0 CB A:CYS48 3.3 7.1 1.0 CB A:CYS22 3.3 10.5 1.0 CB A:CYS45 3.5 7.1 1.0 N A:CYS22 3.7 10.8 1.0 N A:CYS45 4.0 7.2 1.0 N A:CYS48 4.0 8.6 1.0 CA A:CYS22 4.1 11.8 1.0 O A:HOH343 4.1 21.1 1.0 O A:HOH312 4.2 20.9 1.0 CA A:CYS48 4.2 9.3 1.0 CA A:CYS45 4.2 5.1 1.0 O A:HOH298 4.5 18.5 1.0 CA A:CYS19 4.6 4.1 1.0 C A:CYS45 4.8 10.2 1.0 C A:CYS22 4.8 13.5 1.0 O A:CYS45 4.8 5.7 1.0 CB A:HIS21 4.8 15.2 1.0 C A:HIS21 4.8 20.3 1.0 N A:ASN23 5.0 10.6 1.0 CB A:SER47 5.0 13.8 1.0

J.Gatchalian, M.Ali, F.H.Andrews, Y.Zhang, A.S.Barrett, T.G.Kutateladze. Structural Insight Into Recognition of Methylated Histone H3K4 By SET3. J. Mol. Biol. V. 429 2066 2017.
ISSN: ESSN 1089-8638
PubMed: 27697561
DOI: 10.1016/J.JMB.2016.09.020