Zinc in PDB 8t4r: RAG2-Phd Finger in Complex with H3K4TBUNLE Peptide

The structure of RAG2-Phd Finger in Complex with H3K4TBUNLE Peptide, PDB code: 8t4r was solved by K.M.Kean, C.R.Travis, M.L.Waters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.27 / 1.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	46.499, 46.499, 79.896, 90, 90, 120
R / Rfree (%)	14 / 16

The binding sites of Zinc atom in the RAG2-Phd Finger in Complex with H3K4TBUNLE Peptide (pdb code 8t4r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the RAG2-Phd Finger in Complex with H3K4TBUNLE Peptide, PDB code: 8t4r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the RAG2-Phd Finger in Complex with H3K4TBUNLE Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RAG2-Phd Finger in Complex with H3K4TBUNLE Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:16.9 occ:1.00 ND1 A:HIS455 2.1 15.9 1.0 SG A:CYS423 2.3 18.4 1.0 SG A:CYS458 2.3 17.3 1.0 SG A:CYS419 2.3 18.2 1.0 HB2 A:HIS455 2.8 17.5 1.0 CE1 A:HIS455 3.0 15.8 1.0 HB2 A:CYS423 3.0 24.1 1.0 CG A:HIS455 3.1 14.5 1.0 HB3 A:CYS419 3.1 22.6 1.0 H A:CYS419 3.1 23.4 1.0 CB A:CYS423 3.2 20.1 1.0 HE1 A:HIS455 3.2 18.9 1.0 HB2 A:CYS458 3.2 20.1 1.0 HA A:CYS423 3.3 25.5 1.0 CB A:CYS458 3.3 16.8 1.0 CB A:CYS419 3.3 18.9 1.0 H A:HIS455 3.4 17.6 1.0 HB3 A:CYS458 3.4 20.1 1.0 CB A:HIS455 3.5 14.6 1.0 HB A:VAL425 3.5 27.8 1.0 H A:VAL425 3.7 27.3 1.0 CA A:CYS423 3.7 21.2 1.0 HG23 A:VAL425 3.8 28.4 1.0 H A:ASP424 3.9 30.8 1.0 N A:CYS419 3.9 19.5 1.0 HB3 A:CYS423 4.0 24.1 1.0 HB2 A:CYS419 4.1 22.6 1.0 HB3 A:HIS455 4.1 17.5 1.0 HG21 A:VAL425 4.1 28.4 1.0 NE2 A:HIS455 4.1 16.6 1.0 CA A:CYS419 4.2 20.4 1.0 N A:HIS455 4.2 14.7 1.0 CD2 A:HIS455 4.2 15.8 1.0 CG2 A:VAL425 4.3 23.7 1.0 CB A:VAL425 4.3 23.2 1.0 N A:ASP424 4.4 25.6 1.0 CA A:HIS455 4.4 14.0 1.0 C A:CYS423 4.4 24.0 1.0 N A:VAL425 4.5 22.7 1.0 H A:CYS458 4.5 18.8 1.0 H A:CYS420 4.6 26.4 1.0 CA A:CYS458 4.7 15.6 1.0 HA A:THR418 4.8 27.4 1.0 C A:CYS419 4.8 20.4 1.0 O A:ILE417 4.9 18.8 1.0 SG A:CYS420 4.9 24.8 1.0 HE2 A:HIS455 4.9 19.9 1.0 N A:CYS420 4.9 22.0 1.0 N A:CYS423 4.9 22.2 1.0 O A:HIS455 4.9 14.0 1.0 HA A:CYS419 5.0 24.4 1.0 HA A:CYS458 5.0 18.7 1.0

Zinc binding site 2 out of 2 in the RAG2-Phd Finger in Complex with H3K4TBUNLE Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RAG2-Phd Finger in Complex with H3K4TBUNLE Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:20.8 occ:1.00 ND1 A:HIS481 2.0 23.9 1.0 NE2 A:HIS452 2.0 20.0 1.0 SG A:CYS446 2.3 19.3 1.0 SG A:CYS478 2.3 21.7 1.0 HB2 A:HIS481 2.9 32.1 1.0 CE1 A:HIS452 2.9 20.1 1.0 CE1 A:HIS481 2.9 25.4 1.0 CG A:HIS481 3.1 25.2 1.0 HE1 A:HIS452 3.1 24.1 1.0 CD2 A:HIS452 3.1 19.6 1.0 HE1 A:HIS481 3.1 30.4 1.0 H A:CYS478 3.1 26.7 1.0 HB3 A:CYS446 3.1 22.2 1.0 HB3 A:CYS478 3.1 25.6 1.0 CB A:CYS446 3.2 18.5 1.0 HB2 A:CYS446 3.3 22.2 1.0 HD2 A:HIS452 3.3 23.5 1.0 CB A:CYS478 3.3 21.3 1.0 HB3 A:HIS448 3.4 35.5 1.0 CB A:HIS481 3.5 26.7 1.0 N A:CYS478 3.9 22.3 1.0 HB3 A:HIS481 4.0 32.1 1.0 HB2 A:HIS448 4.0 35.5 1.0 NE2 A:HIS481 4.1 28.1 1.0 ND1 A:HIS452 4.1 21.0 1.0 HB2 A:CYS478 4.1 25.6 1.0 CB A:HIS448 4.1 29.6 1.0 CD2 A:HIS481 4.2 27.4 1.0 CA A:CYS478 4.2 21.5 1.0 CG A:HIS452 4.2 20.1 1.0 HB2 A:GLU480 4.3 38.5 1.0 H A:HIS448 4.3 27.6 1.0 H A:HIS481 4.3 32.1 1.0 N A:HIS481 4.6 26.8 1.0 CA A:CYS446 4.6 18.1 1.0 HG11 A:VAL454 4.7 20.8 1.0 HA A:TYR477 4.7 24.6 1.0 CA A:HIS481 4.7 26.1 1.0 C A:CYS478 4.8 20.4 1.0 HD2 A:HIS448 4.8 42.5 1.0 HG13 A:VAL454 4.8 20.8 1.0 HE2 A:HIS481 4.8 33.7 1.0 CG A:HIS448 4.8 30.5 1.0 HD1 A:HIS452 4.9 25.2 1.0 O A:CYS478 4.9 21.9 1.0 H A:GLU480 4.9 32.1 1.0 HA A:CYS446 5.0 21.8 1.0

C.R.Travis, K.M.Kean, K.I.Albanese, H.C.Henriksen, J.W.Treacy, E.Y.Chao, K.N.Houk, M.L.Waters. Trimethyllysine Reader Proteins Exhibit Widespread Charge-Agnostic Binding Via Different Mechanisms to Cationic and Neutral Ligands. J.Am.Chem.Soc. V. 146 3086 2024.
ISSN: ESSN 1520-5126
PubMed: 38266163
DOI: 10.1021/JACS.3C10031