Zinc in PDB 4d1m: Tetramerization Domain of Zebrafish P53 (Crystal Form II)

The structure of Tetramerization Domain of Zebrafish P53 (Crystal Form II), PDB code: 4d1m was solved by A.C.Joerger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.90 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.861, 74.507, 74.945, 90.00, 117.79, 90.00
R / Rfree (%)	22.59 / 27.996

The binding sites of Zinc atom in the Tetramerization Domain of Zebrafish P53 (Crystal Form II) (pdb code 4d1m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Tetramerization Domain of Zebrafish P53 (Crystal Form II), PDB code: 4d1m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Tetramerization Domain of Zebrafish P53 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tetramerization Domain of Zebrafish P53 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1343 b:87.1 occ:1.00 OE2 B:GLU303 2.2 79.7 1.0 CD B:GLU303 3.2 74.0 1.0 OE1 B:GLU303 3.5 78.0 1.0 NE A:ARG312 4.0 67.0 1.0 NH2 A:ARG312 4.1 75.2 1.0 CZ A:ARG312 4.5 71.5 1.0 CG B:GLU303 4.6 69.5 1.0

Zinc binding site 2 out of 2 in the Tetramerization Domain of Zebrafish P53 (Crystal Form II)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tetramerization Domain of Zebrafish P53 (Crystal Form II) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1344 b:81.3 occ:1.00 OD1 F:ASP335 2.5 63.1 1.0 OD2 F:ASP335 2.9 56.8 1.0 CG F:ASP335 3.0 54.7 1.0 NZ F:LYS338 4.0 84.6 1.0 OG F:SER334 4.1 53.1 1.0 CB F:ASP335 4.5 50.0 1.0 CG F:PRO332 4.8 50.8 1.0 CB F:PRO332 4.9 46.9 1.0 N F:ASP335 4.9 45.8 1.0

A.C.Joerger, R.Wilcken, A.Andreeva. Tracing the Evolution of the P53 Tetramerization Domain Structure V. 22 1301 2014.
ISSN: ISSN 0969-2126
PubMed: 25185827
DOI: 10.1016/J.STR.2014.07.010