Zinc in PDB 7z5h: Human Zn Matcap

The structure of Human Zn Matcap, PDB code: 7z5h was solved by J.Bak, A.Adamopoulos, T.Heidebrecht, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.08 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.646, 88.067, 165.581, 90, 90.77, 90
R / Rfree (%)	23.2 / 25.5

The binding sites of Zinc atom in the Human Zn Matcap (pdb code 7z5h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Zn Matcap, PDB code: 7z5h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human Zn Matcap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Zn Matcap within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:46.2 occ:1.00 HE2 A:HIS280 1.3 30.0 0.0 HE2 A:HIS285 1.5 30.0 0.0 NE2 A:HIS280 2.2 44.4 1.0 OE1 A:GLU316 2.2 48.6 1.0 NE2 A:HIS285 2.3 41.8 1.0 OE2 A:GLU316 2.8 49.1 1.0 CD A:GLU316 2.9 48.3 1.0 CD2 A:HIS285 3.1 42.6 1.0 CE1 A:HIS280 3.2 43.1 1.0 CD2 A:HIS280 3.2 45.0 1.0 HD2 A:HIS285 3.2 42.6 1.0 HE1 A:TYR393 3.3 41.2 1.0 HH A:TYR393 3.3 30.0 0.0 HD2 A:HIS280 3.3 45.4 1.0 HE1 A:HIS280 3.3 42.4 1.0 CE1 A:HIS285 3.4 42.1 1.0 HE1 A:HIS285 3.6 41.4 1.0 OE2 A:GLU281 3.7 48.6 1.0 OH A:TYR393 4.1 45.9 1.0 CE1 A:TYR393 4.1 40.9 1.0 HB3 A:ALA319 4.2 44.5 1.0 ND1 A:HIS280 4.3 41.4 1.0 CG A:HIS285 4.3 42.3 1.0 CG A:HIS280 4.3 43.4 1.0 CG A:GLU316 4.3 47.0 1.0 HB2 A:ALA319 4.4 45.1 1.0 ND1 A:HIS285 4.4 41.9 1.0 CD A:GLU281 4.4 49.7 1.0 HA A:GLU316 4.5 46.0 1.0 OE1 A:GLU281 4.6 51.8 1.0 CB A:ALA319 4.6 44.9 1.0 CZ A:TYR393 4.6 42.0 1.0 HB3 A:GLU316 4.7 45.4 1.0 HG3 A:GLU316 4.8 47.2 1.0 HG2 A:GLU316 4.8 47.7 1.0 HB1 A:ALA319 4.8 45.3 1.0 CB A:GLU316 5.0 45.8 1.0

Zinc binding site 2 out of 4 in the Human Zn Matcap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Zn Matcap within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:55.0 occ:1.00 HE2 B:HIS280 1.4 30.0 0.0 HE2 B:HIS285 1.5 30.0 0.0 NE2 B:HIS280 2.3 52.9 1.0 NE2 B:HIS285 2.3 52.7 1.0 OE1 B:GLU316 2.4 56.5 1.0 OE2 B:GLU316 2.8 58.0 1.0 CD B:GLU316 2.9 57.0 1.0 CD2 B:HIS285 3.1 53.4 1.0 HD2 B:HIS285 3.1 53.7 1.0 CD2 B:HIS280 3.2 53.1 1.0 CE1 B:HIS280 3.3 53.3 1.0 HH B:TYR393 3.3 30.0 0.0 HD2 B:HIS280 3.3 53.5 1.0 HE1 B:TYR393 3.4 53.4 1.0 CE1 B:HIS285 3.4 53.2 1.0 HE1 B:HIS280 3.4 53.2 1.0 OE2 B:GLU281 3.6 59.2 1.0 HE1 B:HIS285 3.7 52.8 1.0 OH B:TYR393 4.1 55.1 1.0 CE1 B:TYR393 4.2 53.7 1.0 CG B:HIS285 4.3 53.0 1.0 HB3 B:ALA319 4.3 55.5 1.0 CD B:GLU281 4.3 58.4 1.0 ND1 B:HIS280 4.4 53.5 1.0 CG B:HIS280 4.4 53.8 1.0 ND1 B:HIS285 4.4 53.1 1.0 HB2 B:ALA319 4.5 55.7 1.0 CG B:GLU316 4.5 56.4 1.0 OE1 B:GLU281 4.5 58.0 1.0 HA B:GLU316 4.6 54.2 1.0 CZ B:TYR393 4.7 54.4 1.0 CB B:ALA319 4.8 55.5 1.0 HG3 B:GLU316 4.9 56.8 1.0 HB3 B:GLU316 4.9 55.7 1.0 HG2 B:GLU316 4.9 56.3 1.0 HB1 B:ALA319 4.9 55.3 1.0

Zinc binding site 3 out of 4 in the Human Zn Matcap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Zn Matcap within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:57.6 occ:1.00 HE2 C:HIS285 1.7 30.0 0.0 HE2 C:HIS280 1.7 30.0 0.0 NE2 C:HIS285 2.5 44.9 1.0 NE2 C:HIS280 2.5 49.7 1.0 OE1 C:GLU316 2.5 53.8 1.0 OE2 C:GLU316 2.8 57.0 1.0 CD C:GLU316 3.0 53.5 1.0 HD2 C:HIS285 3.2 45.6 1.0 CD2 C:HIS285 3.2 45.4 1.0 HH C:TYR393 3.3 30.0 0.0 CD2 C:HIS280 3.4 49.5 1.0 HE1 C:TYR393 3.4 46.5 1.0 HD2 C:HIS280 3.5 49.9 1.0 CE1 C:HIS280 3.5 49.3 1.0 OE2 C:GLU281 3.5 52.4 1.0 CE1 C:HIS285 3.6 45.0 1.0 HE1 C:HIS280 3.7 48.8 1.0 HE1 C:HIS285 3.8 44.4 1.0 OH C:TYR393 4.1 48.5 1.0 CD C:GLU281 4.3 53.2 1.0 CE1 C:TYR393 4.3 46.4 1.0 OE1 C:GLU281 4.3 57.4 1.0 CG C:HIS285 4.4 44.9 1.0 CG C:GLU316 4.5 52.0 1.0 ND1 C:HIS285 4.6 44.7 1.0 CG C:HIS280 4.6 49.0 1.0 HB3 C:ALA319 4.6 48.6 1.0 ND1 C:HIS280 4.6 48.7 1.0 HB2 C:ALA319 4.7 49.2 1.0 CZ C:TYR393 4.7 46.5 1.0 HA C:GLU316 4.8 51.5 1.0 HG3 C:GLU316 4.9 52.1 1.0 HG2 C:GLU316 5.0 52.3 1.0 HB3 C:GLU316 5.0 51.6 1.0

Zinc binding site 4 out of 4 in the Human Zn Matcap


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Zn Matcap within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:44.8 occ:1.00 HE2 D:HIS285 1.4 30.0 0.0 HE2 D:HIS280 1.4 30.0 0.0 NE2 D:HIS285 2.2 38.2 1.0 OE1 D:GLU316 2.3 47.3 1.0 NE2 D:HIS280 2.3 36.8 1.0 OE2 D:GLU316 2.7 50.0 1.0 CD D:GLU316 2.8 46.6 1.0 CD2 D:HIS285 3.0 38.3 1.0 HD2 D:HIS285 3.1 38.2 1.0 CD2 D:HIS280 3.2 37.2 1.0 CE1 D:HIS280 3.3 35.8 1.0 CE1 D:HIS285 3.3 38.4 1.0 HD2 D:HIS280 3.3 37.8 1.0 HE1 D:TYR393 3.4 30.1 1.0 HH D:TYR393 3.4 30.0 0.0 HE1 D:HIS280 3.5 35.3 1.0 HE1 D:HIS285 3.6 37.6 1.0 OE2 D:GLU281 3.7 46.5 1.0 OH D:TYR393 4.2 31.8 1.0 CE1 D:TYR393 4.2 29.6 1.0 CG D:HIS285 4.2 36.9 1.0 HB3 D:ALA319 4.3 37.0 1.0 ND1 D:HIS285 4.3 38.0 1.0 CG D:GLU316 4.4 44.4 1.0 CD D:GLU281 4.4 46.1 1.0 CG D:HIS280 4.4 36.8 1.0 ND1 D:HIS280 4.4 35.2 1.0 HB2 D:ALA319 4.4 37.7 1.0 OE1 D:GLU281 4.5 48.9 1.0 HA D:GLU316 4.5 41.0 1.0 CB D:ALA319 4.7 37.5 1.0 CZ D:TYR393 4.7 30.1 1.0 HG3 D:GLU316 4.8 44.4 1.0 HG2 D:GLU316 4.8 44.9 1.0 HB3 D:GLU316 4.8 42.0 1.0 O D:HOH616 4.8 45.4 1.0 HB1 D:ALA319 4.8 37.9 1.0

L.Landskron, J.Bak, A.Adamopoulos, K.Kaplani, M.Moraiti, L.G.Van Den Hengel, J.Y.Song, O.B.Bleijerveld, J.Nieuwenhuis, T.Heidebrecht, L.Henneman, M.J.Moutin, M.Barisic, S.Taraviras, A.Perrakis, T.R.Brummelkamp. Posttranslational Modification of Microtubules By the Matcap Detyrosinase. Science V. 376 N6020 2022.
ISSN: ESSN 1095-9203
PubMed: 35482892
DOI: 10.1126/SCIENCE.ABN6020