Zinc in PDB 1hr6: Yeast Mitochondrial Processing Peptidase

All present enzymatic activity of Yeast Mitochondrial Processing Peptidase:
3.4.24.64;

The structure of Yeast Mitochondrial Processing Peptidase, PDB code: 1hr6 was solved by A.B.Taylor, B.S.Smith, S.Kitada, K.Kojima, H.Miyaura, Z.Otwinowski, A.Ito, J.Deisenhofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.96 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	134.180, 178.500, 202.070, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 27.9

The binding sites of Zinc atom in the Yeast Mitochondrial Processing Peptidase (pdb code 1hr6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Yeast Mitochondrial Processing Peptidase, PDB code: 1hr6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Yeast Mitochondrial Processing Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Mitochondrial Processing Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:62.6 occ:1.00 NE2 B:HIS74 2.0 61.4 1.0 NE2 B:HIS70 2.1 46.2 1.0 O B:HOH502 2.1 49.5 1.0 OE2 B:GLU150 2.2 80.2 1.0 OE1 B:GLU150 2.2 79.3 1.0 CD B:GLU150 2.4 77.9 1.0 CE1 B:HIS70 2.8 44.4 1.0 CE1 B:HIS74 2.9 57.6 1.0 CD2 B:HIS74 3.2 62.5 1.0 CD2 B:HIS70 3.2 43.7 1.0 CG B:GLU150 3.9 74.6 1.0 ND1 B:HIS70 4.0 43.2 1.0 ND1 B:HIS74 4.1 58.6 1.0 CG B:HIS74 4.2 59.7 1.0 CG B:HIS70 4.3 45.5 1.0 OE2 B:GLU73 4.3 59.4 1.0 CB B:GLU150 4.8 71.0 1.0 CD B:GLU73 5.0 57.9 1.0

Zinc binding site 2 out of 4 in the Yeast Mitochondrial Processing Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Mitochondrial Processing Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:79.3 occ:1.00 NE2 D:HIS74 2.0 71.9 1.0 O D:HOH503 2.1 65.9 1.0 NE2 D:HIS70 2.1 73.5 1.0 OE2 D:GLU150 2.2 84.4 1.0 OE1 D:GLU150 2.2 89.0 1.0 CD D:GLU150 2.4 86.4 1.0 CE1 D:HIS74 2.9 71.5 1.0 CE1 D:HIS70 2.9 73.1 1.0 CD2 D:HIS74 3.1 71.5 1.0 CD2 D:HIS70 3.3 69.7 1.0 CG D:GLU150 4.0 85.0 1.0 ND1 D:HIS74 4.0 70.4 1.0 ND1 D:HIS70 4.1 70.7 1.0 CG D:HIS74 4.2 71.5 1.0 OE2 D:GLU73 4.3 76.6 1.0 CG D:HIS70 4.3 68.8 1.0 CB D:GLU150 4.9 83.2 1.0 CD D:GLU73 5.0 74.4 1.0

Zinc binding site 3 out of 4 in the Yeast Mitochondrial Processing Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Mitochondrial Processing Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn503 b:84.2 occ:1.00 NE2 F:HIS74 2.0 87.9 1.0 O F:HOH504 2.0 55.1 1.0 NE2 F:HIS70 2.1 71.5 1.0 OE2 F:GLU150 2.2 86.5 1.0 OE1 F:GLU150 2.2 86.0 1.0 CD F:GLU150 2.5 85.5 1.0 CE1 F:HIS70 2.8 71.9 1.0 CE1 F:HIS74 2.9 86.5 1.0 CD2 F:HIS74 3.2 86.4 1.0 CD2 F:HIS70 3.2 71.4 1.0 CG F:GLU150 4.0 84.4 1.0 ND1 F:HIS70 4.0 72.7 1.0 ND1 F:HIS74 4.1 86.2 1.0 CG F:HIS74 4.2 85.1 1.0 CG F:HIS70 4.2 72.7 1.0 OE2 F:GLU73 4.3 82.9 1.0 CB F:GLU150 4.9 84.4 1.0 CD F:GLU73 4.9 81.7 1.0

Zinc binding site 4 out of 4 in the Yeast Mitochondrial Processing Peptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Mitochondrial Processing Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn504 b:0.1 occ:1.00 NE2 H:HIS70 2.0 91.8 1.0 NE2 H:HIS74 2.0 88.2 1.0 OE1 H:GLU150 2.1 90.2 1.0 OE2 H:GLU150 2.1 89.7 1.0 O H:HOH505 2.2 81.1 1.0 CD H:GLU150 2.3 90.5 1.0 CE1 H:HIS70 2.7 90.9 1.0 CE1 H:HIS74 2.9 87.0 1.0 CD2 H:HIS74 3.2 86.9 1.0 CD2 H:HIS70 3.2 89.6 1.0 CG H:GLU150 3.8 90.6 1.0 ND1 H:HIS70 3.9 89.6 1.0 ND1 H:HIS74 4.1 86.2 1.0 CG H:HIS70 4.2 88.1 1.0 CG H:HIS74 4.2 86.1 1.0 OE2 H:GLU73 4.3 88.8 1.0 CB H:GLU150 4.7 90.8 1.0 CD1 H:LEU181 4.9 81.1 1.0 CD1 H:ILE147 5.0 88.7 1.0 CD H:GLU73 5.0 88.8 1.0

A.B.Taylor, B.S.Smith, S.Kitada, K.Kojima, H.Miyaura, Z.Otwinowski, A.Ito, J.Deisenhofer. Crystal Structures of Mitochondrial Processing Peptidase Reveal the Mode For Specific Cleavage of Import Signal Sequences. Structure V. 9 615 2001.
ISSN: ISSN 0969-2126
PubMed: 11470436
DOI: 10.1016/S0969-2126(01)00621-9