Zinc in PDB 1hr7: Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant

All present enzymatic activity of Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant:
3.4.24.64;

The structure of Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant, PDB code: 1hr7 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)	47.53 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	134.200, 178.620, 201.970, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 25.6

The binding sites of Zinc atom in the Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant (pdb code 1hr7). 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 Beta-E73Q Mutant, PDB code: 1hr7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant


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 Beta-E73Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:46.0 occ:1.00 NE2 B:HIS74 2.0 56.0 1.0 NE2 B:HIS70 2.1 39.2 1.0 O B:HOH502 2.1 36.9 1.0 OE1 B:GLU150 2.2 63.8 1.0 OE2 B:GLU150 2.2 70.4 1.0 CD B:GLU150 2.5 68.0 1.0 CE1 B:HIS70 2.9 38.8 1.0 CE1 B:HIS74 2.9 53.4 1.0 CD2 B:HIS74 3.1 58.0 1.0 CD2 B:HIS70 3.2 39.8 1.0 CG B:GLU150 4.0 67.9 1.0 ND1 B:HIS74 4.1 55.5 1.0 ND1 B:HIS70 4.1 39.0 1.0 CG B:HIS74 4.2 55.9 1.0 CG B:HIS70 4.3 39.6 1.0 CD1 B:ILE147 4.7 65.6 1.0 CB B:GLU150 5.0 66.2 1.0

Zinc binding site 2 out of 4 in the Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant


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 Beta-E73Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:65.0 occ:1.00 NE2 D:HIS74 2.0 65.0 1.0 NE2 D:HIS70 2.0 66.2 1.0 O D:HOH503 2.2 47.3 1.0 OE2 D:GLU150 2.3 83.6 1.0 OE1 D:GLU150 2.3 84.4 1.0 CD D:GLU150 2.6 82.7 1.0 CE1 D:HIS70 2.9 65.2 1.0 CE1 D:HIS74 2.9 65.5 1.0 CD2 D:HIS74 3.1 66.6 1.0 CD2 D:HIS70 3.2 63.3 1.0 CG D:GLU150 4.0 79.4 1.0 ND1 D:HIS70 4.0 62.5 1.0 ND1 D:HIS74 4.1 67.0 1.0 CG D:HIS74 4.2 67.8 1.0 CG D:HIS70 4.2 62.1 1.0 CD1 D:ILE147 4.7 75.8 1.0 NE2 D:GLN73 4.9 70.7 1.0 CB D:GLU150 5.0 76.3 1.0

Zinc binding site 3 out of 4 in the Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant


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 Beta-E73Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn503 b:73.6 occ:1.00 NE2 F:HIS70 2.0 64.2 1.0 NE2 F:HIS74 2.0 81.0 1.0 O F:HOH504 2.1 65.5 1.0 OE2 F:GLU150 2.2 77.7 1.0 OE1 F:GLU150 2.2 76.6 1.0 CD F:GLU150 2.5 78.0 1.0 CE1 F:HIS70 2.8 65.4 1.0 CE1 F:HIS74 2.9 79.6 1.0 CD2 F:HIS74 3.1 79.0 1.0 CD2 F:HIS70 3.1 64.2 1.0 CG F:GLU150 4.0 78.6 1.0 ND1 F:HIS70 4.0 66.6 1.0 ND1 F:HIS74 4.1 79.4 1.0 CG F:HIS70 4.2 66.9 1.0 CG F:HIS74 4.2 79.2 1.0 CD1 F:ILE147 4.7 79.5 1.0 CB F:GLU150 5.0 79.3 1.0

Zinc binding site 4 out of 4 in the Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant


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 Beta-E73Q Mutant within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn504 b:0.8 occ:1.00 NE2 H:HIS70 2.0 81.3 1.0 NE2 H:HIS74 2.1 79.4 1.0 OE2 H:GLU150 2.2 82.4 1.0 OE1 H:GLU150 2.3 82.7 1.0 O H:HOH4 2.3 63.2 1.0 CD H:GLU150 2.5 83.9 1.0 CE1 H:HIS70 2.8 82.1 1.0 CE1 H:HIS74 3.0 79.2 1.0 CD2 H:HIS70 3.2 80.3 1.0 CD2 H:HIS74 3.2 79.5 1.0 CG H:GLU150 4.0 83.7 1.0 ND1 H:HIS70 4.0 81.3 1.0 ND1 H:HIS74 4.1 78.2 1.0 CG H:HIS70 4.2 80.4 1.0 CG H:HIS74 4.3 79.7 1.0 CD1 H:ILE147 4.7 81.8 1.0 NE2 H:GLN73 4.8 80.2 1.0 CB H:GLU150 4.9 83.4 1.0 CD1 H:LEU181 5.0 81.1 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