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

Enzymatic activity of Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant

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

Protein crystallography data

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

Zinc Binding Sites:

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 1hr7

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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 1hr7

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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 1hr7

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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 1hr7

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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

Reference:

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
Page generated: Wed Dec 16 02:51:43 2020

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