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Zinc in PDB 1hr8: Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant Complexed with Cytochrome C Oxidase IV Signal Peptide

Enzymatic activity of Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant Complexed with Cytochrome C Oxidase IV Signal Peptide

All present enzymatic activity of Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant Complexed with Cytochrome C Oxidase IV Signal Peptide:
1.9.3.1; 3.4.24.64;

Protein crystallography data

The structure of Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant Complexed with Cytochrome C Oxidase IV Signal Peptide, PDB code: 1hr8 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) 48.63 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 134.260, 178.120, 202.210, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 26.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant Complexed with Cytochrome C Oxidase IV Signal Peptide (pdb code 1hr8). 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 Complexed with Cytochrome C Oxidase IV Signal Peptide, PDB code: 1hr8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1hr8

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Zinc binding site 1 out of 4 in the Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant Complexed with Cytochrome C Oxidase IV Signal Peptide


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 Complexed with Cytochrome C Oxidase IV Signal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:72.8
occ:1.00
O O:HOH1 2.0 47.9 1.0
NE2 B:HIS74 2.0 59.2 1.0
NE2 B:HIS70 2.0 40.7 1.0
OE1 B:GLU150 2.2 84.2 1.0
OE2 B:GLU150 2.2 84.2 1.0
CD B:GLU150 2.5 84.2 1.0
CE1 B:HIS70 2.7 40.7 1.0
CE1 B:HIS74 2.9 59.2 1.0
CD2 B:HIS74 3.0 59.2 1.0
CD2 B:HIS70 3.2 40.7 1.0
ND1 B:HIS70 3.9 40.7 1.0
CG B:GLU150 4.0 84.2 1.0
ND1 B:HIS74 4.1 59.2 1.0
CG B:HIS74 4.1 59.2 1.0
CG B:HIS70 4.2 40.7 1.0
NE2 B:GLN73 4.5 61.9 1.0
O O:THR17 4.6 94.0 1.0
CD1 B:ILE147 4.7 42.6 1.0
CB O:ARG16 4.7 74.5 1.0
CB B:GLU150 4.7 84.2 1.0
CD1 B:LEU181 4.7 43.7 1.0

Zinc binding site 2 out of 4 in 1hr8

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Zinc binding site 2 out of 4 in the Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant Complexed with Cytochrome C Oxidase IV Signal Peptide


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 Complexed with Cytochrome C Oxidase IV Signal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:91.1
occ:1.00
NE2 D:HIS74 2.0 77.5 1.0
NE2 D:HIS70 2.0 59.5 1.0
O P:HOH26 2.1 75.6 1.0
OE1 D:GLU150 2.1 0.4 1.0
OE2 D:GLU150 2.2 0.4 1.0
CD D:GLU150 2.5 0.4 1.0
CE1 D:HIS70 2.7 59.5 1.0
CE1 D:HIS74 2.9 77.5 1.0
CD2 D:HIS74 3.0 77.5 1.0
CD2 D:HIS70 3.2 59.5 1.0
ND1 D:HIS70 3.9 59.5 1.0
CG D:GLU150 4.0 0.4 1.0
ND1 D:HIS74 4.1 77.5 1.0
CG D:HIS74 4.1 77.5 1.0
CG D:HIS70 4.2 59.5 1.0
NE2 D:GLN73 4.5 68.1 1.0
CB P:ARG16 4.6 83.7 1.0
O P:THR17 4.6 90.3 1.0
CB D:GLU150 4.7 0.4 1.0
CD1 D:LEU181 4.8 55.5 1.0
CD1 D:ILE147 4.8 57.7 1.0

Zinc binding site 3 out of 4 in 1hr8

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Zinc binding site 3 out of 4 in the Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant Complexed with Cytochrome C Oxidase IV Signal Peptide


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 Complexed with Cytochrome C Oxidase IV Signal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn503

b:0.4
occ:1.00
NE2 F:HIS70 2.0 77.0 1.0
NE2 F:HIS74 2.0 0.4 1.0
O F:HOH3 2.0 57.1 1.0
OE1 F:GLU150 2.2 0.4 1.0
OE2 F:GLU150 2.2 0.4 1.0
CD F:GLU150 2.4 0.4 1.0
CE1 F:HIS70 2.7 77.0 1.0
CE1 F:HIS74 3.0 0.4 1.0
CD2 F:HIS74 3.0 0.4 1.0
CD2 F:HIS70 3.2 77.0 1.0
ND1 F:HIS70 3.9 77.0 1.0
CG F:GLU150 4.0 0.4 1.0
ND1 F:HIS74 4.1 0.4 1.0
CG F:HIS74 4.2 0.4 1.0
CG F:HIS70 4.2 77.0 1.0
NE2 F:GLN73 4.5 90.5 1.0
CB Q:ARG16 4.6 0.4 1.0
CD1 F:ILE147 4.7 68.0 1.0
CD1 F:LEU181 4.7 85.5 1.0
CB F:GLU150 4.7 0.4 1.0
O Q:THR17 4.8 0.4 1.0

Zinc binding site 4 out of 4 in 1hr8

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Zinc binding site 4 out of 4 in the Yeast Mitochondrial Processing Peptidase Beta-E73Q Mutant Complexed with Cytochrome C Oxidase IV Signal Peptide


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 Complexed with Cytochrome C Oxidase IV Signal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn504

b:0.4
occ:1.00
NE2 H:HIS70 2.0 0.4 1.0
NE2 H:HIS74 2.0 0.2 1.0
O H:HOH4 2.1 71.6 1.0
OE2 H:GLU150 2.2 0.4 1.0
OE1 H:GLU150 2.3 0.4 1.0
CD H:GLU150 2.6 0.4 1.0
CE1 H:HIS70 2.8 0.4 1.0
CE1 H:HIS74 3.0 0.2 1.0
CD2 H:HIS74 3.1 0.2 1.0
CD2 H:HIS70 3.2 0.4 1.0
ND1 H:HIS70 4.0 0.4 1.0
CG H:GLU150 4.1 0.4 1.0
ND1 H:HIS74 4.1 0.2 1.0
CG H:HIS70 4.2 0.4 1.0
CG H:HIS74 4.2 0.2 1.0
O R:THR17 4.2 0.4 1.0
NE2 H:GLN73 4.3 0.3 1.0
CB R:ARG16 4.6 0.1 1.0
CD1 H:LEU181 4.7 87.6 1.0
C R:THR17 4.8 0.4 1.0
CB H:GLU150 4.9 0.4 1.0
CD1 H:ILE147 4.9 98.5 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: Sun Oct 13 02:28:35 2024

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