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Zinc in PDB 6az0: Mitochondrial Atpase Protease YME1

Other elements in 6az0:

The structure of Mitochondrial Atpase Protease YME1 also contains other interesting chemical elements:

Magnesium (Mg) 20 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Mitochondrial Atpase Protease YME1 (pdb code 6az0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Mitochondrial Atpase Protease YME1, PDB code: 6az0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6az0

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Zinc binding site 1 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mitochondrial Atpase Protease YME1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:64.2
occ:1.00
OD2 A:ASP618 2.1 38.2 1.0
NE2 A:HIS544 2.2 36.8 1.0
NE2 A:HIS540 2.2 39.3 1.0
OD1 A:ASP618 2.6 38.2 1.0
CG A:ASP618 2.7 38.2 1.0
CE1 A:HIS544 3.1 36.8 1.0
CD2 A:HIS544 3.1 36.8 1.0
CE1 A:HIS540 3.1 39.3 1.0
CD2 A:HIS540 3.2 39.3 1.0
ND1 A:HIS544 4.1 36.8 1.0
CG A:HIS544 4.2 36.8 1.0
CB A:ASP618 4.2 38.2 1.0
ND1 A:HIS540 4.3 39.3 1.0
CG A:HIS540 4.4 39.3 1.0

Zinc binding site 2 out of 6 in 6az0

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Zinc binding site 2 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mitochondrial Atpase Protease YME1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:89.8
occ:1.00
OD2 B:ASP618 2.0 41.6 1.0
NE2 B:HIS544 2.1 42.2 1.0
NE2 B:HIS540 2.2 48.0 1.0
OD1 B:ASP618 2.5 41.6 1.0
CG B:ASP618 2.6 41.6 1.0
CE1 B:HIS540 2.7 48.0 1.0
CE1 B:HIS544 2.9 42.2 1.0
CD2 B:HIS544 3.3 42.2 1.0
CD2 B:HIS540 3.4 48.0 1.0
ND1 B:HIS540 3.9 48.0 1.0
CB B:ASP618 4.1 41.6 1.0
ND1 B:HIS544 4.1 42.2 1.0
CG B:HIS544 4.3 42.2 1.0
CG B:HIS540 4.3 48.0 1.0
CA B:GLY598 4.7 44.7 1.0
O B:GLY614 5.0 48.5 1.0
CA B:ASP618 5.0 41.6 1.0

Zinc binding site 3 out of 6 in 6az0

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Zinc binding site 3 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mitochondrial Atpase Protease YME1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:72.0
occ:1.00
OD2 C:ASP618 2.0 40.0 1.0
NE2 C:HIS540 2.2 45.2 1.0
NE2 C:HIS544 2.2 42.7 1.0
OD1 C:ASP618 2.4 40.0 1.0
CG C:ASP618 2.5 40.0 1.0
CE1 C:HIS540 3.0 45.2 1.0
CE1 C:HIS544 3.0 42.7 1.0
CD2 C:HIS540 3.2 45.2 1.0
CD2 C:HIS544 3.2 42.7 1.0
CB C:ASP618 4.0 40.0 1.0
ND1 C:HIS544 4.2 42.7 1.0
ND1 C:HIS540 4.2 45.2 1.0
CG C:HIS540 4.2 45.2 1.0
CG C:HIS544 4.3 42.7 1.0
CA C:ASP618 4.9 40.0 1.0

Zinc binding site 4 out of 6 in 6az0

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Zinc binding site 4 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mitochondrial Atpase Protease YME1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:75.4
occ:1.00
OD2 D:ASP618 2.0 45.5 1.0
NE2 D:HIS544 2.1 48.4 1.0
NE2 D:HIS540 2.1 53.4 1.0
CE1 D:HIS540 3.0 53.4 1.0
CE1 D:HIS544 3.1 48.4 1.0
CD2 D:HIS544 3.1 48.4 1.0
CG D:ASP618 3.1 45.5 1.0
CD2 D:HIS540 3.2 53.4 1.0
CB D:ASP618 3.8 45.5 1.0
OD1 D:ASP618 4.0 45.5 1.0
ND1 D:HIS540 4.2 53.4 1.0
ND1 D:HIS544 4.2 48.4 1.0
CG D:HIS544 4.2 48.4 1.0
CG D:HIS540 4.2 53.4 1.0
CA D:GLY598 5.0 51.2 1.0

Zinc binding site 5 out of 6 in 6az0

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Zinc binding site 5 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mitochondrial Atpase Protease YME1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn802

b:45.0
occ:1.00
OD2 E:ASP618 2.0 43.6 1.0
NE2 E:HIS540 2.1 51.6 1.0
NE2 E:HIS544 2.2 47.0 1.0
OD1 E:ASP618 2.4 43.6 1.0
CG E:ASP618 2.5 43.6 1.0
CE1 E:HIS540 2.6 51.6 1.0
CE1 E:HIS544 3.0 47.0 1.0
CD2 E:HIS544 3.3 47.0 1.0
CD2 E:HIS540 3.4 51.6 1.0
ND1 E:HIS540 3.9 51.6 1.0
CB E:ASP618 4.0 43.6 1.0
ND1 E:HIS544 4.1 47.0 1.0
CG E:HIS540 4.3 51.6 1.0
CG E:HIS544 4.3 47.0 1.0
CA E:GLY598 4.9 46.9 1.0
CA E:ASP618 4.9 43.6 1.0

Zinc binding site 6 out of 6 in 6az0

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Zinc binding site 6 out of 6 in the Mitochondrial Atpase Protease YME1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mitochondrial Atpase Protease YME1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn801

b:0.8
occ:1.00
OD2 F:ASP618 1.7 56.5 1.0
NE2 F:HIS540 2.1 59.7 1.0
CG F:ASP618 2.5 56.5 1.0
NE2 F:HIS544 2.6 57.1 1.0
CE1 F:HIS540 2.7 59.7 1.0
OD1 F:ASP618 2.7 56.5 1.0
CD2 F:HIS540 3.3 59.7 1.0
CE1 F:HIS544 3.5 57.1 1.0
CD2 F:HIS544 3.5 57.1 1.0
CB F:ASP618 3.9 56.5 1.0
ND1 F:HIS540 3.9 59.7 1.0
CG F:HIS540 4.3 59.7 1.0
ND1 F:HIS544 4.6 57.1 1.0
CG F:HIS544 4.6 57.1 1.0
CA F:ASP618 5.0 56.5 1.0

Reference:

C.Puchades, A.J.Rampello, M.Shin, C.J.Giuliano, R.L.Wiseman, S.E.Glynn, G.C.Lander. Structure of the Mitochondrial Inner Membrane Aaa+ Protease YME1 Gives Insight Into Substrate Processing. Science V. 358 2017.
ISSN: ESSN 1095-9203
PubMed: 29097521
DOI: 10.1126/SCIENCE.AAO0464
Page generated: Mon Oct 28 17:45:58 2024

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