Zinc in PDB 8uy3: FEM1B with FNIP1 and TOM20 Fragment

The structure of FEM1B with FNIP1 and TOM20 Fragment, PDB code: 8uy3 was solved by C.L.Gee, A.G.Manford, R.Mcminimy, M.Rape, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.93 / 3.20
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	183.715, 183.715, 183.715, 90, 90, 90
R / Rfree (%)	23.9 / 26.4

The binding sites of Zinc atom in the FEM1B with FNIP1 and TOM20 Fragment (pdb code 8uy3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the FEM1B with FNIP1 and TOM20 Fragment, PDB code: 8uy3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the FEM1B with FNIP1 and TOM20 Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of FEM1B with FNIP1 and TOM20 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:68.7 occ:1.00 NE2 A:HIS218 2.1 73.0 1.0 SG E:CYS25 2.3 81.9 1.0 SG A:CYS186 2.3 49.3 1.0 SG E:CYS22 2.3 63.0 1.0 CE1 A:HIS218 3.0 75.5 1.0 CD2 A:HIS218 3.1 75.6 1.0 CB E:CYS22 3.2 67.9 1.0 CB A:CYS186 3.2 66.1 1.0 CB E:CYS25 3.6 77.3 1.0 N E:CYS25 3.7 78.7 1.0 CA E:CYS25 3.9 78.4 1.0 ZN E:ZN601 4.0 62.4 1.0 ND1 A:HIS218 4.1 79.1 1.0 CG A:HIS218 4.2 73.7 1.0 C E:TYR24 4.3 79.0 1.0 CA E:CYS22 4.6 74.2 1.0 NE2 A:HIS185 4.7 74.8 1.0 CA A:CYS186 4.7 70.5 1.0 CB E:TYR24 4.8 74.9 1.0 O E:TYR24 4.9 82.7 1.0 CA E:TYR24 4.9 75.9 1.0 CB A:ALA188 5.0 65.1 1.0 N E:TYR24 5.0 76.4 1.0 SG E:CYS20 5.0 70.5 1.0

Zinc binding site 2 out of 8 in the FEM1B with FNIP1 and TOM20 Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of FEM1B with FNIP1 and TOM20 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:62.0 occ:1.00 NE2 C:HIS218 2.1 68.5 1.0 SG F:CYS25 2.3 76.8 1.0 SG C:CYS186 2.3 55.1 1.0 SG F:CYS22 2.3 70.1 1.0 CD2 C:HIS218 3.1 76.1 1.0 CE1 C:HIS218 3.1 69.3 1.0 CB C:CYS186 3.1 68.2 1.0 CB F:CYS22 3.1 71.1 1.0 CB F:CYS25 3.7 75.3 1.0 N F:CYS25 3.7 70.0 1.0 CA F:CYS25 4.0 74.1 1.0 ZN F:ZN601 4.1 68.1 1.0 ND1 C:HIS218 4.2 71.4 1.0 CG C:HIS218 4.2 77.4 1.0 C F:TYR24 4.4 68.6 1.0 CA F:CYS22 4.6 75.2 1.0 CA C:CYS186 4.6 69.2 1.0 NE2 C:HIS185 4.7 69.4 1.0 CB F:TYR24 4.7 72.1 1.0 CA F:TYR24 4.9 72.1 1.0 N F:TYR24 5.0 72.5 1.0 C F:CYS22 5.0 71.2 1.0

Zinc binding site 3 out of 8 in the FEM1B with FNIP1 and TOM20 Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of FEM1B with FNIP1 and TOM20 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:94.2 occ:1.00 NE2 B:HIS218 2.1 104.8 1.0 SG H:CYS25 2.3 91.3 1.0 SG B:CYS186 2.3 90.3 1.0 SG H:CYS22 2.3 108.3 1.0 CD2 B:HIS218 3.0 102.9 1.0 CB H:CYS22 3.0 102.3 1.0 CE1 B:HIS218 3.1 101.6 1.0 CB B:CYS186 3.1 92.6 1.0 CB H:CYS25 3.9 102.2 1.0 ZN H:ZN601 3.9 94.8 1.0 CG B:HIS218 4.2 99.8 1.0 ND1 B:HIS218 4.2 100.4 1.0 N H:CYS25 4.2 104.8 1.0 C H:TYR24 4.4 105.2 1.0 CA H:CYS25 4.4 103.6 1.0 CA H:CYS22 4.5 101.3 1.0 O H:TYR24 4.5 112.8 1.0 CA B:CYS186 4.6 95.5 1.0 CB H:TYR24 4.8 99.3 1.0 NE2 B:HIS185 4.9 97.3 1.0 SG H:CYS20 4.9 90.5 1.0 CB B:ALA188 4.9 88.8 1.0 CA H:TYR24 4.9 100.8 1.0 C H:CYS22 5.0 100.8 1.0

Zinc binding site 4 out of 8 in the FEM1B with FNIP1 and TOM20 Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of FEM1B with FNIP1 and TOM20 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:119.3 occ:1.00 NE2 D:HIS218 2.1 110.4 1.0 SG I:CYS25 2.3 114.7 1.0 SG I:CYS22 2.3 108.7 1.0 SG D:CYS186 2.3 123.2 1.0 CD2 D:HIS218 2.9 107.7 1.0 CB I:CYS22 3.0 115.0 1.0 CE1 D:HIS218 3.2 108.7 1.0 CB D:CYS186 3.4 114.3 1.0 CB I:CYS25 3.7 118.5 1.0 ZN I:ZN601 3.9 119.2 1.0 CG D:HIS218 4.1 104.7 1.0 ND1 D:HIS218 4.2 107.9 1.0 N I:CYS25 4.3 112.3 1.0 CA I:CYS25 4.3 115.7 1.0 C I:TYR24 4.4 111.1 1.0 CA I:CYS22 4.5 116.8 1.0 O I:TYR24 4.5 111.9 1.0 CB D:ALA188 4.7 110.6 1.0 CA D:CYS186 4.8 111.8 1.0 SG I:CYS20 4.9 122.7 1.0 C I:CYS22 5.0 113.9 1.0 NE2 D:HIS185 5.0 121.0 1.0

Zinc binding site 5 out of 8 in the FEM1B with FNIP1 and TOM20 Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of FEM1B with FNIP1 and TOM20 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn601 b:62.4 occ:1.00 NE2 A:HIS185 2.0 74.8 1.0 NE2 E:HIS27 2.1 84.9 1.0 SG E:CYS20 2.3 70.5 1.0 SG E:CYS25 2.3 81.9 1.0 CE1 E:HIS27 3.0 82.9 1.0 CD2 A:HIS185 3.0 73.3 1.0 CE1 A:HIS185 3.1 74.5 1.0 CD2 E:HIS27 3.1 83.0 1.0 CB E:CYS25 3.2 77.3 1.0 CB E:CYS20 3.4 73.7 1.0 ZN A:ZN401 4.0 68.7 1.0 ND1 E:HIS27 4.1 83.3 1.0 CG A:HIS185 4.1 70.0 1.0 ND1 A:HIS185 4.2 71.0 1.0 CG E:HIS27 4.2 85.4 1.0 CB E:CYS22 4.4 67.9 1.0 SG A:CYS186 4.6 49.3 1.0 CB A:TYR153 4.6 65.8 1.0 CA E:CYS25 4.7 78.4 1.0 CG A:TYR153 4.7 68.5 1.0 CD1 A:TYR153 4.8 69.1 1.0 CA E:CYS20 4.8 75.1 1.0 CB A:CYS186 5.0 66.1 1.0

Zinc binding site 6 out of 8 in the FEM1B with FNIP1 and TOM20 Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of FEM1B with FNIP1 and TOM20 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn601 b:68.1 occ:1.00 NE2 C:HIS185 2.0 69.4 1.0 NE2 F:HIS27 2.0 81.2 1.0 SG F:CYS20 2.3 77.5 1.0 SG F:CYS25 2.3 76.8 1.0 CD2 C:HIS185 3.0 69.8 1.0 CE1 F:HIS27 3.0 82.2 1.0 CD2 F:HIS27 3.0 82.2 1.0 CE1 C:HIS185 3.0 71.9 1.0 CB F:CYS25 3.2 75.3 1.0 CB F:CYS20 3.5 83.2 1.0 ZN C:ZN401 4.1 62.0 1.0 ND1 F:HIS27 4.1 83.2 1.0 CG C:HIS185 4.1 69.9 1.0 ND1 C:HIS185 4.1 74.0 1.0 CG F:HIS27 4.2 87.2 1.0 CB F:CYS22 4.4 71.1 1.0 SG C:CYS186 4.6 55.1 1.0 CB C:TYR153 4.6 75.5 1.0 CA F:CYS25 4.7 74.1 1.0 CG C:TYR153 4.7 76.6 1.0 CD1 C:TYR153 4.8 80.9 1.0 CA F:CYS20 4.9 78.7 1.0 CB C:CYS186 4.9 68.2 1.0

Zinc binding site 7 out of 8 in the FEM1B with FNIP1 and TOM20 Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of FEM1B with FNIP1 and TOM20 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn601 b:94.8 occ:1.00 NE2 H:HIS27 2.0 98.1 1.0 NE2 B:HIS185 2.0 97.3 1.0 SG H:CYS20 2.3 90.5 1.0 SG H:CYS25 2.3 91.3 1.0 CE1 B:HIS185 2.7 97.5 1.0 CD2 H:HIS27 2.9 98.6 1.0 CB H:CYS25 2.9 102.2 1.0 CE1 H:HIS27 3.1 98.8 1.0 CD2 B:HIS185 3.2 94.6 1.0 CB H:CYS20 3.5 102.4 1.0 ZN B:ZN401 3.9 94.2 1.0 ND1 B:HIS185 4.0 95.7 1.0 CG H:HIS27 4.1 100.8 1.0 ND1 H:HIS27 4.1 100.4 1.0 CG B:HIS185 4.2 91.7 1.0 SG B:CYS186 4.3 90.3 1.0 CB H:CYS22 4.4 102.3 1.0 CA H:CYS25 4.4 103.6 1.0 CB B:CYS186 4.6 92.6 1.0 CA H:CYS20 4.9 103.6 1.0

Zinc binding site 8 out of 8 in the FEM1B with FNIP1 and TOM20 Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of FEM1B with FNIP1 and TOM20 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn601 b:119.2 occ:1.00 NE2 D:HIS185 2.0 121.0 1.0 NE2 I:HIS27 2.0 117.4 1.0 SG I:CYS20 2.3 122.7 1.0 SG I:CYS25 2.3 114.7 1.0 CD2 I:HIS27 3.0 118.2 1.0 CE1 D:HIS185 3.0 120.8 1.0 CD2 D:HIS185 3.0 119.9 1.0 CE1 I:HIS27 3.1 118.6 1.0 CB I:CYS25 3.2 118.5 1.0 CB I:CYS20 3.4 123.6 1.0 ZN D:ZN401 3.9 119.3 1.0 ND1 D:HIS185 4.1 120.9 1.0 CG I:HIS27 4.1 117.7 1.0 ND1 I:HIS27 4.1 119.2 1.0 CG D:HIS185 4.1 117.5 1.0 SG D:CYS186 4.2 123.2 1.0 CB I:CYS22 4.4 115.0 1.0 CB D:CYS186 4.4 114.3 1.0 CA I:CYS25 4.6 115.7 1.0 CA I:CYS20 4.8 124.4 1.0 O I:CYS20 4.9 126.5 1.0

R.Mcminimy, A.G.Manford, C.L.Gee, S.Chandrasekhar, G.A.Mousa, J.Chuang, L.Phu, K.Y.Shih, C.M.Rose, J.Kuriyan, B.Bingol, M.Rape. Reactive Oxygen Species Control Protein Degradation at the Mitochondrial Import Gate. Mol.Cell V. 84 4612 2024.
ISSN: ISSN 1097-2765
PubMed: 39642856
DOI: 10.1016/J.MOLCEL.2024.11.004