Zinc in PDB 9lky: Dimer of CRL2-FEM1B Bound with PLD6

The binding sites of Zinc atom in the Dimer of CRL2-FEM1B Bound with PLD6 (pdb code 9lky). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Dimer of CRL2-FEM1B Bound with PLD6, PDB code: 9lky:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Dimer of CRL2-FEM1B Bound with PLD6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dimer of CRL2-FEM1B Bound with PLD6 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn200 b:131.2 occ:1.00 ND1 E:HIS82 2.0 101.3 1.0 SG E:CYS53 2.3 115.2 1.0 SG E:CYS56 2.3 124.6 1.0 SG E:CYS68 2.3 108.8 1.0 CE1 E:HIS82 2.6 101.3 1.0 CB E:CYS56 2.7 124.6 1.0 CG E:HIS82 3.0 101.3 1.0 OE1 E:GLU55 3.5 121.6 1.0 CB E:CYS53 3.6 115.2 1.0 NE2 E:HIS82 3.6 101.3 1.0 CB E:HIS82 3.7 101.3 1.0 N E:CYS56 3.8 124.6 1.0 CA E:CYS56 3.8 124.6 1.0 CD2 E:HIS82 3.9 101.3 1.0 CB E:CYS68 4.1 108.8 1.0 N E:CYS53 4.1 115.2 1.0 CA E:CYS53 4.4 115.2 1.0 CD E:GLU55 4.7 121.6 1.0 CA E:CYS68 4.7 108.8 1.0 O E:CYS53 4.7 115.2 1.0 C E:GLU55 4.8 121.6 1.0 C E:CYS53 4.8 115.2 1.0 C E:CYS56 5.0 124.6 1.0

Zinc binding site 2 out of 6 in the Dimer of CRL2-FEM1B Bound with PLD6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dimer of CRL2-FEM1B Bound with PLD6 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:113.5 occ:1.00 ND1 E:HIS80 2.0 85.9 1.0 SG E:CYS83 2.3 94.1 1.0 SG E:CYS45 2.3 89.0 1.0 SG E:CYS42 2.3 84.4 1.0 CE1 E:HIS80 2.7 85.9 1.0 CB E:CYS45 2.9 89.0 1.0 CG E:HIS80 3.1 85.9 1.0 CB E:CYS42 3.4 84.4 1.0 N E:CYS45 3.5 89.0 1.0 CB E:CYS83 3.7 94.1 1.0 CB E:HIS80 3.7 85.9 1.0 NE2 E:HIS80 3.8 85.9 1.0 CA E:CYS45 3.8 89.0 1.0 CB E:CYS53 3.9 115.2 1.0 CD2 E:HIS80 4.0 85.9 1.0 CA E:CYS53 4.2 115.2 1.0 N E:HIS80 4.4 85.9 1.0 OD1 E:ASN47 4.5 91.2 1.0 CB E:ILE44 4.6 76.7 1.0 C E:ILE44 4.6 76.7 1.0 N E:ILE54 4.7 114.5 1.0 CA E:HIS80 4.7 85.9 1.0 CA E:CYS42 4.8 84.4 1.0 CA E:CYS83 5.0 94.1 1.0

Zinc binding site 3 out of 6 in the Dimer of CRL2-FEM1B Bound with PLD6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dimer of CRL2-FEM1B Bound with PLD6 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn202 b:95.4 occ:1.00 OD1 E:ASP97 2.0 64.4 1.0 SG E:CYS75 2.3 76.8 1.0 SG E:CYS94 2.3 69.6 1.0 ND1 E:HIS77 2.3 67.9 1.0 CG E:ASP97 3.0 64.4 1.0 CG E:HIS77 3.2 67.9 1.0 CE1 E:HIS77 3.3 67.9 1.0 CB E:HIS77 3.4 67.9 1.0 CB E:CYS94 3.4 69.6 1.0 OD2 E:ASP97 3.4 64.4 1.0 CB E:CYS75 3.8 76.8 1.0 CZ3 E:TRP101 4.0 74.6 1.0 N E:ASP97 4.1 64.4 1.0 CB E:LEU96 4.2 64.7 1.0 CB E:ASP97 4.4 64.4 1.0 CD2 E:HIS77 4.4 67.9 1.0 NE2 E:HIS77 4.4 67.9 1.0 CE3 E:TRP101 4.4 74.6 1.0 O E:ASP97 4.5 64.4 1.0 CA E:ASP97 4.7 64.4 1.0 CE2 E:PHE79 4.8 77.9 1.0 CA E:HIS77 4.8 67.9 1.0 CZ E:PHE79 4.8 77.9 1.0 CA E:CYS94 4.8 69.6 1.0 N E:LEU96 4.8 64.7 1.0 CA E:LEU96 4.9 64.7 1.0 C E:LEU96 4.9 64.7 1.0

Zinc binding site 4 out of 6 in the Dimer of CRL2-FEM1B Bound with PLD6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dimer of CRL2-FEM1B Bound with PLD6 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn200 b:179.2 occ:1.00 CE1 I:HIS82 1.5 131.3 1.0 ND1 I:HIS82 2.1 131.3 1.0 SG I:CYS56 2.3 160.3 1.0 SG I:CYS53 2.3 140.2 1.0 SG I:CYS68 2.3 150.8 1.0 NE2 I:HIS82 2.7 131.3 1.0 CB I:CYS56 3.2 160.3 1.0 CG I:HIS82 3.4 131.3 1.0 CD2 I:HIS82 3.6 131.3 1.0 CB I:CYS68 3.6 150.8 1.0 CA I:CYS68 3.8 150.8 1.0 CB I:CYS53 4.0 140.2 1.0 N I:CYS56 4.2 160.3 1.0 N I:CYS68 4.2 150.8 1.0 CA I:CYS56 4.3 160.3 1.0 O I:THR64 4.3 206.0 1.0 N I:CYS53 4.4 140.2 1.0 CB I:HIS82 4.6 131.3 1.0 CA I:CYS53 4.7 140.2 1.0 CB I:GLU55 5.0 155.6 1.0

Zinc binding site 5 out of 6 in the Dimer of CRL2-FEM1B Bound with PLD6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Dimer of CRL2-FEM1B Bound with PLD6 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:99.1 occ:1.00 ND1 I:HIS80 2.0 121.1 1.0 SG I:CYS45 2.3 125.9 1.0 SG I:CYS83 2.3 124.9 1.0 SG I:CYS42 2.3 124.2 1.0 CE1 I:HIS80 2.7 121.1 1.0 CG I:HIS80 3.2 121.1 1.0 CB I:CYS42 3.4 124.2 1.0 CB I:CYS83 3.5 124.9 1.0 CB I:CYS45 3.6 125.9 1.0 CB I:HIS80 3.7 121.1 1.0 N I:CYS45 3.8 125.9 1.0 NE2 I:HIS80 3.9 121.1 1.0 CD2 I:HIS80 4.1 121.1 1.0 N I:HIS80 4.3 121.1 1.0 CA I:CYS45 4.3 125.9 1.0 CB I:ILE44 4.4 121.7 1.0 O I:CYS42 4.4 124.2 1.0 CB I:CYS53 4.6 140.2 1.0 CA I:CYS42 4.7 124.2 1.0 CA I:HIS80 4.7 121.1 1.0 C I:CYS42 4.8 124.2 1.0 C I:ILE44 4.8 121.7 1.0 CA I:CYS83 4.8 124.9 1.0 N I:ILE44 4.9 121.7 1.0 CG2 I:ILE44 4.9 121.7 1.0 CA I:ILE44 5.0 121.7 1.0

Zinc binding site 6 out of 6 in the Dimer of CRL2-FEM1B Bound with PLD6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Dimer of CRL2-FEM1B Bound with PLD6 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:140.2 occ:1.00 CD2 I:HIS77 2.2 124.4 1.0 CG I:HIS77 2.2 124.4 1.0 NE2 I:HIS77 2.3 124.4 1.0 ND1 I:HIS77 2.3 124.4 1.0 SG I:CYS94 2.3 128.1 1.0 SG I:CYS75 2.3 130.8 1.0 CE1 I:HIS77 2.4 124.4 1.0 CB I:CYS94 2.7 128.1 1.0 OD1 I:ASP97 3.2 129.2 1.0 CB I:HIS77 3.2 124.4 1.0 CB I:CYS75 3.8 130.8 1.0 CA I:CYS94 4.0 128.1 1.0 CG I:ASP97 4.2 129.2 1.0 CA I:HIS77 4.6 124.4 1.0 OD2 I:ASP97 4.6 129.2 1.0 O I:CYS75 4.6 130.8 1.0 CZ3 I:TRP101 4.7 120.9 1.0 C I:CYS94 4.7 128.1 1.0 CD I:PRO95 4.7 123.4 1.0 CE3 I:TRP101 4.8 120.9 1.0 CB I:ARG99 4.9 127.4 1.0 N I:PRO95 4.9 123.4 1.0 CA I:CYS75 4.9 130.8 1.0 N I:HIS77 5.0 124.4 1.0 N I:ASP97 5.0 129.2 1.0 C I:CYS75 5.0 130.8 1.0

C.Xu, S.Zhao. TOM20-Driven E3 Ligase Recruitment Regulates Mitochondrial Dynamics Through PLD6 Nat.Chem.Biol. 2025.
ISSN: ESSN 1552-4469