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Zinc in PDB 9j77: Cryo-Em Structure of CRL2-FEM1B (Dimer 1)

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of CRL2-FEM1B (Dimer 1) (pdb code 9j77). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of CRL2-FEM1B (Dimer 1), PDB code: 9j77:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9j77

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of CRL2-FEM1B (Dimer 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of CRL2-FEM1B (Dimer 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn200

b:140.6
occ:1.00
CB I:CYS56 2.0 99.2 1.0
ND1 I:HIS82 2.1 90.8 1.0
CE1 I:HIS82 2.2 90.8 1.0
SG I:CYS68 2.3 86.9 1.0
SG I:CYS53 2.3 90.3 1.0
SG I:CYS56 2.3 99.2 1.0
CB I:CYS68 3.1 86.9 1.0
CA I:CYS56 3.3 99.2 1.0
CG I:HIS82 3.3 90.8 1.0
NE2 I:HIS82 3.4 90.8 1.0
N I:CYS68 3.6 86.9 1.0
N I:CYS56 3.8 99.2 1.0
CD2 I:HIS82 3.9 90.8 1.0
CA I:CYS68 4.0 86.9 1.0
CB I:CYS53 4.1 90.3 1.0
CB I:HIS82 4.3 90.8 1.0
C I:CYS56 4.5 99.2 1.0
N I:CYS53 4.5 90.3 1.0
C I:GLU55 4.7 104.6 1.0
CA I:CYS53 4.8 90.3 1.0
O I:CYS56 5.0 99.2 1.0
C I:CYS68 5.0 86.9 1.0

Zinc binding site 2 out of 6 in 9j77

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of CRL2-FEM1B (Dimer 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of CRL2-FEM1B (Dimer 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:97.9
occ:1.00
ND1 I:HIS80 2.1 80.6 1.0
SG I:CYS83 2.3 91.3 1.0
SG I:CYS45 2.3 90.0 1.0
SG I:CYS42 2.3 80.5 1.0
CE1 I:HIS80 3.1 80.6 1.0
CG I:HIS80 3.1 80.6 1.0
CB I:CYS42 3.2 80.5 1.0
CB I:HIS80 3.4 80.6 1.0
CB I:CYS83 3.5 91.3 1.0
CB I:CYS45 3.7 90.0 1.0
N I:CYS45 4.0 90.0 1.0
CB I:CYS53 4.0 90.3 1.0
N I:HIS80 4.1 80.6 1.0
NE2 I:HIS80 4.2 80.6 1.0
CD2 I:HIS80 4.2 80.6 1.0
CB I:ILE44 4.4 85.4 1.0
CA I:HIS80 4.4 80.6 1.0
CA I:CYS45 4.5 90.0 1.0
CA I:CYS42 4.6 80.5 1.0
CA I:CYS53 4.8 90.3 1.0
O I:CYS42 4.8 80.5 1.0
CA I:CYS83 4.8 91.3 1.0
C I:CYS42 4.9 80.5 1.0
C I:ILE44 4.9 85.4 1.0
CG2 I:ILE44 5.0 85.4 1.0
N I:ILE44 5.0 85.4 1.0

Zinc binding site 3 out of 6 in 9j77

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of CRL2-FEM1B (Dimer 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of CRL2-FEM1B (Dimer 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:151.4
occ:1.00
SG I:CYS75 2.3 117.1 1.0
SG I:CYS94 2.3 119.0 1.0
ND1 I:HIS77 2.3 111.6 1.0
CG I:HIS77 2.6 111.6 1.0
CB I:HIS77 2.8 111.6 1.0
CB I:CYS94 3.0 119.0 1.0
CE1 I:HIS77 3.3 111.6 1.0
CD2 I:HIS77 3.6 111.6 1.0
CZ3 I:TRP101 3.7 116.1 1.0
CE3 I:TRP101 3.8 116.1 1.0
NE2 I:HIS77 3.9 111.6 1.0
CB I:CYS75 4.1 117.1 1.0
CA I:CYS94 4.2 119.0 1.0
OD1 I:ASP97 4.2 118.0 1.0
CA I:HIS77 4.2 111.6 1.0
CD I:PRO95 4.4 106.7 1.0
N I:HIS77 4.5 111.6 1.0
CE2 I:PHE79 4.8 84.3 1.0
O I:CYS75 4.9 117.1 1.0
O I:HIS77 4.9 111.6 1.0
C I:CYS94 4.9 119.0 1.0
CA I:CYS75 4.9 117.1 1.0
N I:PRO95 4.9 106.7 1.0
N I:CYS75 5.0 117.1 1.0
C I:HIS77 5.0 111.6 1.0
C I:CYS75 5.0 117.1 1.0

Zinc binding site 4 out of 6 in 9j77

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of CRL2-FEM1B (Dimer 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of CRL2-FEM1B (Dimer 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn200

b:111.3
occ:1.00
CD2 E:HIS82 1.8 74.9 1.0
NE2 E:HIS82 2.1 74.9 1.0
SG E:CYS56 2.3 99.6 1.0
SG E:CYS53 2.3 85.2 1.0
SG E:CYS68 2.3 89.6 1.0
CB E:CYS56 2.7 99.6 1.0
CG E:HIS82 2.9 74.9 1.0
CE1 E:HIS82 3.1 74.9 1.0
CB E:CYS53 3.4 85.2 1.0
ND1 E:HIS82 3.5 74.9 1.0
N E:CYS56 3.8 99.6 1.0
CA E:CYS56 3.8 99.6 1.0
CB E:HIS82 3.9 74.9 1.0
N E:CYS53 3.9 85.2 1.0
CB E:CYS68 4.0 89.6 1.0
CA E:CYS53 4.2 85.2 1.0
CA E:CYS68 4.5 89.6 1.0
OE1 E:GLU55 4.7 98.2 1.0
CG E:GLU67 4.8 106.0 1.0
C E:CYS53 4.8 85.2 1.0
O E:CYS53 4.8 85.2 1.0
C E:GLU55 4.8 98.2 1.0
N E:CYS68 4.9 89.6 1.0

Zinc binding site 5 out of 6 in 9j77

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of CRL2-FEM1B (Dimer 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of CRL2-FEM1B (Dimer 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:81.3
occ:1.00
ND1 E:HIS80 2.1 65.2 1.0
SG E:CYS45 2.3 66.0 1.0
SG E:CYS83 2.3 64.2 1.0
SG E:CYS42 2.3 60.9 1.0
CG E:HIS80 3.0 65.2 1.0
CB E:CYS45 3.1 66.0 1.0
CE1 E:HIS80 3.1 65.2 1.0
CB E:HIS80 3.2 65.2 1.0
CB E:CYS42 3.4 60.9 1.0
CB E:CYS83 3.6 64.2 1.0
N E:CYS45 3.7 66.0 1.0
CA E:CYS45 3.9 66.0 1.0
CB E:CYS53 4.0 85.2 1.0
CD2 E:HIS80 4.2 65.2 1.0
NE2 E:HIS80 4.2 65.2 1.0
CA E:CYS53 4.2 85.2 1.0
N E:HIS80 4.4 65.2 1.0
CA E:HIS80 4.4 65.2 1.0
N E:ILE54 4.6 91.2 1.0
C E:ILE44 4.8 56.0 1.0
CA E:CYS42 4.8 60.9 1.0
CB E:ILE44 4.9 56.0 1.0
CA E:CYS83 4.9 64.2 1.0

Zinc binding site 6 out of 6 in 9j77

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Zinc binding site 6 out of 6 in the Cryo-Em Structure of CRL2-FEM1B (Dimer 1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of CRL2-FEM1B (Dimer 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:47.7
occ:1.00
OD1 E:ASP97 2.1 33.6 1.0
SG E:CYS94 2.3 34.1 1.0
SG E:CYS75 2.3 46.3 1.0
ND1 E:HIS77 2.3 41.6 1.0
CG E:ASP97 3.0 33.6 1.0
OD2 E:ASP97 3.2 33.6 1.0
CE1 E:HIS77 3.2 41.6 1.0
CB E:CYS94 3.2 34.1 1.0
CG E:HIS77 3.3 41.6 1.0
CB E:CYS75 3.5 46.3 1.0
CB E:HIS77 3.7 41.6 1.0
CZ3 E:TRP101 4.2 48.0 1.0
N E:ASP97 4.2 33.6 1.0
NE2 E:HIS77 4.4 41.6 1.0
CB E:ASP97 4.4 33.6 1.0
O E:ASP97 4.4 33.6 1.0
CE3 E:TRP101 4.4 48.0 1.0
CD2 E:HIS77 4.4 41.6 1.0
CA E:CYS94 4.7 34.1 1.0
CB E:LEU96 4.7 31.1 1.0
CE2 E:PHE79 4.7 48.9 1.0
CA E:ASP97 4.8 33.6 1.0
CA E:CYS75 4.8 46.3 1.0

Reference:

C.Xu, S.Zhao. TOM20-Driven E3 Ligase Recruitment Regulates Mitochondrial Dynamics Through PLD6 Nat.Chem.Biol. 2025.
ISSN: ESSN 1552-4469
Page generated: Fri Aug 22 18:19:41 2025

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