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Zinc in PDB 9j79: Cryo-Em Structure of CRL2-FEM1B Bound with TOM20(Tetramer)

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of CRL2-FEM1B Bound with TOM20(Tetramer) (pdb code 9j79). 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 Bound with TOM20(Tetramer), PDB code: 9j79:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9j79

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of CRL2-FEM1B Bound with TOM20(Tetramer)


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 Bound with TOM20(Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn200

b:535.7
occ:1.00
 ND1 I:HIS82 2.1 481.4 1.0
CE1 I:HIS82 2.1 481.4 1.0
SG I:CYS68 2.3 487.7 1.0
SG I:CYS53 2.3 494.2 1.0
SG I:CYS56 2.3 496.1 1.0
NE2 I:HIS82 2.6 481.4 1.0
CG I:HIS82 2.6 481.4 1.0
CD2 I:HIS82 2.9 481.4 1.0
CB I:CYS56 2.9 496.1 1.0
CB I:HIS82 3.6 481.4 1.0
CB I:CYS68 3.6 487.7 1.0
CB I:CYS53 3.7 494.2 1.0
N I:CYS56 3.7 496.1 1.0
CA I:CYS56 3.9 496.1 1.0
N I:CYS53 4.6 494.2 1.0
CG I:GLU55 4.6 500.1 1.0
C I:GLU55 4.7 500.1 1.0
CB I:GLU55 4.7 500.1 1.0
CA I:CYS53 4.7 494.2 1.0
OG1 I:THR69 4.8 459.0 1.0
N I:THR69 4.9 459.0 1.0
CA I:CYS68 4.9 487.7 1.0
CA I:HIS82 5.0 481.4 1.0

Zinc binding site 2 out of 6 in 9j79

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of CRL2-FEM1B Bound with TOM20(Tetramer)


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 Bound with TOM20(Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:466.7
occ:1.00
 ND1 I:HIS80 2.1 465.1 1.0
SG I:CYS45 2.3 479.2 1.0
SG I:CYS83 2.3 467.0 1.0
SG I:CYS42 2.3 462.1 1.0
CE1 I:HIS80 2.6 465.1 1.0
CG I:HIS80 3.3 465.1 1.0
CB I:CYS42 3.5 462.1 1.0
CB I:CYS83 3.5 467.0 1.0
CB I:CYS45 3.7 479.2 1.0
N I:CYS45 3.8 479.2 1.0
NE2 I:HIS80 3.9 465.1 1.0
CB I:HIS80 4.0 465.1 1.0
CB I:ILE44 4.2 455.2 1.0
CD2 I:HIS80 4.2 465.1 1.0
CA I:CYS45 4.4 479.2 1.0
N I:HIS80 4.4 465.1 1.0
O I:CYS42 4.5 462.1 1.0
CG1 I:ILE44 4.6 455.2 1.0
CA I:CYS42 4.8 462.1 1.0
C I:ILE44 4.8 455.2 1.0
CA I:HIS80 4.8 465.1 1.0
N I:ILE44 4.8 455.2 1.0
CA I:ILE44 4.9 455.2 1.0
CA I:CYS83 4.9 467.0 1.0
C I:CYS42 4.9 462.1 1.0
CB I:CYS53 4.9 494.2 1.0

Zinc binding site 3 out of 6 in 9j79

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of CRL2-FEM1B Bound with TOM20(Tetramer)


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 Bound with TOM20(Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:539.3
occ:1.00
 CB I:CYS75 2.1 489.6 1.0
OD1 I:ASP97 2.1 515.6 1.0
CE1 I:HIS77 2.2 480.6 1.0
SG I:CYS75 2.3 489.6 1.0
SG I:CYS94 2.3 514.0 1.0
ND1 I:HIS77 2.3 480.6 1.0
CG I:ASP97 3.0 515.6 1.0
CB I:CYS94 3.2 514.0 1.0
OD2 I:ASP97 3.2 515.6 1.0
NE2 I:HIS77 3.3 480.6 1.0
CG I:HIS77 3.5 480.6 1.0
CA I:CYS75 3.5 489.6 1.0
O I:CYS75 3.8 489.6 1.0
CD2 I:HIS77 4.0 480.6 1.0
C I:CYS75 4.0 489.6 1.0
CB I:ASP97 4.3 515.6 1.0
N I:ASP97 4.4 515.6 1.0
N I:CYS75 4.5 489.6 1.0
CB I:HIS77 4.5 480.6 1.0
CA I:CYS94 4.6 514.0 1.0
O I:ASP97 4.8 515.6 1.0
CA I:ASP97 4.9 515.6 1.0
CB I:ARG99 4.9 500.5 1.0

Zinc binding site 4 out of 6 in 9j79

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of CRL2-FEM1B Bound with TOM20(Tetramer)


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 Bound with TOM20(Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn200

b:207.8
occ:1.00
 ND1 N:HIS82 2.1 163.6 1.0
CE1 N:HIS82 2.1 163.6 1.0
SG N:CYS53 2.3 173.7 1.0
SG N:CYS56 2.3 196.6 1.0
SG N:CYS68 2.3 172.4 1.0
CB N:CYS56 2.8 196.6 1.0
CG N:HIS82 3.1 163.6 1.0
NE2 N:HIS82 3.2 163.6 1.0
CB N:CYS53 3.3 173.7 1.0
CD2 N:HIS82 3.7 163.6 1.0
N N:CYS56 3.9 196.6 1.0
N N:CYS53 3.9 173.7 1.0
CB N:CYS68 3.9 172.4 1.0
CA N:CYS56 3.9 196.6 1.0
CB N:HIS82 4.1 163.6 1.0
CA N:CYS53 4.1 173.7 1.0
CA N:CYS68 4.4 172.4 1.0
N N:CYS68 4.5 172.4 1.0
O N:CYS53 4.6 173.7 1.0
C N:CYS53 4.7 173.7 1.0
CG N:GLU67 4.7 205.5 1.0
OE1 N:GLU55 4.8 194.5 1.0
C N:GLU55 4.9 194.5 1.0

Zinc binding site 5 out of 6 in 9j79

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of CRL2-FEM1B Bound with TOM20(Tetramer)


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 Bound with TOM20(Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn201

b:192.4
occ:1.00
 ND1 N:HIS80 2.1 160.8 1.0
SG N:CYS83 2.3 159.6 1.0
SG N:CYS42 2.3 157.5 1.0
SG N:CYS45 2.3 161.4 1.0
CB N:CYS45 2.7 161.4 1.0
CE1 N:HIS80 2.9 160.8 1.0
CG N:HIS80 3.2 160.8 1.0
CB N:CYS42 3.7 157.5 1.0
CB N:HIS80 3.7 160.8 1.0
CB N:CYS53 3.8 173.7 1.0
CA N:CYS45 3.9 161.4 1.0
N N:CYS45 3.9 161.4 1.0
CB N:CYS83 3.9 159.6 1.0
N N:HIS80 4.0 160.8 1.0
CA N:CYS53 4.1 173.7 1.0
NE2 N:HIS80 4.1 160.8 1.0
CD2 N:HIS80 4.3 160.8 1.0
CA N:HIS80 4.4 160.8 1.0
OD1 N:ASN47 4.7 154.7 1.0
N N:ILE54 4.7 180.1 1.0
CA N:CYS83 4.9 159.6 1.0
CB N:PHE79 4.9 139.7 1.0
CA N:CYS42 5.0 157.5 1.0
C N:CYS53 5.0 173.7 1.0
N N:CYS83 5.0 159.6 1.0

Zinc binding site 6 out of 6 in 9j79

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Zinc binding site 6 out of 6 in the Cryo-Em Structure of CRL2-FEM1B Bound with TOM20(Tetramer)


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 Bound with TOM20(Tetramer) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn202

b:135.1
occ:1.00
 CB N:CYS75 2.0 113.9 1.0
OD1 N:ASP97 2.0 106.9 1.0
SG N:CYS75 2.3 113.9 1.0
ND1 N:HIS77 2.3 107.2 1.0
SG N:CYS94 2.3 112.6 1.0
CE1 N:HIS77 2.5 107.2 1.0
CG N:ASP97 2.8 106.9 1.0
OD2 N:ASP97 3.0 106.9 1.0
CB N:CYS94 3.3 112.6 1.0
CA N:CYS75 3.4 113.9 1.0
CG N:HIS77 3.6 107.2 1.0
NE2 N:HIS77 3.8 107.2 1.0
O N:CYS75 3.8 113.9 1.0
C N:CYS75 3.9 113.9 1.0
N N:ASP97 4.2 106.9 1.0
CB N:ASP97 4.3 106.9 1.0
CD2 N:HIS77 4.3 107.2 1.0
CB N:HIS77 4.4 107.2 1.0
N N:CYS75 4.4 113.9 1.0
O N:ASP97 4.5 106.9 1.0
CA N:CYS94 4.7 112.6 1.0
CB N:LEU96 4.7 98.4 1.0
CA N:ASP97 4.8 106.9 1.0
N N:ASN76 4.9 102.9 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 18:19:46 2025

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