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
Go back to
Zinc Binding Sites List in 9j77
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
Go back to
Zinc Binding Sites List in 9j77
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
Go back to
Zinc Binding Sites List in 9j77
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
Go back to
Zinc Binding Sites List in 9j77
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
Go back to
Zinc Binding Sites List in 9j77
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
Go back to
Zinc Binding Sites List in 9j77
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
|