Zinc in PDB 8wqb: Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) (pdb code 8wqb). 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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2), PDB code: 8wqb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8wqb

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn200

b:59.7
occ:1.00
 ND1 I:HIS82 2.1 38.1 1.0
CB I:CYS56 2.2 35.6 1.0
SG I:CYS68 2.3 41.6 1.0
SG I:CYS56 2.3 35.6 1.0
SG I:CYS53 2.3 33.0 1.0
CE1 I:HIS82 2.4 38.1 1.0
CB I:CYS68 2.9 41.6 1.0
CG I:HIS82 3.2 38.1 1.0
NE2 I:HIS82 3.5 38.1 1.0
CA I:CYS56 3.7 35.6 1.0
CD2 I:HIS82 3.9 38.1 1.0
CB I:CYS53 3.9 33.0 1.0
CB I:HIS82 4.0 38.1 1.0
CA I:CYS68 4.2 41.6 1.0
N I:CYS56 4.2 35.6 1.0
N I:CYS53 4.2 33.0 1.0
N I:CYS68 4.3 41.6 1.0
CA I:CYS53 4.6 33.0 1.0
C I:CYS56 4.7 35.6 1.0
N I:HIS82 4.8 38.1 1.0
O I:CYS53 5.0 33.0 1.0

Zinc binding site 2 out of 6 in 8wqb

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:25.4
occ:1.00
 ND1 I:HIS80 2.1 34.1 1.0
SG I:CYS45 2.3 36.8 1.0
SG I:CYS83 2.3 41.1 1.0
SG I:CYS42 2.3 41.4 1.0
CG I:HIS80 3.0 34.1 1.0
CE1 I:HIS80 3.1 34.1 1.0
CB I:HIS80 3.2 34.1 1.0
CB I:CYS42 3.4 41.4 1.0
CB I:CYS83 3.5 41.1 1.0
CB I:CYS53 3.6 33.0 1.0
CB I:CYS45 3.7 36.8 1.0
N I:CYS45 4.0 36.8 1.0
CD2 I:HIS80 4.2 34.1 1.0
NE2 I:HIS80 4.2 34.1 1.0
CA I:CYS53 4.2 33.0 1.0
N I:HIS80 4.4 34.1 1.0
CB I:ILE44 4.4 41.7 1.0
CA I:HIS80 4.4 34.1 1.0
CA I:CYS45 4.4 36.8 1.0
O I:CYS42 4.7 41.4 1.0
CA I:CYS42 4.7 41.4 1.0
CA I:CYS83 4.8 41.1 1.0
CG1 I:ILE44 4.9 41.7 1.0
C I:CYS42 4.9 41.4 1.0
C I:ILE44 5.0 41.7 1.0

Zinc binding site 3 out of 6 in 8wqb

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:76.4
occ:1.00
 SG I:CYS75 2.3 52.6 1.0
SG I:CYS94 2.3 53.0 1.0
ND1 I:HIS77 2.3 50.9 1.0
CG I:HIS77 2.4 50.9 1.0
CE1 I:HIS77 2.5 50.9 1.0
CD2 I:HIS77 2.7 50.9 1.0
NE2 I:HIS77 2.7 50.9 1.0
OD1 I:ASP97 3.2 54.7 1.0
CB I:CYS94 3.2 53.0 1.0
CB I:HIS77 3.2 50.9 1.0
CB I:CYS75 3.7 52.6 1.0
OD2 I:ASP97 3.8 54.7 1.0
CG I:ASP97 3.9 54.7 1.0
O I:CYS75 4.4 52.6 1.0
CA I:CYS94 4.5 53.0 1.0
CZ3 I:TRP101 4.6 58.5 1.0
CA I:HIS77 4.6 50.9 1.0
CA I:CYS75 4.8 52.6 1.0
CE3 I:TRP101 4.8 58.5 1.0
C I:CYS75 4.8 52.6 1.0
N I:HIS77 5.0 50.9 1.0

Zinc binding site 4 out of 6 in 8wqb

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn200

b:108.6
occ:1.00
 ND1 E:HIS82 2.1 42.3 1.0
SG E:CYS56 2.3 56.5 1.0
SG E:CYS68 2.3 52.7 1.0
SG E:CYS53 2.3 47.7 1.0
CB E:CYS56 2.5 56.5 1.0
CE1 E:HIS82 2.6 42.3 1.0
CG E:HIS82 3.3 42.3 1.0
CB E:CYS53 3.6 47.7 1.0
CA E:CYS56 3.7 56.5 1.0
N E:CYS56 3.8 56.5 1.0
NE2 E:HIS82 3.8 42.3 1.0
CB E:CYS68 3.9 52.7 1.0
CB E:HIS82 3.9 42.3 1.0
CD2 E:HIS82 4.2 42.3 1.0
OE1 E:GLU55 4.2 51.0 1.0
N E:CYS53 4.3 47.7 1.0
CA E:CYS53 4.4 47.7 1.0
CA E:CYS68 4.4 52.7 1.0
O E:CYS53 4.8 47.7 1.0
C E:GLU55 4.8 51.0 1.0
C E:CYS56 4.8 56.5 1.0
N E:CYS68 4.9 52.7 1.0
C E:CYS53 4.9 47.7 1.0

Zinc binding site 5 out of 6 in 8wqb

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:27.1
occ:1.00
 ND1 E:HIS80 2.1 31.6 1.0
SG E:CYS45 2.3 23.4 1.0
SG E:CYS83 2.3 32.4 1.0
SG E:CYS42 2.3 23.2 1.0
CE1 E:HIS80 3.0 31.6 1.0
CG E:HIS80 3.2 31.6 1.0
CB E:CYS42 3.3 23.2 1.0
CB E:CYS83 3.5 32.4 1.0
CB E:HIS80 3.6 31.6 1.0
CB E:CYS45 3.6 23.4 1.0
CB E:CYS53 3.9 47.7 1.0
N E:HIS80 4.1 31.6 1.0
NE2 E:HIS80 4.1 31.6 1.0
CA E:CYS53 4.1 47.7 1.0
CD2 E:HIS80 4.2 31.6 1.0
OD1 E:ASN47 4.3 28.2 1.0
N E:CYS45 4.3 23.4 1.0
CA E:HIS80 4.4 31.6 1.0
CA E:CYS45 4.6 23.4 1.0
CA E:CYS42 4.7 23.2 1.0
N E:ILE54 4.7 46.9 1.0
CA E:CYS83 4.8 32.4 1.0
CB E:ILE44 4.9 20.5 1.0

Zinc binding site 6 out of 6 in 8wqb

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Zinc binding site 6 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:12.5
occ:1.00
 OD1 E:ASP97 2.0 10.8 1.0
SG E:CYS94 2.3 11.5 1.0
SG E:CYS75 2.3 12.9 1.0
ND1 E:HIS77 2.3 12.2 1.0
CG E:ASP97 3.1 10.8 1.0
CG E:HIS77 3.2 12.2 1.0
CE1 E:HIS77 3.3 12.2 1.0
CB E:HIS77 3.3 12.2 1.0
CB E:CYS94 3.4 11.5 1.0
CB E:CYS75 3.5 12.9 1.0
OD2 E:ASP97 3.6 10.8 1.0
N E:ASP97 4.1 10.8 1.0
CZ3 E:TRP101 4.3 17.7 1.0
CD2 E:HIS77 4.4 12.2 1.0
O E:ASP97 4.4 10.8 1.0
CB E:ASP97 4.4 10.8 1.0
NE2 E:HIS77 4.4 12.2 1.0
CB E:LEU96 4.5 10.6 1.0
CA E:HIS77 4.7 12.2 1.0
O E:CYS75 4.7 12.9 1.0
CA E:ASP97 4.7 10.8 1.0
CE3 E:TRP101 4.8 17.7 1.0
CA E:CYS94 4.8 11.5 1.0
CA E:CYS75 4.8 12.9 1.0
N E:LEU96 4.8 10.6 1.0
N E:HIS77 4.9 12.2 1.0
C E:CYS75 4.9 12.9 1.0
C E:LEU96 4.9 10.6 1.0

Reference:

X.Chen, K.Zhang, C.Xu. Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) To Be Published.
Page generated: Thu Oct 31 13:37:29 2024

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