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Zinc in PDB 8h38: Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn(Mutate) Complex

Enzymatic activity of Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn(Mutate) Complex

All present enzymatic activity of Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn(Mutate) Complex:
2.3.2.27; 2.3.2.32;

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn(Mutate) Complex (pdb code 8h38). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn(Mutate) Complex, PDB code: 8h38:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8h38

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Zinc binding site 1 out of 4 in the Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn(Mutate) Complex


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 the KBTBD2-CRL3~N8-Csn(Mutate) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:149.1
occ:1.00
 OD2 E:ASP151 2.0 184.6 1.0
NE2 E:HIS140 2.0 174.3 1.0
CG E:ASP151 2.7 179.9 1.0
OD1 E:ASP151 2.8 180.8 1.0
CD2 E:HIS140 3.0 172.8 1.0
CE1 E:HIS140 3.1 173.5 1.0
OG E:SER148 4.0 167.7 1.0
CG E:HIS140 4.1 173.1 1.0
CB E:ASP151 4.1 176.3 1.0
ND1 E:HIS140 4.1 173.5 1.0
O E:TRP146 4.6 163.7 1.0
CB E:SER148 4.6 167.0 1.0
N E:SER148 4.6 163.0 1.0
OH E:TYR143 4.7 175.8 1.0
CB E:ALA138 4.7 30.0 1.0

Zinc binding site 2 out of 4 in 8h38

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Zinc binding site 2 out of 4 in the Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn(Mutate) Complex


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 the KBTBD2-CRL3~N8-Csn(Mutate) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn4001

b:104.2
occ:1.00
 ND1 R:HIS80 2.1 112.2 1.0
SG R:CYS42 2.3 136.0 1.0
SG R:CYS45 2.3 137.7 1.0
SG R:CYS83 2.3 118.1 1.0
CB R:CYS42 2.8 136.2 1.0
CB R:CYS45 2.8 137.7 1.0
CG R:HIS80 2.9 112.4 1.0
CB R:HIS80 3.0 112.5 1.0
CE1 R:HIS80 3.2 112.3 1.0
CB R:CYS83 3.2 117.6 1.0
CB R:CYS53 3.7 143.4 1.0
N R:CYS45 3.7 137.4 1.0
CA R:CYS45 3.9 137.8 1.0
N R:HIS80 4.0 112.2 1.0
O R:CYS42 4.1 136.3 1.0
CD2 R:HIS80 4.1 112.3 1.0
CA R:HIS80 4.1 112.5 1.0
CA R:CYS42 4.2 136.3 1.0
NE2 R:HIS80 4.2 112.3 1.0
C R:CYS42 4.4 136.2 1.0
CA R:CYS83 4.6 117.7 1.0
CA R:CYS53 4.6 143.5 1.0
N R:CYS83 4.8 116.9 1.0
C R:ILE44 4.8 137.0 1.0
O R:HIS48 4.8 141.4 1.0
C R:CYS45 4.9 138.1 1.0
CB R:ILE44 5.0 136.6 1.0

Zinc binding site 3 out of 4 in 8h38

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Zinc binding site 3 out of 4 in the Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn(Mutate) Complex


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 the KBTBD2-CRL3~N8-Csn(Mutate) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn4002

b:92.5
occ:1.00
 ND1 R:HIS77 2.3 113.1 1.0
SG R:CYS75 2.3 115.9 1.0
SG R:CYS94 2.3 129.2 1.0
OD2 R:ASP97 2.8 131.3 1.0
OD1 R:ASP97 2.9 131.1 1.0
CE1 R:HIS77 3.0 113.2 1.0
CG R:ASP97 3.1 131.3 1.0
CG R:HIS77 3.4 112.9 1.0
CB R:CYS75 3.6 116.0 1.0
CB R:CYS94 3.7 130.0 1.0
CB R:HIS77 4.0 112.9 1.0
CE3 R:TRP101 4.1 129.1 1.0
NE2 R:HIS77 4.2 113.1 1.0
CZ3 R:TRP101 4.3 128.8 1.0
CB R:ASP97 4.3 131.3 1.0
CB R:LEU96 4.3 130.6 1.0
O R:CYS94 4.4 130.2 1.0
CD2 R:HIS77 4.4 113.0 1.0
N R:ASP97 4.5 131.1 1.0
CZ B:PHE259 4.8 96.6 1.0
C R:LEU96 4.9 130.8 1.0
CA R:CYS94 4.9 130.1 1.0
CA R:CYS75 4.9 116.0 1.0
C R:CYS94 4.9 130.2 1.0
O R:CYS75 4.9 115.6 1.0
CB R:ARG99 5.0 132.2 1.0

Zinc binding site 4 out of 4 in 8h38

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Zinc binding site 4 out of 4 in the Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn(Mutate) Complex


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 the KBTBD2-CRL3~N8-Csn(Mutate) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn4003

b:104.9
occ:1.00
 ND1 R:HIS82 2.1 115.0 1.0
SG R:CYS53 2.3 143.1 1.0
SG R:CYS56 2.3 146.0 1.0
SG R:CYS68 2.3 133.8 1.0
CG R:HIS82 2.7 115.1 1.0
CB R:HIS82 2.9 115.4 1.0
CE1 R:HIS82 3.1 114.9 1.0
CB R:CYS56 3.3 146.0 1.0
CB R:CYS68 3.4 134.2 1.0
CB R:CYS53 3.7 143.4 1.0
CD2 R:HIS82 3.8 114.8 1.0
NE2 R:HIS82 3.9 114.7 1.0
N R:CYS56 4.2 145.7 1.0
N R:CYS53 4.2 143.3 1.0
CA R:CYS68 4.2 134.1 1.0
CA R:CYS56 4.3 146.0 1.0
C R:GLU55 4.4 145.4 1.0
CA R:HIS82 4.4 115.5 1.0
CA R:CYS53 4.5 143.5 1.0
O R:GLU55 4.6 145.5 1.0
CB R:GLU55 4.7 145.1 1.0
N R:HIS82 4.8 114.8 1.0
NE2 R:GLN60 4.8 148.2 1.0
OE1 R:GLU66 4.9 140.9 1.0
CA R:GLU55 5.0 145.1 1.0

Reference:

Y.Hu, Q.Mao, Z.Chen, L.Sun. Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn(Mutate) Complex To Be Published.
Page generated: Thu Dec 28 13:07:15 2023

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