Zinc in PDB 8h3a: Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn Complex

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

All present enzymatic activity of Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn 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 Complex (pdb code 8h3a). 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 Complex, PDB code: 8h3a:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8h3a

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Zinc binding site 1 out of 4 in the Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:149.1
occ:1.00
 NE2 E:HIS140 2.0 174.3 1.0
OD2 E:ASP151 2.0 184.6 1.0
NE2 E:HIS138 2.1 175.2 1.0
CG E:ASP151 2.8 179.9 1.0
CD2 E:HIS138 3.0 173.9 1.0
CD2 E:HIS140 3.0 172.8 1.0
OD1 E:ASP151 3.0 180.8 1.0
CE1 E:HIS140 3.0 173.5 1.0
CE1 E:HIS138 3.2 173.2 1.0
CB E:ASP151 4.1 176.3 1.0
ND1 E:HIS140 4.1 173.5 1.0
CG E:HIS140 4.1 173.1 1.0
CG E:HIS138 4.1 172.8 1.0
ND1 E:HIS138 4.2 173.1 1.0
OG E:SER148 4.4 167.7 1.0
O E:TRP146 4.5 163.7 1.0
N E:SER148 4.5 163.0 1.0
CB E:SER148 4.6 167.0 1.0
OH E:TYR143 4.7 175.8 1.0

Zinc binding site 2 out of 4 in 8h3a

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Zinc binding site 2 out of 4 in the Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn4001

b:104.2
occ:1.00
 CG R:HIS80 1.9 112.4 1.0
CB R:HIS80 2.3 112.5 1.0
ND1 R:HIS80 2.3 112.2 1.0
CD2 R:HIS80 2.5 112.3 1.0
CB R:CYS53 2.8 143.4 1.0
CE1 R:HIS80 3.0 112.3 1.0
NE2 R:HIS80 3.1 112.3 1.0
SG R:CYS53 3.3 143.1 1.0
N R:CYS53 3.7 143.3 1.0
CA R:CYS53 3.7 143.5 1.0
CA R:HIS80 3.7 112.5 1.0
SG R:CYS68 3.8 133.8 1.0
C R:LEU52 3.8 143.2 1.0
O R:LEU52 3.9 143.1 1.0
SG R:CYS83 4.1 118.1 1.0
CA R:LEU52 4.5 143.2 1.0
N R:HIS80 4.6 112.2 1.0
C R:HIS80 4.6 112.8 1.0
SG R:CYS45 4.8 137.7 1.0

Zinc binding site 3 out of 4 in 8h3a

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Zinc binding site 3 out of 4 in the Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn4002

b:92.5
occ:1.00
 O R:GLU102 2.1 130.2 1.0
NE1 R:TRP101 2.2 129.4 1.0
CE2 R:TRP101 2.3 129.1 1.0
CA R:GLY73 2.5 118.8 1.0
CZ2 R:TRP101 2.6 128.8 1.0
N R:GLY73 3.0 119.5 1.0
CD1 R:TRP101 3.1 129.7 1.0
O R:TRP72 3.1 120.2 1.0
CD2 R:TRP101 3.2 129.3 1.0
C R:GLU102 3.3 130.1 1.0
C R:TRP72 3.3 120.2 1.0
CG R:TRP101 3.6 129.8 1.0
CH2 R:TRP101 3.6 128.8 1.0
C R:GLY73 3.8 118.3 1.0
CA R:PHE103 3.9 129.7 1.0
N R:PHE103 4.0 129.9 1.0
CE3 R:TRP101 4.2 129.1 1.0
N R:GLU102 4.2 130.3 1.0
N R:VAL74 4.2 117.9 1.0
CZ3 R:TRP101 4.3 128.8 1.0
CA R:GLU102 4.3 130.3 1.0
CG R:PHE103 4.5 129.8 1.0
CA R:TRP72 4.5 120.7 1.0
CD1 R:PHE103 4.6 129.8 1.0
N R:GLN104 4.7 129.3 1.0
N R:TRP72 4.8 121.8 1.0
CD2 R:PHE103 4.8 130.1 1.0
C R:TRP101 4.8 130.4 1.0
O R:GLY73 4.8 118.3 1.0
CB R:PHE103 4.9 129.8 1.0
CE1 R:PHE103 4.9 129.8 1.0
C R:PHE103 4.9 129.6 1.0
CB R:TRP101 5.0 130.4 1.0

Zinc binding site 4 out of 4 in 8h3a

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Zinc binding site 4 out of 4 in the Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn 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 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn4003

b:104.9
occ:1.00
 CB R:CYS56 2.2 146.0 1.0
SG R:CYS56 2.3 146.0 1.0
OE1 R:GLU66 3.2 140.9 1.0
CD1 R:LEU52 3.3 143.2 1.0
CA R:CYS56 3.4 146.0 1.0
OE2 R:GLU66 3.8 140.9 1.0
O R:CYS56 3.9 146.3 1.0
CD R:GLU66 3.9 140.9 1.0
C R:CYS56 4.0 146.2 1.0
O R:ALA58 4.1 147.7 1.0
CG R:LEU52 4.6 143.3 1.0
N R:CYS56 4.6 145.7 1.0
CB R:CYS68 4.8 134.2 1.0

Reference:

Y.Hu, Q.Mao, Z.Chen, L.Sun. Cryo-Em Structure of the KBTBD2-CRL3~N8-Csn Complex To Be Published.
Page generated: Thu Oct 31 07:00:38 2024

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