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Zinc in PDB 6x67: Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc)

Other elements in 6x67:

The structure of Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc) also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc) (pdb code 6x67). 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 Piggybac Transposase Strand Transfer Complex (Stc), PDB code: 6x67:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6x67

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Zinc binding site 1 out of 4 in the Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc)


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 Piggybac Transposase Strand Transfer Complex (Stc) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:0.2
occ:1.00
 SG C:CYS562 2.0 99.5 1.0
SG C:CYS582 2.0 0.3 1.0
SG C:CYS559 2.1 96.7 1.0
ND1 C:HIS585 2.2 0.8 1.0
CE1 C:HIS585 2.3 0.8 1.0
CB C:CYS582 3.2 0.8 1.0
CG C:HIS585 3.2 0.6 1.0
NE2 C:HIS585 3.3 0.7 1.0
CB C:CYS559 3.4 94.4 1.0
CB C:CYS562 3.4 90.1 1.0
CD2 C:HIS585 3.8 0.7 1.0
N C:CYS562 4.0 89.3 1.0
CA C:CYS562 4.1 88.6 1.0
N C:CYS582 4.1 0.2 1.0
CB C:HIS585 4.2 0.9 1.0
CA C:CYS582 4.2 0.3 1.0
C C:TYR561 4.4 93.8 1.0
NH1 C:ARG568 4.5 0.2 1.0
O C:CYS582 4.6 0.3 1.0
N C:HIS585 4.7 0.6 1.0
CD C:ARG568 4.7 88.8 1.0
CA C:CYS559 4.7 91.1 1.0
C C:CYS582 4.8 0.9 1.0
O C:TYR561 4.8 96.9 1.0
N C:TYR561 4.8 98.2 1.0
CB C:TYR561 4.9 0.7 1.0
CA C:TYR561 5.0 99.3 1.0

Zinc binding site 2 out of 4 in 6x67

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Zinc binding site 2 out of 4 in the Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc)


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 Piggybac Transposase Strand Transfer Complex (Stc) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:0.4
occ:1.00
 SG C:CYS590 2.0 0.8 1.0
SG C:CYS574 2.0 0.5 1.0
SG C:CYS593 2.2 0.7 1.0
SG C:CYS577 2.2 0.6 1.0
CB C:CYS574 3.0 0.1 1.0
CB C:CYS577 3.1 0.6 1.0
CB C:CYS590 3.2 0.0 1.0
CB C:CYS593 3.2 0.4 1.0
N C:CYS577 3.8 0.2 1.0
N C:CYS590 3.9 0.5 1.0
OG C:SER592 4.0 0.2 1.0
CA C:CYS577 4.0 0.5 1.0
CA C:CYS590 4.1 0.1 1.0
N C:CYS593 4.2 1.0 1.0
CA C:CYS593 4.3 1.0 1.0
C C:LYS576 4.3 0.6 1.0
OH C:TYR561 4.4 0.3 1.0
CA C:CYS574 4.4 0.2 1.0
O C:CYS590 4.7 0.7 1.0
C C:CYS590 4.7 0.8 1.0
C C:CYS577 4.7 0.2 1.0
CB C:LYS576 4.7 0.2 1.0
C C:CYS574 4.8 0.0 1.0
O C:LYS576 4.8 0.8 1.0
O C:CYS574 4.8 0.6 1.0
C C:SER592 4.9 0.0 1.0
CA C:LYS576 4.9 0.6 1.0
N C:LYS576 4.9 0.5 1.0

Zinc binding site 3 out of 4 in 6x67

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Zinc binding site 3 out of 4 in the Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc)


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 Piggybac Transposase Strand Transfer Complex (Stc) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:1.0
occ:1.00
 SG D:CYS562 2.0 0.2 1.0
ND1 D:HIS585 2.0 0.8 1.0
SG D:CYS582 2.0 0.3 1.0
SG D:CYS559 2.1 0.7 1.0
CE1 D:HIS585 2.6 0.6 1.0
CB D:CYS582 2.9 0.1 1.0
CB D:CYS559 3.0 0.8 1.0
CB D:CYS562 3.1 0.4 1.0
CG D:HIS585 3.2 0.8 1.0
NE2 D:HIS585 3.7 0.2 1.0
N D:CYS562 3.7 0.2 1.0
CA D:CYS562 3.8 0.6 1.0
CB D:HIS585 3.9 1.0 1.0
CD2 D:HIS585 4.0 0.1 1.0
CA D:CYS582 4.1 0.2 1.0
C D:TYR561 4.1 0.8 1.0
N D:CYS582 4.2 1.0 1.0
O D:TYR561 4.4 0.0 1.0
CA D:CYS559 4.5 0.3 1.0
CG D:ARG568 4.6 0.9 1.0
CB D:ARG568 4.6 0.6 1.0
O D:CYS582 4.6 0.4 1.0
N D:HIS585 4.6 0.1 1.0
C D:CYS582 4.7 0.3 1.0
CB D:TYR561 4.7 0.1 1.0
NH1 D:ARG568 4.8 0.7 1.0
CA D:TYR561 4.8 0.8 1.0
C D:CYS559 4.9 0.1 1.0
CA D:HIS585 4.9 0.5 1.0
N D:TYR561 4.9 0.1 1.0

Zinc binding site 4 out of 4 in 6x67

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Zinc binding site 4 out of 4 in the Cryo-Em Structure of Piggybac Transposase Strand Transfer Complex (Stc)


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 Piggybac Transposase Strand Transfer Complex (Stc) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:0.8
occ:1.00
 SG D:CYS574 1.9 0.6 1.0
SG D:CYS590 2.0 0.6 1.0
SG D:CYS593 2.1 0.6 1.0
SG D:CYS577 2.1 0.7 1.0
CB D:CYS590 2.9 0.3 1.0
CB D:CYS574 3.0 0.8 1.0
CB D:CYS577 3.1 0.6 1.0
CB D:CYS593 3.1 0.1 1.0
N D:CYS577 3.8 0.8 1.0
CA D:CYS590 4.0 0.2 1.0
CA D:CYS577 4.0 0.9 1.0
N D:CYS590 4.0 0.7 1.0
N D:CYS593 4.1 0.3 1.0
CA D:CYS593 4.2 0.2 1.0
CA D:CYS574 4.4 0.7 1.0
C D:LYS576 4.4 0.1 1.0
C D:SER592 4.6 0.5 1.0
C D:CYS590 4.6 0.0 1.0
C D:CYS577 4.6 0.1 1.0
CB D:LYS579 4.7 0.6 1.0
O D:CYS590 4.7 0.4 1.0
N D:LYS578 4.9 0.7 1.0
C D:CYS574 4.9 0.6 1.0
CB D:SER592 4.9 0.4 1.0
N D:LYS576 4.9 0.0 1.0
OH D:TYR561 5.0 0.9 1.0
O D:LYS576 5.0 0.5 1.0
N D:SER592 5.0 0.7 1.0

Reference:

Q.Chen, W.Luo, R.A.Veach, A.B.Hickman, M.H.Wilson, F.Dyda. Structural Basis of Seamless Excision and Specific Targeting By Piggybac Transposase Nat Commun V. 11 3446 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-17128-1
Page generated: Tue Oct 29 10:37:05 2024

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