Zinc in PDB 8bd4: Tniq-Capped Tns-Atp-Dsdna Complex

The structure of Tniq-Capped Tns-Atp-Dsdna Complex also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Zinc atom in the Tniq-Capped Tns-Atp-Dsdna Complex (pdb code 8bd4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Tniq-Capped Tns-Atp-Dsdna Complex, PDB code: 8bd4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:30.0 occ:1.00 CZ A:ARG128 1.1 215.5 1.0 NH1 A:ARG128 1.2 215.8 1.0 NH2 A:ARG128 1.3 215.7 1.0 SG S:CYS154 2.3 30.0 1.0 SG S:CYS151 2.3 30.0 1.0 SG S:CYS136 2.3 30.0 1.0 SG S:CYS133 2.3 30.0 1.0 NE A:ARG128 2.4 215.0 1.0 OE2 A:GLU131 2.9 227.1 1.0 CB S:CYS133 3.1 30.0 1.0 CB S:CYS151 3.2 30.0 1.0 CB S:CYS154 3.3 30.0 1.0 CB S:CYS136 3.3 30.0 1.0 OE1 A:GLU131 3.3 227.7 1.0 CD A:GLU131 3.4 227.7 1.0 CD A:ARG128 3.4 215.0 1.0 N S:CYS154 3.7 30.0 1.0 N S:CYS136 3.7 30.0 1.0 CA S:CYS154 4.0 30.0 1.0 CA S:CYS136 4.0 30.0 1.0 CG1 A:VAL132 4.3 234.9 1.0 CB S:ASN135 4.5 30.0 1.0 CD2 A:TYR115 4.5 215.6 1.0 CA S:CYS133 4.6 30.0 1.0 C S:CYS136 4.6 30.0 1.0 CA S:CYS151 4.6 30.0 1.0 CB S:ALA138 4.6 30.0 1.0 CE2 A:TYR115 4.6 215.9 1.0 CB S:ARG153 4.7 30.0 1.0 CG A:GLU131 4.7 227.9 1.0 C S:ASN135 4.7 30.0 1.0 CG A:ARG128 4.7 214.7 1.0 C S:CYS154 4.7 30.0 1.0 N S:ARG155 4.8 30.0 1.0 N S:GLN137 4.8 30.0 1.0 C S:ARG153 4.8 30.0 1.0 N S:ALA138 4.9 30.0 1.0 ND2 S:ASN135 4.9 30.0 1.0 CB S:MET156 4.9 30.0 1.0 CA S:ASN135 5.0 30.0 1.0 CE S:MET161 5.0 30.0 1.0

Zinc binding site 2 out of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn303 b:30.0 occ:1.00 NH1 E:ARG128 1.6 215.8 1.0 CZ E:ARG128 2.3 215.5 1.0 SG R:CYS154 2.3 30.0 1.0 SG R:CYS151 2.3 30.0 1.0 SG R:CYS136 2.3 30.0 1.0 SG R:CYS133 2.3 30.0 1.0 NH2 E:ARG128 2.6 215.7 1.0 CB R:CYS133 3.1 30.0 1.0 CB R:CYS151 3.2 30.0 1.0 CB R:CYS154 3.3 30.0 1.0 NE E:ARG128 3.3 215.0 1.0 CB R:CYS136 3.3 30.0 1.0 N R:CYS154 3.7 30.0 1.0 N R:CYS136 3.7 30.0 1.0 OE2 E:GLU131 3.9 227.1 1.0 OE1 E:GLU131 3.9 227.7 1.0 CD E:ARG128 4.0 215.0 1.0 CA R:CYS154 4.0 30.0 1.0 CA R:CYS136 4.0 30.0 1.0 CD E:GLU131 4.4 227.7 1.0 CB R:ASN135 4.5 30.0 1.0 CA R:CYS133 4.6 30.0 1.0 CA R:CYS151 4.6 30.0 1.0 C R:CYS136 4.6 30.0 1.0 CB R:ALA138 4.6 30.0 1.0 CB R:ARG153 4.7 30.0 1.0 C R:ASN135 4.7 30.0 1.0 C R:CYS154 4.7 30.0 1.0 N R:ARG155 4.8 30.0 1.0 N R:GLN137 4.8 30.0 1.0 C R:ARG153 4.8 30.0 1.0 N R:ALA138 4.9 30.0 1.0 ND2 R:ASN135 4.9 30.0 1.0 CB R:MET156 4.9 30.0 1.0 CE R:MET161 5.0 30.0 1.0 CA R:ASN135 5.0 30.0 1.0

Zinc binding site 3 out of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:30.0 occ:1.00 ND1 R:HIS125 2.1 30.0 1.0 SG R:CYS103 2.3 30.0 1.0 SG R:CYS122 2.3 30.0 1.0 SG R:CYS100 2.3 30.0 1.0 CE1 R:HIS125 3.0 30.0 1.0 CG R:HIS125 3.2 30.0 1.0 CB R:CYS100 3.3 30.0 1.0 CB R:CYS122 3.3 30.0 1.0 CB R:CYS103 3.4 30.0 1.0 N R:CYS103 3.5 30.0 1.0 CB R:HIS125 3.6 30.0 1.0 CA R:CYS103 3.9 30.0 1.0 NE2 R:HIS125 4.1 30.0 1.0 CD2 R:HIS125 4.3 30.0 1.0 N R:HIS125 4.4 30.0 1.0 C R:ALA102 4.4 30.0 1.0 CB R:ALA102 4.4 30.0 1.0 CA R:HIS125 4.7 30.0 1.0 CA R:CYS100 4.7 30.0 1.0 CA R:CYS122 4.7 30.0 1.0 CB R:ARG124 4.8 30.0 1.0 CA R:ALA102 4.9 30.0 1.0 O R:CYS100 5.0 30.0 1.0 C R:CYS100 5.0 30.0 1.0

Zinc binding site 4 out of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn201 b:30.0 occ:1.00 ND1 S:HIS125 2.1 30.0 1.0 SG S:CYS103 2.3 30.0 1.0 SG S:CYS122 2.3 30.0 1.0 SG S:CYS100 2.3 30.0 1.0 CE1 S:HIS125 3.0 30.0 1.0 CG S:HIS125 3.2 30.0 1.0 CB S:CYS100 3.3 30.0 1.0 CB S:CYS122 3.3 30.0 1.0 CB S:CYS103 3.4 30.0 1.0 N S:CYS103 3.5 30.0 1.0 CB S:HIS125 3.6 30.0 1.0 CA S:CYS103 3.9 30.0 1.0 NE2 S:HIS125 4.1 30.0 1.0 CD2 S:HIS125 4.3 30.0 1.0 N S:HIS125 4.4 30.0 1.0 C S:ALA102 4.4 30.0 1.0 CB S:ALA102 4.4 30.0 1.0 CA S:CYS100 4.7 30.0 1.0 CA S:HIS125 4.7 30.0 1.0 CA S:CYS122 4.7 30.0 1.0 CB S:ARG124 4.8 30.0 1.0 CA S:ALA102 4.9 30.0 1.0 O S:CYS100 5.0 30.0 1.0 C S:CYS100 5.0 30.0 1.0

Zinc binding site 5 out of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Zn201 b:30.0 occ:1.00 NH1 C:ARG128 0.6 215.8 1.0 CZ C:ARG128 1.8 215.5 1.0 SG T:CYS154 2.3 30.0 1.0 SG T:CYS151 2.3 30.0 1.0 SG T:CYS136 2.3 30.0 1.0 SG T:CYS133 2.3 30.0 1.0 NH2 C:ARG128 2.5 215.7 1.0 OE1 C:GLU131 2.7 227.7 1.0 NE C:ARG128 2.8 215.0 1.0 OE2 C:GLU131 3.0 227.1 1.0 CB T:CYS133 3.1 30.0 1.0 CB T:CYS151 3.2 30.0 1.0 CD C:GLU131 3.2 227.7 1.0 CB T:CYS154 3.3 30.0 1.0 CD C:ARG128 3.3 215.0 1.0 CB T:CYS136 3.3 30.0 1.0 N T:CYS154 3.7 30.0 1.0 N T:CYS136 3.7 30.0 1.0 CA T:CYS154 4.0 30.0 1.0 CA T:CYS136 4.0 30.0 1.0 CB T:ASN135 4.5 30.0 1.0 CA T:CYS133 4.6 30.0 1.0 CG C:GLU131 4.6 227.9 1.0 CA T:CYS151 4.6 30.0 1.0 C T:CYS136 4.6 30.0 1.0 CB T:ALA138 4.6 30.0 1.0 CB T:ARG153 4.7 30.0 1.0 C T:ASN135 4.7 30.0 1.0 C T:CYS154 4.7 30.0 1.0 N T:ARG155 4.8 30.0 1.0 CG C:ARG128 4.8 214.7 1.0 N T:GLN137 4.8 30.0 1.0 C T:ARG153 4.8 30.0 1.0 N T:ALA138 4.9 30.0 1.0 ND2 T:ASN135 4.9 30.0 1.0 CB T:MET156 4.9 30.0 1.0 CA T:ASN135 5.0 30.0 1.0 CE T:MET161 5.0 30.0 1.0

Zinc binding site 6 out of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:Zn202 b:30.0 occ:1.00 ND1 T:HIS125 2.1 30.0 1.0 SG T:CYS103 2.3 30.0 1.0 SG T:CYS122 2.3 30.0 1.0 SG T:CYS100 2.3 30.0 1.0 CE1 T:HIS125 3.0 30.0 1.0 CG T:HIS125 3.2 30.0 1.0 CB T:CYS100 3.3 30.0 1.0 CB T:CYS122 3.3 30.0 1.0 CB T:CYS103 3.4 30.0 1.0 N T:CYS103 3.5 30.0 1.0 CB T:HIS125 3.6 30.0 1.0 CA T:CYS103 3.9 30.0 1.0 NE2 T:HIS125 4.1 30.0 1.0 CD2 T:HIS125 4.3 30.0 1.0 N T:HIS125 4.4 30.0 1.0 C T:ALA102 4.4 30.0 1.0 CB T:ALA102 4.4 30.0 1.0 CA T:HIS125 4.7 30.0 1.0 CA T:CYS100 4.7 30.0 1.0 CA T:CYS122 4.7 30.0 1.0 CB T:ARG124 4.8 30.0 1.0 CA T:ALA102 4.9 30.0 1.0 O T:CYS100 5.0 30.0 1.0 C T:CYS100 5.0 30.0 1.0

M.Schmitz, I.Querques, S.Oberli, C.Chanez, M.Jinek. Structural Basis For the Assembly of the Type V Crispr-Associated Transposon Complex. Cell V. 185 4999 2022.
ISSN: ISSN 1097-4172
PubMed: 36435179
DOI: 10.1016/J.CELL.2022.11.009