Zinc in PDB 8edg: Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon

The binding sites of Zinc atom in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon (pdb code 8edg). 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 the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon, PDB code: 8edg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon


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 Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:236.4 occ:1.00 CB A:CYS54 1.5 149.7 1.0 NE2 A:HIS71 2.1 132.9 1.0 SG A:CYS73 2.3 166.3 1.0 SG A:CYS51 2.3 140.5 1.0 SG A:CYS54 2.3 149.7 1.0 CA A:CYS54 2.8 149.7 1.0 CD2 A:HIS71 2.8 132.9 1.0 CB A:CYS73 2.9 166.3 1.0 N A:CYS54 3.2 149.7 1.0 CE1 A:HIS71 3.2 132.9 1.0 CB A:CYS51 3.6 140.5 1.0 C A:CYS54 4.0 149.7 1.0 CG A:HIS71 4.1 132.9 1.0 CA A:CYS73 4.1 166.3 1.0 ND1 A:HIS71 4.2 132.9 1.0 C A:LYS53 4.2 137.3 1.0 N A:CYS73 4.2 166.3 1.0 CE A:LYS72 4.3 144.4 1.0 O A:CYS54 4.5 149.7 1.0 NZ A:LYS72 4.6 144.4 1.0 N A:GLU55 4.8 134.5 1.0 O A:LYS53 4.8 137.3 1.0 CD A:LYS72 4.8 144.4 1.0 CA A:CYS51 5.0 140.5 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon


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 Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:289.9 occ:1.00 CB C:CYS73 2.0 186.2 1.0 NE2 C:HIS71 2.1 174.4 1.0 SG C:CYS51 2.3 176.1 1.0 SG C:CYS54 2.3 183.9 1.0 SG C:CYS73 2.3 186.2 1.0 CD2 C:HIS71 3.0 174.4 1.0 CE1 C:HIS71 3.1 174.4 1.0 CA C:CYS73 3.5 186.2 1.0 CB C:CYS51 3.6 176.1 1.0 CB C:CYS54 3.9 183.9 1.0 N C:CYS54 4.0 183.9 1.0 N C:CYS73 4.1 186.2 1.0 CG C:HIS71 4.2 174.4 1.0 ND1 C:HIS71 4.2 174.4 1.0 C C:CYS73 4.3 186.2 1.0 CA C:CYS54 4.6 183.9 1.0 CB C:LYS53 4.7 168.7 1.0 O C:CYS73 4.8 186.2 1.0 N C:LYS53 4.9 168.7 1.0 N C:CYS74 4.9 160.8 1.0 CA C:CYS51 5.0 176.1 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon


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 Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn701 b:289.4 occ:1.00 NE2 I:HIS71 2.1 159.2 1.0 SG I:CYS54 2.3 166.9 1.0 SG I:CYS51 2.3 157.6 1.0 SG I:CYS73 2.3 176.8 1.0 CD2 I:HIS71 2.7 159.2 1.0 CB I:CYS73 2.8 176.8 1.0 CB I:CYS51 3.1 157.6 1.0 CB I:CYS54 3.2 166.9 1.0 CE1 I:HIS71 3.3 159.2 1.0 N I:CYS54 3.5 166.9 1.0 CA I:CYS54 3.9 166.9 1.0 CG I:HIS71 4.0 159.2 1.0 CA I:CYS73 4.1 176.8 1.0 ND1 I:HIS71 4.2 159.2 1.0 N I:CYS73 4.3 176.8 1.0 N I:LYS53 4.4 146.4 1.0 C I:LYS53 4.4 146.4 1.0 CA I:CYS51 4.6 157.6 1.0 CB I:LYS53 4.6 146.4 1.0 CA I:LYS53 4.7 146.4 1.0 N I:GLU55 4.7 157.2 1.0 C I:CYS54 4.8 166.9 1.0 N I:ARG52 4.8 156.1 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon


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 Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn701 b:236.0 occ:1.00 NE2 E:HIS71 2.1 140.9 1.0 SG E:CYS54 2.3 169.5 1.0 SG E:CYS73 2.3 153.2 1.0 SG E:CYS51 2.3 162.3 1.0 CD2 E:HIS71 2.5 140.9 1.0 CB E:CYS54 2.8 169.5 1.0 CB E:CYS73 2.9 153.2 1.0 CB E:CYS51 3.0 162.3 1.0 CE1 E:HIS71 3.3 140.9 1.0 N E:CYS54 3.5 169.5 1.0 CA E:CYS54 3.7 169.5 1.0 CG E:HIS71 3.8 140.9 1.0 ND1 E:HIS71 4.2 140.9 1.0 CA E:CYS73 4.2 153.2 1.0 N E:CYS73 4.3 153.2 1.0 CA E:CYS51 4.5 162.3 1.0 C E:CYS54 4.6 169.5 1.0 C E:LYS53 4.6 159.1 1.0 N E:GLU55 4.7 159.2 1.0 N E:LYS53 4.8 159.1 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon


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 the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn701 b:236.6 occ:1.00 NE2 G:HIS71 2.1 103.8 1.0 SG G:CYS73 2.3 124.0 1.0 SG G:CYS54 2.3 158.5 1.0 SG G:CYS51 2.3 147.5 1.0 CD2 G:HIS71 2.6 103.8 1.0 CB G:CYS54 2.8 158.5 1.0 CB G:CYS51 3.0 147.5 1.0 CB G:CYS73 3.1 124.0 1.0 N G:CYS54 3.2 158.5 1.0 CE1 G:HIS71 3.3 103.8 1.0 CA G:CYS54 3.5 158.5 1.0 CG G:HIS71 3.9 103.8 1.0 ND1 G:HIS71 4.2 103.8 1.0 C G:LYS53 4.3 145.7 1.0 CB G:LYS53 4.4 145.7 1.0 CA G:CYS73 4.4 124.0 1.0 CA G:CYS51 4.5 147.5 1.0 C G:CYS54 4.5 158.5 1.0 N G:CYS73 4.5 124.0 1.0 N G:LYS53 4.6 145.7 1.0 CA G:LYS53 4.6 145.7 1.0 N G:GLU55 4.7 142.2 1.0 C G:CYS51 4.9 147.5 1.0 CD1 G:LEU34 5.0 111.6 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon


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 the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn701 b:254.6 occ:1.00 NE2 K:HIS71 2.1 151.5 1.0 SG K:CYS54 2.3 165.2 1.0 SG K:CYS73 2.3 156.7 1.0 SG K:CYS51 2.3 176.2 1.0 CD2 K:HIS71 2.9 151.5 1.0 CE1 K:HIS71 3.1 151.5 1.0 CB K:CYS51 3.2 176.2 1.0 CG K:LYS56 3.8 164.7 1.0 CB K:CYS54 3.8 165.2 1.0 CG K:HIS71 4.1 151.5 1.0 CB K:CYS73 4.1 156.7 1.0 ND1 K:HIS71 4.1 151.5 1.0 CD K:LYS56 4.1 164.7 1.0 CE K:LYS56 4.4 164.7 1.0 CA K:CYS51 4.6 176.2 1.0 CA K:CYS54 4.8 165.2 1.0 N K:CYS54 4.8 165.2 1.0 N K:CYS73 4.9 156.7 1.0 CG K:LYS72 4.9 149.3 1.0

L.Lannes, C.M.Furman, A.B.Hickman, F.Dyda. Zinc-Finger Bed Domains Drive the Formation of the Active Hermes Transpososome By Asymmetric Dna Binding. Nat Commun V. 14 4470 2023.
ISSN: ESSN 2041-1723
PubMed: 37491363
DOI: 10.1038/S41467-023-40210-3