Zinc in PDB 8zay: Crystal Structure of Fab

The structure of Crystal Structure of Fab, PDB code: 8zay was solved by Y.Adachi, T.Nogi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.91 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.78, 70.44, 132.46, 90, 96.69, 90
R / Rfree (%)	21.8 / 26.9

The binding sites of Zinc atom in the Crystal Structure of Fab (pdb code 8zay). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Fab, PDB code: 8zay:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:63.8 occ:1.00 OD2 L:ASP167 2.1 50.1 1.0 NE2 H:HIS175 2.3 29.8 1.0 CG L:ASP167 3.0 38.9 1.0 CE1 H:HIS175 3.1 30.9 1.0 CD2 H:HIS175 3.3 25.6 1.0 OD1 L:ASP167 3.5 35.3 1.0 OD1 L:ASN138 3.9 31.5 1.0 OD2 L:ASP170 4.0 41.7 1.0 CB L:ASP167 4.2 30.3 1.0 ND1 H:HIS175 4.2 22.9 1.0 O L:HOH444 4.3 25.3 1.0 CG H:HIS175 4.4 19.9 1.0 OD1 L:ASP170 4.6 28.9 1.0 CG L:ASP170 4.6 31.3 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn302 b:25.8 occ:1.00 NE2 L:HIS55 2.3 24.5 1.0 OD2 H:ASP112 2.4 23.1 1.0 O H:HOH456 2.5 5.0 1.0 O L:HOH465 2.5 19.7 1.0 CE1 L:HIS55 3.2 22.5 1.0 CD2 L:HIS55 3.3 27.1 1.0 CG H:ASP112 3.3 25.3 1.0 NH1 H:ARG104 3.3 33.4 1.0 CB H:ASP112 3.5 20.9 1.0 NH2 H:ARG102 4.1 26.5 1.0 CE2 H:TYR113 4.2 38.5 1.0 ND1 L:HIS55 4.4 22.2 1.0 CG L:HIS55 4.4 24.6 1.0 CG H:ARG104 4.5 25.9 1.0 CZ H:ARG104 4.5 32.9 1.0 OD1 H:ASP112 4.5 36.0 1.0 CD2 H:TYR113 4.6 33.1 1.0 CG2 L:THR56 4.8 31.3 1.0 CA H:ASP112 4.8 21.2 1.0 O H:ASP112 4.9 20.8 1.0 CD H:ARG104 5.0 25.4 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Fab within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn301 b:22.5 occ:1.00 NE2 M:HIS55 2.3 17.9 1.0 OD2 I:ASP112 2.3 22.5 1.0 O I:HOH435 2.5 5.2 1.0 CE1 M:HIS55 3.3 20.2 1.0 CD2 M:HIS55 3.3 21.6 1.0 CG I:ASP112 3.3 23.5 1.0 NH1 I:ARG104 3.3 26.3 1.0 CB I:ASP112 3.5 19.8 1.0 NH2 I:ARG102 4.0 20.7 1.0 CE2 I:TYR113 4.1 29.1 1.0 CZ I:ARG104 4.3 24.2 1.0 ND1 M:HIS55 4.4 15.1 1.0 CG M:HIS55 4.4 20.7 1.0 CG I:ARG104 4.4 21.1 1.0 OD1 I:ASP112 4.4 24.3 1.0 CD2 I:TYR113 4.5 21.8 1.0 CG2 M:THR56 4.6 24.8 1.0 O I:ASP112 4.9 19.5 1.0 CA I:ASP112 4.9 18.7 1.0 CZ I:TYR113 4.9 24.6 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Fab within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn302 b:58.8 occ:1.00 OD2 M:ASP167 2.1 57.3 1.0 NE2 I:HIS175 2.3 33.0 1.0 O M:HOH413 2.4 47.8 1.0 O M:HOH454 2.6 48.2 1.0 CG M:ASP167 2.9 43.9 1.0 CE1 I:HIS175 3.3 31.2 1.0 CD2 I:HIS175 3.3 29.4 1.0 OD1 M:ASP167 3.4 40.6 1.0 CE M:LYS169 3.5 52.4 1.0 OD1 M:ASN138 3.7 44.2 1.0 NZ M:LYS169 3.9 45.6 1.0 CB M:ASP167 4.0 41.6 1.0 O M:HOH444 4.2 32.8 1.0 OD2 M:ASP170 4.3 45.5 1.0 OD1 M:ASP170 4.3 42.1 1.0 ND1 I:HIS175 4.4 29.9 1.0 CG I:HIS175 4.4 26.9 1.0 CG M:ASP170 4.7 41.2 1.0 CD M:LYS169 4.8 44.1 1.0 CG M:ASN138 4.8 40.6 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:34.3 occ:1.00 OD2 L:ASP32 2.0 24.8 1.0 O L:HOH427 2.3 39.5 1.0 O L:HOH446 2.3 26.6 1.0 O L:HOH463 2.4 32.5 1.0 CG L:ASP32 3.1 23.8 1.0 OD1 L:ASP32 3.7 23.1 1.0 O L:TYR91 4.3 20.6 1.0 CB L:ASP32 4.3 18.7 1.0 CA L:SER92 4.6 17.9 1.0 O L:SER92 4.8 26.0 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn302 b:17.7 occ:1.00 OE1 L:GLU185 2.2 23.9 1.0 NE2 L:HIS189 2.3 12.3 1.0 OE2 L:GLU185 2.8 21.0 1.0 CD L:GLU185 2.8 16.1 1.0 CD2 L:HIS189 3.2 15.6 1.0 CE1 L:HIS189 3.3 17.6 1.0 CG L:GLU185 4.3 15.6 1.0 ND1 L:HIS189 4.4 13.8 1.0 CG L:HIS189 4.4 16.0 1.0 NH2 L:ARG155 4.4 15.6 1.0 O L:GLU185 4.5 15.1 1.0 CB L:ARG188 4.6 14.4 1.0 CB L:GLU185 4.9 16.3 1.0 CD L:ARG188 5.0 24.4 1.0 CA L:GLU185 5.0 14.5 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn303 b:58.0 occ:1.00 O M:HOH460 2.2 47.0 1.0 NE2 M:HIS8 2.3 36.9 1.0 OE1 L:GLU105 2.7 41.7 1.0 CE1 M:HIS8 2.9 33.7 1.0 CE L:LYS142 3.2 43.3 1.0 CD L:GLU105 3.5 43.6 1.0 OE2 L:GLU105 3.5 46.7 1.0 CD2 M:HIS8 3.5 31.8 1.0 CD L:LYS142 3.6 43.7 1.0 NZ L:LYS142 4.0 46.3 1.0 ND1 M:HIS8 4.1 33.0 1.0 CG L:PHE10 4.2 30.5 1.0 CB L:PHE10 4.3 24.5 1.0 CG L:LYS142 4.4 34.5 1.0 CG M:HIS8 4.5 28.6 1.0 CD1 L:PHE10 4.5 23.6 1.0 CD2 L:PHE10 4.6 27.5 1.0 O M:HOH459 4.9 32.5 1.0 CG L:GLU105 4.9 39.9 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Fab within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn301 b:45.3 occ:1.00 NZ M:LYS142 2.1 42.8 1.0 O L:HOH461 2.1 40.3 1.0 OE2 M:GLU105 2.2 42.6 1.0 NE2 L:HIS8 2.3 28.9 1.0 CE M:LYS142 2.8 43.8 1.0 CD M:GLU105 3.1 40.2 1.0 OE1 M:GLU105 3.2 42.3 1.0 CE1 L:HIS8 3.2 28.0 1.0 CD2 L:HIS8 3.3 23.7 1.0 CG M:PHE10 4.2 21.9 1.0 CB M:PHE10 4.2 18.8 1.0 CD M:LYS142 4.2 45.1 1.0 ND1 L:HIS8 4.4 27.1 1.0 CD1 M:PHE10 4.4 20.3 1.0 CG L:HIS8 4.4 25.6 1.0 CG M:GLU105 4.5 31.0 1.0 CD2 M:PHE10 4.6 20.4 1.0 O M:HOH405 4.6 27.2 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Fab within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn302 b:23.5 occ:1.00 NE2 M:HIS189 2.3 11.6 1.0 OE1 M:GLU185 2.3 23.7 1.0 OE2 M:GLU185 2.8 23.2 1.0 CD M:GLU185 2.9 21.6 1.0 CD2 M:HIS189 3.1 18.1 1.0 CE1 M:HIS189 3.4 25.2 1.0 CG M:HIS189 4.3 17.4 1.0 CG M:GLU185 4.4 17.2 1.0 NH2 M:ARG155 4.4 23.5 1.0 ND1 M:HIS189 4.4 21.2 1.0 CB M:ARG188 4.6 21.2 1.0 O M:GLU185 4.6 24.6 1.0 CD M:ARG188 5.0 28.7 1.0 CB M:GLU185 5.0 18.9 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Fab within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn303 b:32.9 occ:1.00 OD2 M:ASP32 2.0 26.8 1.0 O M:HOH446 2.1 24.3 1.0 O M:HOH430 2.3 30.4 1.0 O M:HOH436 2.4 28.8 1.0 CG M:ASP32 3.2 26.8 1.0 OD1 M:ASP32 3.7 26.4 1.0 O M:HOH403 3.9 29.6 1.0 O M:TYR91 4.3 15.2 1.0 CB M:ASP32 4.4 20.4 1.0 CA M:SER92 4.7 18.6 1.0 O M:SER92 4.8 23.4 1.0

K.Asahi, M.Hirose, R.Aruga, Y.Shimizu, M.Tajiri, T.Tanaka, Y.Adachi, Y.Tanaka, M.K.Kaneko, Y.Kato, S.Akashi, Y.Akiyama, Y.Hizukuri, T.Kato, T.Nogi. Cryo-Em Structure of the Bacterial Intramembrane Metalloprotease Rsep in the Substrate-Bound State. Sci Adv 2025.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ADU0925