Zinc in PDB 5yi0: Structure of Lactococcus Lactis Zitr, C30AH42A Mutant

The structure of Structure of Lactococcus Lactis Zitr, C30AH42A Mutant, PDB code: 5yi0 was solved by Y.Song, H.Liu, R.Zhu, C.Yi, P.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.55 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.038, 86.864, 126.783, 90.00, 90.69, 90.00
R / Rfree (%)	25.1 / 30.1

The binding sites of Zinc atom in the Structure of Lactococcus Lactis Zitr, C30AH42A Mutant (pdb code 5yi0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Lactococcus Lactis Zitr, C30AH42A Mutant, PDB code: 5yi0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Lactococcus Lactis Zitr, C30AH42A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Lactococcus Lactis Zitr, C30AH42A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:60.3 occ:1.00 NE2 B:HIS112 1.9 65.5 1.0 NE2 B:HIS108 2.0 63.6 1.0 OE2 B:GLU24 2.1 54.7 1.0 OE1 B:GLU41 2.1 66.8 1.0 OE1 B:GLU24 2.5 54.0 1.0 CD B:GLU24 2.6 64.1 1.0 CD B:GLU41 2.8 59.1 1.0 CE1 B:HIS112 2.8 63.8 1.0 OE2 B:GLU41 2.9 63.9 1.0 CE1 B:HIS108 2.9 65.3 1.0 CD2 B:HIS108 3.0 60.0 1.0 CD2 B:HIS112 3.0 61.7 1.0 ND1 B:HIS112 4.0 58.3 1.0 ND1 B:HIS108 4.0 64.8 1.0 CG B:HIS112 4.1 60.2 1.0 CG B:GLU24 4.1 64.7 1.0 CG B:HIS108 4.1 66.2 1.0 CG B:GLU41 4.3 58.3 1.0 CD1 B:LEU26 4.6 64.0 1.0 CB B:GLU24 4.8 66.5 1.0

Zinc binding site 2 out of 4 in the Structure of Lactococcus Lactis Zitr, C30AH42A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Lactococcus Lactis Zitr, C30AH42A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:61.6 occ:1.00 NE2 A:HIS112 2.0 68.1 1.0 NE2 A:HIS108 2.0 64.7 1.0 OE2 A:GLU24 2.0 57.0 1.0 OE1 A:GLU41 2.2 68.1 1.0 OE1 A:GLU24 2.3 61.0 1.0 CD A:GLU24 2.5 66.6 1.0 OE2 A:GLU41 2.8 61.7 1.0 CD A:GLU41 2.8 59.8 1.0 CE1 A:HIS112 2.8 61.0 1.0 CE1 A:HIS108 2.9 66.3 1.0 CD2 A:HIS108 3.1 63.6 1.0 CD2 A:HIS112 3.1 61.0 1.0 O A:HOH302 3.9 63.4 1.0 CG A:GLU24 4.0 65.0 1.0 ND1 A:HIS112 4.0 59.5 1.0 ND1 A:HIS108 4.0 65.5 1.0 CG A:HIS108 4.1 68.4 1.0 CG A:HIS112 4.2 61.2 1.0 CG A:GLU41 4.2 63.2 1.0 CD1 A:LEU26 4.4 64.5 1.0 O A:HOH317 4.6 63.4 1.0 CB A:GLU24 4.8 66.2 1.0

Zinc binding site 3 out of 4 in the Structure of Lactococcus Lactis Zitr, C30AH42A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Lactococcus Lactis Zitr, C30AH42A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:60.9 occ:1.00 NE2 C:HIS112 1.9 67.8 1.0 NE2 C:HIS108 2.1 64.9 1.0 OE1 C:GLU41 2.2 66.7 1.0 OE2 C:GLU24 2.2 59.7 1.0 OE1 C:GLU24 2.4 65.0 1.0 CD C:GLU24 2.6 69.2 1.0 CE1 C:HIS112 2.8 61.7 1.0 CD C:GLU41 2.9 58.8 1.0 OE2 C:GLU41 2.9 63.9 1.0 CE1 C:HIS108 3.0 64.1 1.0 CD2 C:HIS108 3.0 61.2 1.0 CD2 C:HIS112 3.1 63.3 1.0 ND1 C:HIS112 4.0 59.7 1.0 CG C:GLU24 4.1 68.3 1.0 CG C:HIS112 4.1 60.8 1.0 ND1 C:HIS108 4.1 61.6 1.0 O C:HOH307 4.2 63.3 1.0 CG C:HIS108 4.2 65.5 1.0 CG C:GLU41 4.3 58.3 1.0 CD1 C:LEU26 4.6 63.4 1.0 CB C:GLU24 4.8 67.4 1.0

Zinc binding site 4 out of 4 in the Structure of Lactococcus Lactis Zitr, C30AH42A Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Lactococcus Lactis Zitr, C30AH42A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:60.7 occ:1.00 NE2 D:HIS108 2.0 67.9 1.0 NE2 D:HIS112 2.0 65.4 1.0 OE2 D:GLU24 2.1 57.8 1.0 OE1 D:GLU41 2.1 65.9 1.0 OE1 D:GLU24 2.4 60.6 1.0 CD D:GLU24 2.6 66.0 1.0 CD D:GLU41 2.8 59.2 1.0 OE2 D:GLU41 2.8 62.5 1.0 CE1 D:HIS108 2.9 67.9 1.0 CD2 D:HIS112 3.0 64.8 1.0 CD2 D:HIS108 3.0 63.0 1.0 CE1 D:HIS112 3.1 61.2 1.0 ND1 D:HIS108 4.0 63.0 1.0 CG D:GLU24 4.1 65.1 1.0 O D:HOH318 4.1 61.6 1.0 CG D:HIS108 4.1 66.3 1.0 ND1 D:HIS112 4.1 60.0 1.0 CG D:HIS112 4.2 59.7 1.0 CG D:GLU41 4.3 60.1 1.0 CD1 D:LEU26 4.3 66.6 1.0 CB D:GLU24 4.8 65.9 1.0

Y.Song, H.Liu, R.Zhu, C.Yi, P.Chen. Structure of Lactococcus Lactis Zitr Proc.Natl.Acad.Sci.Usa 2017.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1708563115