Zinc in PDB 4ad9: Crystal Structure of Human LACTB2.

The structure of Crystal Structure of Human LACTB2., PDB code: 4ad9 was solved by C.K.Allerston, T.Krojer, B.Shrestha, N.Burgess Brown, R.Chalk, J.M.Elkins, P.Filippakopoulos, A.C.W.Pike, J.R.C.Muniz, M.Vollmar, C.H.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, F.Von Delft, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.85 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.470, 95.690, 135.760, 90.00, 112.84, 90.00
R / Rfree (%)	17.8 / 22.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Human LACTB2. (pdb code 4ad9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Human LACTB2., PDB code: 4ad9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Human LACTB2.


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 Human LACTB2. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:28.2 occ:1.00 OD2 A:ASP81 2.1 27.3 1.0 OD2 A:ASP164 2.1 29.1 1.0 NE2 A:HIS199 2.1 17.8 1.0 NE2 A:HIS82 2.3 18.8 1.0 O A:HOH2042 2.4 18.3 1.0 O A:HOH2083 2.5 13.3 1.0 CG A:ASP164 2.9 26.1 1.0 OD1 A:ASP164 3.0 27.3 1.0 CD2 A:HIS199 3.1 17.9 1.0 CD2 A:HIS82 3.1 19.5 1.0 CE1 A:HIS199 3.2 17.9 1.0 CG A:ASP81 3.2 27.9 1.0 CE1 A:HIS82 3.3 18.4 1.0 ZN A:ZN1001 3.6 30.1 1.0 OD1 A:ASP81 3.7 27.0 1.0 OE1 C:GLU118 3.9 54.6 1.0 OE2 C:GLU118 4.1 52.3 1.0 CG A:HIS199 4.2 17.1 1.0 ND1 A:HIS199 4.3 19.3 1.0 CG A:HIS82 4.3 18.2 1.0 NE2 A:HIS77 4.3 18.5 1.0 CB A:ASP164 4.3 21.8 1.0 CD C:GLU118 4.3 51.4 1.0 ND1 A:HIS82 4.4 19.8 1.0 CB A:ASP81 4.4 16.6 1.0 CE1 A:HIS77 4.4 18.0 1.0 O A:MET26 4.7 31.5 1.0 O A:HOH2162 4.9 19.4 1.0 CG2 A:THR27 4.9 16.3 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Human LACTB2.


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 Human LACTB2. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:30.1 occ:1.00 O A:HOH2083 2.0 13.3 1.0 NE2 A:HIS145 2.2 22.4 1.0 ND1 A:HIS79 2.2 18.5 1.0 OD2 A:ASP164 2.2 29.1 1.0 NE2 A:HIS77 2.3 18.5 1.0 OE2 C:GLU118 2.8 52.3 1.0 CE1 A:HIS145 3.1 22.4 1.0 CE1 A:HIS79 3.2 17.5 1.0 CD2 A:HIS77 3.2 19.6 1.0 CD2 A:HIS145 3.2 22.6 1.0 CG A:ASP164 3.2 26.1 1.0 CE1 A:HIS77 3.3 18.0 1.0 CG A:HIS79 3.3 17.9 1.0 CD C:GLU118 3.3 51.4 1.0 CB A:ASP164 3.5 21.8 1.0 ZN A:ZN1000 3.6 28.2 1.0 CB A:HIS79 3.7 15.5 1.0 OE1 C:GLU118 3.9 54.6 1.0 CG C:GLU118 3.9 38.9 1.0 ND1 A:HIS145 4.2 23.7 1.0 CG A:HIS145 4.3 22.3 1.0 CG A:HIS77 4.3 18.9 1.0 NE2 A:HIS79 4.3 18.4 1.0 OD1 A:ASP164 4.4 27.3 1.0 ND1 A:HIS77 4.4 19.6 1.0 NE2 A:HIS82 4.4 18.8 1.0 CD2 A:HIS79 4.4 19.1 1.0 CD2 A:HIS82 4.4 19.5 1.0 O A:HOH2042 4.5 18.3 1.0 OD1 A:ASP81 4.7 27.0 1.0 OD2 A:ASP81 4.7 27.3 1.0 O A:HOH2162 4.9 19.4 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Human LACTB2.


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 Human LACTB2. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1000 b:50.3 occ:1.00 OD2 B:ASP81 2.1 41.2 1.0 NE2 B:HIS199 2.2 47.1 1.0 OD2 B:ASP164 2.3 45.8 1.0 NE2 B:HIS82 2.3 37.3 1.0 O A:HOH2130 2.5 26.7 1.0 OD1 B:ASP164 2.9 44.2 1.0 CG B:ASP164 2.9 43.4 1.0 CD2 B:HIS82 3.0 36.5 1.0 CD2 B:HIS199 3.1 49.3 1.0 CG B:ASP81 3.2 36.8 1.0 CE1 B:HIS199 3.2 47.0 1.0 CE1 B:HIS82 3.5 37.8 1.0 ZN B:ZN1001 3.5 48.9 1.0 OD1 B:ASP81 3.7 39.1 1.0 OE1 A:GLU118 3.9 88.0 1.0 OE2 A:GLU118 4.1 74.9 1.0 CG B:HIS82 4.3 35.5 1.0 CG B:HIS199 4.3 49.1 1.0 NE2 B:HIS77 4.3 29.4 1.0 ND1 B:HIS199 4.4 49.6 1.0 CD A:GLU118 4.4 78.4 1.0 CB B:ASP164 4.4 39.5 1.0 CB B:ASP81 4.5 32.9 1.0 ND1 B:HIS82 4.5 38.0 1.0 CE1 B:HIS77 4.5 29.6 1.0 O A:HOH2131 4.7 44.0 1.0 O B:MET26 4.8 53.8 1.0 CG2 B:THR27 4.9 45.8 1.0 O A:HOH2128 5.0 42.8 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Human LACTB2.


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 Human LACTB2. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:48.9 occ:1.00 OD2 B:ASP164 2.1 45.8 1.0 O A:HOH2130 2.1 26.7 1.0 NE2 B:HIS145 2.2 41.1 1.0 ND1 B:HIS79 2.2 33.2 1.0 NE2 B:HIS77 2.3 29.4 1.0 OE2 A:GLU118 3.0 74.9 1.0 CE1 B:HIS145 3.0 41.9 1.0 CD2 B:HIS77 3.1 29.4 1.0 CE1 B:HIS79 3.1 32.8 1.0 CG B:ASP164 3.2 43.4 1.0 CG B:HIS79 3.2 31.7 1.0 CD2 B:HIS145 3.3 41.8 1.0 CD A:GLU118 3.3 78.4 1.0 CE1 B:HIS77 3.5 29.6 1.0 ZN B:ZN1000 3.5 50.3 1.0 CB B:ASP164 3.6 39.5 1.0 CB B:HIS79 3.6 29.1 1.0 OE1 A:GLU118 3.8 88.0 1.0 CG A:GLU118 3.9 57.0 1.0 ND1 B:HIS145 4.2 44.1 1.0 OD1 B:ASP164 4.3 44.2 1.0 NE2 B:HIS79 4.3 32.7 1.0 CG B:HIS77 4.3 29.6 1.0 CG B:HIS145 4.3 42.3 1.0 CD2 B:HIS79 4.4 32.5 1.0 CD2 B:HIS82 4.4 36.5 1.0 NE2 B:HIS82 4.4 37.3 1.0 ND1 B:HIS77 4.5 31.4 1.0 OD1 B:ASP81 4.6 39.1 1.0 OD2 B:ASP81 4.7 41.2 1.0 O A:HOH2131 4.9 44.0 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Human LACTB2.


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 Human LACTB2. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1000 b:39.7 occ:1.00 OD2 C:ASP164 2.0 24.8 1.0 NE2 C:HIS199 2.1 29.8 1.0 OD2 C:ASP81 2.1 39.8 1.0 NE2 C:HIS82 2.3 22.2 1.0 O B:HOH2064 2.5 30.1 1.0 CG C:ASP164 2.9 25.2 1.0 OD1 C:ASP164 3.0 27.7 1.0 CD2 C:HIS199 3.1 29.7 1.0 CD2 C:HIS82 3.1 22.8 1.0 CE1 C:HIS199 3.1 29.7 1.0 OE2 B:GLU118 3.1 58.4 1.0 CG C:ASP81 3.2 32.9 1.0 CE1 C:HIS82 3.5 21.5 1.0 ZN C:ZN1001 3.6 31.0 1.0 OD1 C:ASP81 3.7 37.7 1.0 O B:HOH2061 4.2 31.1 1.0 CG C:HIS199 4.2 28.2 1.0 ND1 C:HIS199 4.2 31.0 1.0 CD B:GLU118 4.3 54.5 1.0 CB C:ASP164 4.3 22.5 1.0 CG C:HIS82 4.3 21.9 1.0 CB C:ASP81 4.5 19.4 1.0 ND1 C:HIS82 4.5 22.6 1.0 O C:MET26 4.5 32.7 1.0 NE2 C:HIS77 4.5 14.7 1.0 CG2 C:THR27 4.6 25.3 1.0 OE1 B:GLU118 4.7 76.1 1.0 CE1 C:HIS77 4.7 14.7 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Human LACTB2.


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 Human LACTB2. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:31.0 occ:1.00 O B:HOH2064 1.9 30.1 1.0 ND1 C:HIS79 2.2 19.7 1.0 NE2 C:HIS145 2.2 18.4 1.0 NE2 C:HIS77 2.3 14.7 1.0 OD2 C:ASP164 2.4 24.8 1.0 OE2 B:GLU118 2.7 58.4 1.0 CE1 C:HIS79 3.1 18.6 1.0 CD2 C:HIS77 3.2 15.2 1.0 CE1 C:HIS145 3.2 18.1 1.0 CD2 C:HIS145 3.2 19.5 1.0 CG C:HIS79 3.3 17.4 1.0 CG C:ASP164 3.3 25.2 1.0 CD B:GLU118 3.3 54.5 1.0 CE1 C:HIS77 3.4 14.7 1.0 CB C:ASP164 3.5 22.5 1.0 ZN C:ZN1000 3.6 39.7 1.0 CB C:HIS79 3.6 14.0 1.0 CG B:GLU118 3.8 36.9 1.0 OE1 B:GLU118 4.0 76.1 1.0 CD2 C:HIS82 4.2 22.8 1.0 NE2 C:HIS82 4.2 22.2 1.0 NE2 C:HIS79 4.3 19.4 1.0 CG C:HIS145 4.3 18.5 1.0 ND1 C:HIS145 4.3 20.1 1.0 CG C:HIS77 4.3 15.0 1.0 CD2 C:HIS79 4.4 19.5 1.0 OD1 C:ASP164 4.4 27.7 1.0 ND1 C:HIS77 4.4 16.5 1.0 OD1 C:ASP81 4.6 37.7 1.0 OD2 C:ASP81 4.7 39.8 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Human LACTB2.


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 Human LACTB2. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1000 b:37.6 occ:1.00 OD2 D:ASP164 2.1 36.8 1.0 OD2 D:ASP81 2.1 24.7 1.0 NE2 D:HIS199 2.2 24.7 1.0 NE2 D:HIS82 2.3 21.3 1.0 O D:HOH2031 2.4 28.1 1.0 O D:HOH2060 2.5 29.4 1.0 CG D:ASP164 2.9 29.7 1.0 OD1 D:ASP164 3.0 26.0 1.0 CD2 D:HIS199 3.1 24.8 1.0 CD2 D:HIS82 3.2 21.9 1.0 CG D:ASP81 3.2 28.0 1.0 CE1 D:HIS199 3.2 25.2 1.0 CE1 D:HIS82 3.3 21.8 1.0 ZN D:ZN1001 3.5 31.6 1.0 OD1 D:ASP81 3.7 28.4 1.0 OE2 F:GLU118 3.8 50.0 1.0 OE1 F:GLU118 3.9 72.0 1.0 CG D:HIS199 4.2 23.9 1.0 CD F:GLU118 4.2 53.7 1.0 CB D:ASP164 4.3 25.8 1.0 ND1 D:HIS199 4.3 26.7 1.0 CG D:HIS82 4.3 21.2 1.0 NE2 D:HIS77 4.4 19.8 1.0 ND1 D:HIS82 4.4 23.5 1.0 CB D:ASP81 4.5 22.4 1.0 CE1 D:HIS77 4.6 20.2 1.0 O D:MET26 4.7 33.5 1.0 O D:HOH2122 4.7 21.4 1.0 CG2 D:THR27 4.9 20.8 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Human LACTB2.


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 Human LACTB2. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:31.6 occ:1.00 O D:HOH2060 1.9 29.4 1.0 NE2 D:HIS145 2.1 21.6 1.0 ND1 D:HIS79 2.2 20.4 1.0 OD2 D:ASP164 2.3 36.8 1.0 NE2 D:HIS77 2.3 19.8 1.0 OE2 F:GLU118 2.7 50.0 1.0 CE1 D:HIS145 3.0 21.3 1.0 CE1 D:HIS79 3.1 19.0 1.0 CD2 D:HIS77 3.2 20.8 1.0 CD2 D:HIS145 3.2 22.2 1.0 CG D:ASP164 3.2 29.7 1.0 CG D:HIS79 3.3 18.7 1.0 CD F:GLU118 3.4 53.7 1.0 CE1 D:HIS77 3.4 20.2 1.0 CB D:ASP164 3.5 25.8 1.0 ZN D:ZN1000 3.5 37.6 1.0 CB D:HIS79 3.7 14.9 1.0 CG F:GLU118 4.0 32.0 1.0 OE1 F:GLU118 4.0 72.0 1.0 ND1 D:HIS145 4.2 22.5 1.0 NE2 D:HIS82 4.2 21.3 1.0 CG D:HIS145 4.3 21.4 1.0 NE2 D:HIS79 4.3 19.8 1.0 CD2 D:HIS82 4.3 21.9 1.0 CG D:HIS77 4.3 21.3 1.0 O D:HOH2031 4.4 28.1 1.0 OD1 D:ASP164 4.4 26.0 1.0 CD2 D:HIS79 4.4 20.2 1.0 ND1 D:HIS77 4.4 22.3 1.0 OD1 D:ASP81 4.6 28.4 1.0 OD2 D:ASP81 4.7 24.7 1.0 O D:HOH2122 4.8 21.4 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Human LACTB2.


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 Human LACTB2. within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1000 b:55.0 occ:1.00 NE2 E:HIS199 2.1 38.8 1.0 OD2 E:ASP164 2.1 47.6 1.0 OD2 E:ASP81 2.1 48.6 1.0 O D:HOH2099 2.2 38.1 1.0 NE2 E:HIS82 2.3 37.9 1.0 O D:HOH2098 2.4 44.6 1.0 CG E:ASP164 2.9 49.5 1.0 CD2 E:HIS199 3.0 41.2 1.0 OD1 E:ASP164 3.0 51.4 1.0 CD2 E:HIS82 3.0 36.8 1.0 CE1 E:HIS199 3.1 39.1 1.0 CG E:ASP81 3.2 45.2 1.0 CE1 E:HIS82 3.4 38.3 1.0 ZN E:ZN1001 3.6 54.4 1.0 OD1 E:ASP81 3.7 49.0 1.0 OE1 D:GLU118 3.9 0.3 1.0 CG E:HIS199 4.1 42.1 1.0 ND1 E:HIS199 4.2 42.1 1.0 CG E:HIS82 4.3 35.9 1.0 CB E:ASP164 4.3 46.7 1.0 OE2 D:GLU118 4.3 95.8 1.0 NE2 E:HIS77 4.3 35.8 1.0 CD D:GLU118 4.4 98.2 1.0 CB E:ASP81 4.4 33.5 1.0 ND1 E:HIS82 4.4 38.5 1.0 CE1 E:HIS77 4.6 35.9 1.0 O E:MET26 4.8 56.0 1.0 CG2 E:THR27 4.9 42.1 1.0 O D:HOH2096 4.9 47.9 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Human LACTB2.


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 Human LACTB2. within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1001 b:54.4 occ:1.00 NE2 E:HIS145 2.1 43.3 1.0 ND1 E:HIS79 2.2 38.6 1.0 O D:HOH2099 2.2 38.1 1.0 OD2 E:ASP164 2.3 47.6 1.0 NE2 E:HIS77 2.4 35.8 1.0 CE1 E:HIS145 2.9 44.5 1.0 CE1 E:HIS79 3.1 38.4 1.0 CD2 E:HIS77 3.1 36.0 1.0 OE2 D:GLU118 3.2 95.8 1.0 CG E:ASP164 3.3 49.5 1.0 CG E:HIS79 3.3 36.1 1.0 CD2 E:HIS145 3.3 43.4 1.0 CD D:GLU118 3.3 98.2 1.0 CB E:ASP164 3.5 46.7 1.0 CE1 E:HIS77 3.5 35.9 1.0 ZN E:ZN1000 3.6 55.0 1.0 CB E:HIS79 3.6 33.2 1.0 CG D:GLU118 3.8 68.5 1.0 OE1 D:GLU118 3.8 0.3 1.0 ND1 E:HIS145 4.2 46.1 1.0 O D:HOH2098 4.2 44.6 1.0 NE2 E:HIS79 4.3 37.7 1.0 CG E:HIS145 4.3 43.6 1.0 CD2 E:HIS79 4.4 37.1 1.0 CG E:HIS77 4.4 34.5 1.0 NE2 E:HIS82 4.4 37.9 1.0 CD2 E:HIS82 4.4 36.8 1.0 OD1 E:ASP164 4.4 51.4 1.0 ND1 E:HIS77 4.6 36.5 1.0 OD1 E:ASP81 4.6 49.0 1.0 OD2 E:ASP81 4.7 48.6 1.0

C.K.Allerston, O.Gileadi, S.Levy, V.Liveanu, M.Rohana, G.Schuster. Identification of LACTB2, A Metallo-Beta-Lactamase Protein, As A Human Mitochondrial Endoribonuclease Nucleic Acids Res. V. 44 1813 2016.
ISSN: ISSN 0305-1048
PubMed: 26826708
DOI: 10.1093/NAR/GKW050