Zinc in PDB 8v24: Lapb Cytoplasmic Domain in Complex with Lpxc

The binding sites of Zinc atom in the Lapb Cytoplasmic Domain in Complex with Lpxc (pdb code 8v24). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Lapb Cytoplasmic Domain in Complex with Lpxc, PDB code: 8v24:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Lapb Cytoplasmic Domain in Complex with Lpxc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lapb Cytoplasmic Domain in Complex with Lpxc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:74.2 occ:1.00 HG A:CYS357 1.2 66.2 1.0 HG A:CYS360 2.2 63.3 1.0 SG A:CYS371 2.3 60.8 1.0 SG A:CYS357 2.3 66.2 1.0 SG A:CYS360 2.3 63.3 1.0 SG A:CYS374 2.3 62.5 1.0 HG A:CYS374 2.5 62.5 1.0 H A:CYS374 3.0 62.5 1.0 HG A:CYS371 3.2 60.8 1.0 HB3 A:CYS371 3.2 60.8 1.0 HB3 A:CYS357 3.2 66.2 1.0 CB A:CYS357 3.3 66.2 1.0 CB A:CYS371 3.3 60.8 1.0 HB2 A:CYS357 3.4 66.2 1.0 HB3 A:CYS374 3.5 62.5 1.0 HB2 A:CYS371 3.6 60.8 1.0 CB A:CYS374 3.6 62.5 1.0 HB3 A:CYS360 3.6 63.3 1.0 CB A:CYS360 3.6 63.3 1.0 HB2 A:SER373 3.7 60.1 1.0 H A:CYS360 3.7 63.3 1.0 N A:CYS374 3.8 62.5 1.0 HB3 A:PHE362 3.9 63.0 1.0 HG1 A:THR379 3.9 65.4 1.0 HB3 A:LYS359 4.0 65.2 1.0 HB2 A:PHE362 4.1 63.0 1.0 N A:CYS360 4.1 63.3 1.0 H A:PHE362 4.2 63.0 1.0 CA A:CYS374 4.3 62.5 1.0 HB2 A:CYS374 4.3 62.5 1.0 HB2 A:CYS360 4.4 63.3 1.0 H A:LYS359 4.4 65.2 1.0 H A:SER373 4.4 60.1 1.0 CA A:CYS360 4.4 63.3 1.0 CB A:SER373 4.5 60.1 1.0 CB A:PHE362 4.5 63.0 1.0 HB3 A:SER373 4.5 60.1 1.0 HB2 A:ALA376 4.5 60.0 1.0 OG1 A:THR379 4.6 65.4 1.0 HB A:THR379 4.6 65.4 1.0 HG13 A:ILE380 4.7 65.5 1.0 CA A:CYS371 4.7 60.8 1.0 CA A:CYS357 4.7 66.2 1.0 HB2 A:LYS359 4.7 65.2 1.0 H A:ALA376 4.7 60.0 1.0 CB A:LYS359 4.7 65.2 1.0 H A:ARG375 4.8 60.1 1.0 C A:LYS359 4.8 65.2 1.0 C A:SER373 4.9 60.1 1.0 N A:SER373 4.9 60.1 1.0 HD12 A:ILE380 5.0 65.5 1.0 C A:CYS371 5.0 60.8 1.0 C A:CYS360 5.0 63.3 1.0

Zinc binding site 2 out of 4 in the Lapb Cytoplasmic Domain in Complex with Lpxc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lapb Cytoplasmic Domain in Complex with Lpxc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:68.8 occ:1.00 OXT B:ACT402 1.9 57.4 1.0 OD1 B:ASP242 1.9 56.1 1.0 OD2 B:ASP242 2.0 56.1 1.0 CG B:ASP242 2.2 56.1 1.0 NE2 B:HIS238 2.3 53.0 1.0 NE2 B:HIS79 2.3 52.1 1.0 HE1 B:HIS238 2.7 53.0 1.0 CE1 B:HIS238 2.8 53.0 1.0 C B:ACT402 3.1 57.4 1.0 CD2 B:HIS79 3.2 52.1 1.0 HG3 B:GLU78 3.3 58.2 1.0 HD2 B:HIS79 3.3 52.1 1.0 CE1 B:HIS79 3.3 52.1 1.0 CD2 B:HIS238 3.4 53.0 1.0 H1 B:ACT402 3.5 57.4 1.0 HE1 B:HIS79 3.5 52.1 1.0 HE1 B:HIS265 3.7 63.7 1.0 CB B:ASP242 3.7 56.1 1.0 OE2 B:GLU78 3.7 58.2 1.0 HB B:THR191 3.8 53.5 1.0 HD2 B:HIS238 3.8 53.0 1.0 CH3 B:ACT402 3.9 57.4 1.0 ND1 B:HIS238 3.9 53.0 1.0 HB3 B:ASP242 4.1 56.1 1.0 CG B:GLU78 4.1 58.2 1.0 O B:ACT402 4.1 57.4 1.0 HB2 B:ASP242 4.2 56.1 1.0 CD B:GLU78 4.2 58.2 1.0 HA B:ASP242 4.3 56.1 1.0 CG B:HIS238 4.3 53.0 1.0 HG2 B:GLU78 4.4 58.2 1.0 CE1 B:HIS265 4.4 63.7 1.0 CG B:HIS79 4.4 52.1 1.0 ND1 B:HIS79 4.4 52.1 1.0 HA B:THR191 4.5 53.5 1.0 NE2 B:HIS265 4.5 63.7 1.0 CA B:ASP242 4.5 56.1 1.0 H2 B:ACT402 4.5 57.4 1.0 OG1 B:THR191 4.5 53.5 1.0 H3 B:ACT402 4.5 57.4 1.0 CB B:THR191 4.6 53.5 1.0 HG1 B:THR191 4.6 53.5 1.0 HD1 B:HIS238 4.6 53.0 1.0 HD23 B:LEU241 4.6 53.7 1.0 H B:ASP242 4.6 56.1 1.0 O B:HIS238 4.7 53.0 1.0 N B:ASP242 4.8 56.1 1.0

Zinc binding site 3 out of 4 in the Lapb Cytoplasmic Domain in Complex with Lpxc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Lapb Cytoplasmic Domain in Complex with Lpxc within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:82.9 occ:1.00 HG C:CYS357 1.2 59.8 1.0 HG C:CYS360 1.6 58.9 1.0 SG C:CYS371 2.3 56.7 1.0 SG C:CYS374 2.3 58.3 1.0 SG C:CYS360 2.3 58.9 1.0 SG C:CYS357 2.3 59.8 1.0 H C:CYS374 3.1 58.3 1.0 HG C:CYS374 3.1 58.3 1.0 HG C:CYS371 3.1 56.7 1.0 HB3 C:CYS357 3.2 59.8 1.0 HB3 C:CYS371 3.2 56.7 1.0 CB C:CYS357 3.2 59.8 1.0 HB2 C:CYS357 3.2 59.8 1.0 CB C:CYS371 3.2 56.7 1.0 HB3 C:CYS360 3.3 58.9 1.0 HB2 C:CYS371 3.4 56.7 1.0 CB C:CYS360 3.5 58.9 1.0 HB3 C:CYS374 3.5 58.3 1.0 CB C:CYS374 3.6 58.3 1.0 H C:CYS360 3.6 58.9 1.0 HB3 C:SER373 3.7 59.1 1.0 HB3 C:PHE362 3.8 59.3 1.0 N C:CYS374 3.9 58.3 1.0 N C:CYS360 4.0 58.9 1.0 HB3 C:LYS359 4.1 58.3 1.0 HB2 C:CYS360 4.2 58.9 1.0 OG1 C:THR379 4.2 57.4 1.0 HB2 C:PHE362 4.2 59.3 1.0 H C:LYS359 4.3 58.3 1.0 CA C:CYS360 4.3 58.9 1.0 CA C:CYS374 4.3 58.3 1.0 HB2 C:CYS374 4.3 58.3 1.0 H C:PHE362 4.4 59.3 1.0 H C:SER373 4.4 59.1 1.0 CB C:PHE362 4.5 59.3 1.0 HG12 C:ILE380 4.5 58.4 1.0 CB C:SER373 4.6 59.1 1.0 CA C:CYS357 4.6 59.8 1.0 HG1 C:THR379 4.6 57.4 1.0 CA C:CYS371 4.7 56.7 1.0 H C:ARG375 4.8 57.4 1.0 C C:LYS359 4.8 58.3 1.0 H C:ALA376 4.8 54.6 1.0 HD12 C:ILE380 4.8 58.4 1.0 HB2 C:ALA376 4.8 54.6 1.0 C C:CYS360 4.9 58.9 1.0 CB C:LYS359 4.9 58.3 1.0 HA C:CYS357 4.9 59.8 1.0 C C:SER373 4.9 59.1 1.0 HG13 C:ILE380 5.0 58.4 1.0 N C:SER373 5.0 59.1 1.0

Zinc binding site 4 out of 4 in the Lapb Cytoplasmic Domain in Complex with Lpxc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Lapb Cytoplasmic Domain in Complex with Lpxc within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn403 b:73.3 occ:1.00 OD1 D:ASP242 2.0 58.0 1.0 OXT D:ACT402 2.0 58.4 1.0 OE2 D:GLU78 2.1 56.9 1.0 OD2 D:ASP242 2.1 58.0 1.0 NE2 D:HIS238 2.3 55.0 1.0 NE2 D:HIS79 2.3 52.8 1.0 CG D:ASP242 2.3 58.0 1.0 HE1 D:HIS238 2.8 55.0 1.0 CE1 D:HIS238 2.9 55.0 1.0 C D:ACT402 3.1 58.4 1.0 CE1 D:HIS79 3.2 52.8 1.0 CD2 D:HIS79 3.2 52.8 1.0 CD D:GLU78 3.3 56.9 1.0 HG3 D:GLU78 3.4 56.9 1.0 H1 D:ACT402 3.4 58.4 1.0 HG23 D:THR191 3.4 55.7 1.0 HD2 D:HIS79 3.4 52.8 1.0 HE1 D:HIS79 3.4 52.8 1.0 CD2 D:HIS238 3.4 55.0 1.0 HD2 D:HIS238 3.8 55.0 1.0 CH3 D:ACT402 3.8 58.4 1.0 CB D:ASP242 3.8 58.0 1.0 CG D:GLU78 3.9 56.9 1.0 HG1 D:THR191 4.0 55.7 1.0 ND1 D:HIS238 4.0 55.0 1.0 HE1 D:HIS265 4.1 61.0 1.0 O D:ACT402 4.2 58.4 1.0 HB3 D:ASP242 4.2 58.0 1.0 OE1 D:GLU78 4.3 56.9 1.0 ND1 D:HIS79 4.3 52.8 1.0 HB2 D:ASP242 4.3 58.0 1.0 CG2 D:THR191 4.3 55.7 1.0 CG D:HIS238 4.3 55.0 1.0 CG D:HIS79 4.3 52.8 1.0 H3 D:ACT402 4.3 58.4 1.0 HA D:ASP242 4.3 58.0 1.0 HA D:THR191 4.5 55.7 1.0 HG2 D:GLU78 4.5 56.9 1.0 HG21 D:THR191 4.5 55.7 1.0 H2 D:ACT402 4.5 58.4 1.0 CA D:ASP242 4.6 58.0 1.0 HD23 D:LEU241 4.6 54.4 1.0 HD1 D:HIS238 4.7 55.0 1.0 CE1 D:HIS265 4.7 61.0 1.0 NE2 D:HIS265 4.7 61.0 1.0 OG1 D:THR191 4.7 55.7 1.0 H D:ASP242 4.7 58.0 1.0 HB2 D:GLU78 4.7 56.9 1.0 O D:HIS238 4.8 55.0 1.0 HG22 D:THR191 4.9 55.7 1.0 N D:ASP242 4.9 58.0 1.0 CB D:GLU78 5.0 56.9 1.0 CB D:THR191 5.0 55.7 1.0

S.Shu, Y.Tsutsui, R.Nathawat, W.Mi. Dual Function of Lapb (Ycim) in Regulating Escherichia Coli Lipopolysaccharide Synthesis Proc.Natl.Acad.Sci.Usa V. 121 2024.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2321510121