Zinc in PDB 6ait: Crystal Structure of E. Coli Bepa

The structure of Crystal Structure of E. Coli Bepa, PDB code: 6ait was solved by M.S.M.Umar, Y.Tanaka, H.Kamikubo, T.Tsukazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.60 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	85.844, 104.674, 104.971, 113.61, 105.84, 104.03
R / Rfree (%)	20.6 / 26.3

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

Zinc binding site 1 out of 6 in the Crystal Structure of E. Coli Bepa


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 E. Coli Bepa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:76.6 occ:1.00 OE1 A:GLU201 2.0 95.5 1.0 NE2 A:HIS140 2.1 75.8 1.0 NE2 A:HIS136 2.1 73.2 1.0 ND1 A:HIS246 2.3 70.6 1.0 OE2 A:GLU201 2.4 97.3 1.0 CD A:GLU201 2.5 93.1 1.0 CE1 A:HIS140 3.0 71.0 1.0 CD2 A:HIS136 3.1 65.4 1.0 CE1 A:HIS136 3.2 67.0 1.0 CD2 A:HIS140 3.2 69.1 1.0 CG A:HIS246 3.2 69.2 1.0 CE1 A:HIS246 3.2 70.0 1.0 CB A:HIS246 3.5 68.9 1.0 CG A:GLU201 3.9 87.6 1.0 CD2 A:PHE196 4.0 83.4 1.0 ND1 A:HIS140 4.2 73.2 1.0 CA A:HIS246 4.2 68.0 1.0 CG A:HIS136 4.2 63.6 1.0 ND1 A:HIS136 4.2 64.6 1.0 CG A:HIS140 4.3 69.7 1.0 NE2 A:HIS246 4.3 68.1 1.0 CD2 A:HIS246 4.3 67.0 1.0 CE2 A:PHE196 4.4 83.1 1.0 CG A:PHE196 4.6 86.3 1.0 CA A:GLU201 4.6 73.8 1.0 OE2 A:GLU137 4.6 74.8 1.0 CB A:GLU201 4.7 78.8 1.0 CB A:ALA204 4.7 52.9 1.0 CB A:PHE196 4.8 90.0 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of E. Coli Bepa


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 E. Coli Bepa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:68.0 occ:1.00 OE2 B:GLU201 2.0 0.0 1.0 NE2 B:HIS136 2.1 91.0 1.0 ND1 B:HIS246 2.1 87.5 1.0 NE2 B:HIS140 2.3 62.8 1.0 OE1 B:GLU201 2.3 99.1 1.0 CD B:GLU201 2.5 95.9 1.0 CE1 B:HIS246 3.0 81.7 1.0 CD2 B:HIS136 3.0 83.3 1.0 CG B:HIS246 3.1 81.1 1.0 CE1 B:HIS136 3.1 90.4 1.0 CD2 B:HIS140 3.2 58.3 1.0 CE1 B:HIS140 3.3 66.9 1.0 CB B:HIS246 3.5 73.9 1.0 CD2 B:PHE196 3.9 81.1 1.0 CG B:GLU201 3.9 88.1 1.0 NE2 B:HIS246 4.0 81.0 1.0 CD2 B:HIS246 4.1 82.5 1.0 CG B:HIS136 4.2 81.2 1.0 ND1 B:HIS136 4.2 88.5 1.0 CA B:HIS246 4.3 75.8 1.0 CE2 B:PHE196 4.4 80.5 1.0 CG B:HIS140 4.4 59.5 1.0 ND1 B:HIS140 4.4 65.5 1.0 OE2 B:GLU137 4.5 78.8 1.0 CB B:GLU201 4.6 82.5 1.0 CB B:ALA204 4.7 75.1 1.0 CA B:GLU201 4.7 83.6 1.0 CG B:PHE196 4.8 83.9 1.0 O B:THR245 5.0 84.0 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of E. Coli Bepa


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 E. Coli Bepa within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:56.3 occ:1.00 NE2 C:HIS136 2.1 78.3 1.0 ND1 C:HIS246 2.1 76.0 1.0 NE2 C:HIS140 2.2 70.4 1.0 OE1 C:GLU201 2.2 67.4 1.0 OE2 C:GLU201 2.5 75.2 1.0 CD C:GLU201 2.7 69.7 1.0 CE1 C:HIS246 2.9 70.7 1.0 CG C:HIS246 3.0 71.3 1.0 CD2 C:HIS136 3.0 74.7 1.0 CE1 C:HIS136 3.0 76.5 1.0 CE1 C:HIS140 3.1 72.2 1.0 CD2 C:HIS140 3.2 70.6 1.0 CB C:HIS246 3.4 69.4 1.0 NE2 C:HIS246 3.9 69.0 1.0 CD2 C:HIS246 3.9 70.2 1.0 ND1 C:HIS136 4.1 76.2 1.0 CG C:GLU201 4.1 66.3 1.0 CG C:HIS136 4.2 72.8 1.0 CD2 C:PHE196 4.2 92.5 1.0 CA C:HIS246 4.2 71.5 1.0 ND1 C:HIS140 4.3 75.2 1.0 CG C:HIS140 4.4 73.9 1.0 OE1 C:GLU137 4.5 79.7 1.0 CE2 C:PHE196 4.6 87.8 1.0 CB C:ALA204 4.8 60.0 1.0 NH2 C:ARG252 4.8 67.0 1.0 CA C:GLU201 4.8 69.3 1.0 CG C:PHE196 4.8 94.0 1.0 CB C:GLU201 4.8 68.6 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of E. Coli Bepa


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 E. Coli Bepa within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:77.9 occ:1.00 OE2 D:GLU201 2.0 0.2 1.0 NE2 D:HIS136 2.0 96.6 1.0 NE2 D:HIS140 2.2 78.6 1.0 ND1 D:HIS246 2.2 81.4 1.0 OE1 D:GLU201 2.4 0.6 1.0 CD D:GLU201 2.4 0.5 1.0 CD2 D:HIS136 2.9 87.5 1.0 CE1 D:HIS246 3.0 81.8 1.0 CE1 D:HIS136 3.1 92.7 1.0 CD2 D:HIS140 3.2 75.9 1.0 CE1 D:HIS140 3.2 79.4 1.0 CG D:HIS246 3.4 79.3 1.0 CG D:GLU201 3.8 0.7 1.0 CB D:HIS246 3.9 80.2 1.0 CG D:HIS136 4.1 85.7 1.0 CD2 D:PHE196 4.1 79.5 1.0 NE2 D:HIS246 4.1 78.8 1.0 ND1 D:HIS136 4.1 91.3 1.0 CG D:HIS140 4.3 78.2 1.0 ND1 D:HIS140 4.3 80.4 1.0 CD2 D:HIS246 4.3 77.8 1.0 OE2 D:GLU137 4.3 79.6 1.0 CA D:HIS246 4.3 81.9 1.0 CG D:PHE196 4.6 84.4 1.0 CE2 D:PHE196 4.6 77.9 1.0 CB D:ALA204 4.7 80.2 1.0 CB D:GLU201 4.7 97.7 1.0 CB D:PHE196 4.7 90.5 1.0 O D:THR245 4.8 89.5 1.0 CA D:GLU201 4.8 91.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of E. Coli Bepa


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 E. Coli Bepa within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:76.6 occ:1.00 OE1 E:GLU201 2.1 0.3 1.0 NE2 E:HIS140 2.1 0.9 1.0 NE2 E:HIS136 2.2 0.3 1.0 OE2 E:GLU201 2.2 0.4 1.0 CD E:GLU201 2.4 1.0 1.0 ND1 E:HIS246 2.4 85.9 1.0 CE1 E:HIS136 2.9 0.2 1.0 CE1 E:HIS140 3.0 0.6 1.0 CD2 E:HIS140 3.1 0.1 1.0 CD2 E:HIS136 3.1 97.7 1.0 CE1 E:HIS246 3.2 84.4 1.0 CG E:HIS246 3.4 86.6 1.0 CB E:HIS246 3.8 94.8 1.0 CG E:GLU201 3.9 0.4 1.0 ND1 E:HIS136 4.0 0.5 1.0 CG E:HIS136 4.1 95.5 1.0 ND1 E:HIS140 4.2 0.7 1.0 CB E:ALA204 4.2 91.0 1.0 CG E:HIS140 4.2 0.6 1.0 NE2 E:HIS246 4.3 83.3 1.0 CA E:HIS246 4.4 0.5 1.0 CD1 E:PHE196 4.4 98.7 1.0 CD2 E:HIS246 4.4 83.0 1.0 CB E:GLU201 4.5 0.6 1.0 CA E:GLU201 4.5 0.5 1.0 OE2 E:GLU137 4.6 96.9 1.0 CE1 E:PHE196 4.8 95.7 1.0 CG E:PHE196 4.9 0.2 1.0 O E:THR245 4.9 96.9 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of E. Coli Bepa


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 E. Coli Bepa within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn501 b:0.3 occ:1.00 NE2 F:HIS136 2.0 0.7 1.0 CG F:GLU201 2.4 0.9 1.0 OE1 F:GLU201 2.5 0.2 1.0 CD F:GLU201 2.5 0.8 1.0 ND1 F:HIS246 2.6 0.4 1.0 NE2 F:HIS140 2.6 0.5 1.0 CE1 F:HIS246 2.9 0.4 1.0 CE1 F:HIS136 2.9 0.3 1.0 CD2 F:HIS136 3.0 0.9 1.0 CD2 F:HIS140 3.4 0.9 1.0 OE2 F:GLU201 3.5 0.9 1.0 CG F:HIS246 3.5 0.3 1.0 CE1 F:HIS140 3.7 0.3 1.0 CB F:GLU201 3.9 0.6 1.0 NE2 F:HIS246 3.9 97.2 1.0 ND1 F:HIS136 4.0 0.0 1.0 CG F:HIS136 4.1 0.1 1.0 CB F:HIS246 4.2 0.7 1.0 CD2 F:HIS246 4.2 98.5 1.0 OE1 F:GLU137 4.4 0.7 1.0 CD2 F:PHE196 4.6 0.2 1.0 CG F:HIS140 4.7 0.5 1.0 CB F:ALA204 4.7 0.2 1.0 CA F:GLU201 4.7 0.2 1.0 ND1 F:HIS140 4.8 0.3 1.0 CE2 F:PHE196 4.9 0.2 1.0

M.Shahrizal, Y.Daimon, Y.Tanaka, Y.Hayashi, S.Nakayama, S.Iwaki, S.I.Narita, H.Kamikubo, Y.Akiyama, T.Tsukazaki. Structural Basis For the Function of the Beta-Barrel Assembly-Enhancing Protease Bepa. J. Mol. Biol. V. 431 625 2019.
ISSN: ESSN 1089-8638
PubMed: 30521812
DOI: 10.1016/J.JMB.2018.11.024