Zinc in PDB 5c22: Crystal Structure of Zn-Bound Hlyd From E. Coli

The structure of Crystal Structure of Zn-Bound Hlyd From E. Coli, PDB code: 5c22 was solved by N.C.Ha, J.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.20 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.865, 94.476, 181.378, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 26.4

The binding sites of Zinc atom in the Crystal Structure of Zn-Bound Hlyd From E. Coli (pdb code 5c22). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Zn-Bound Hlyd From E. Coli, PDB code: 5c22:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Zn-Bound Hlyd From E. Coli


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 Zn-Bound Hlyd From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:0.2 occ:1.00 NE2 A:HIS252 2.2 66.9 1.0 CE1 A:HIS252 2.3 69.9 1.0 CD2 A:HIS252 3.5 65.1 1.0 ND1 A:HIS252 3.6 70.1 1.0 CG A:HIS252 4.2 63.2 1.0 OE1 A:GLU256 4.3 0.8 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Zn-Bound Hlyd From E. Coli


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 Zn-Bound Hlyd From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:71.7 occ:1.00 OE1 B:GLU149 2.3 57.8 1.0 CD B:GLU149 3.2 60.4 1.0 CG B:GLU149 3.3 34.0 1.0 OE2 B:GLU149 4.4 55.6 1.0 NE B:ARG186 4.6 54.1 1.0 NH2 B:ARG186 4.7 47.2 1.0 CB B:GLU149 4.8 32.2 1.0 CZ B:ARG186 4.9 47.3 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Zn-Bound Hlyd From E. Coli


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 Zn-Bound Hlyd From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:63.0 occ:1.00 NE2 B:HIS252 2.1 62.2 1.0 O B:HOH516 2.2 26.8 1.0 OE2 B:GLU256 2.4 47.7 1.0 CE1 B:HIS252 2.7 38.1 1.0 CD2 B:HIS252 3.3 51.5 1.0 CD B:GLU256 3.3 77.2 1.0 OE1 B:GLU256 3.8 94.1 1.0 O B:HOH518 3.8 34.4 1.0 ND1 B:HIS252 4.0 37.7 1.0 CG B:HIS252 4.3 44.0 1.0 CG B:GLU256 4.5 60.6 1.0 CB B:GLU256 4.8 38.2 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Zn-Bound Hlyd From E. Coli


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 Zn-Bound Hlyd From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:56.9 occ:1.00 NE2 D:HIS252 2.2 36.6 1.0 OE1 D:GLU256 2.7 33.8 1.0 O D:HOH565 2.8 14.1 1.0 CE1 D:HIS252 3.1 25.2 1.0 CD2 D:HIS252 3.2 24.4 1.0 CD D:GLU256 3.9 62.3 1.0 ND1 D:HIS252 4.2 29.5 1.0 CG D:HIS252 4.3 28.8 1.0 OE2 D:GLU256 4.6 68.5 1.0 CG D:GLU256 4.9 64.7 1.0 CB D:GLU256 5.0 23.7 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Zn-Bound Hlyd From E. Coli


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 Zn-Bound Hlyd From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:63.7 occ:1.00 O D:HOH567 2.5 29.2 1.0 NE2 D:HIS344 2.5 43.2 1.0 CD2 D:HIS344 3.1 38.4 1.0 CE1 D:HIS344 3.7 50.1 1.0 CG D:HIS344 4.4 39.8 1.0 CG D:LYS342 4.4 44.4 1.0 CD D:LYS342 4.4 42.0 1.0 CE D:LYS342 4.5 41.0 1.0 ND1 D:HIS344 4.6 54.5 1.0 CB D:LYS342 4.8 37.9 1.0

J.S.Kim, S.Song, M.Lee, S.Lee, K.Lee, N.C.Ha. Crystal Structure of A Soluble Fragment of the Membrane Fusion Protein Hlyd in A Type I Secretion System of Gram-Negative Bacteria Structure V. 24 477 2016.
ISSN: ISSN 0969-2126
PubMed: 26833388
DOI: 10.1016/J.STR.2015.12.012