Zinc in PDB 5xlk: Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422

The structure of Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422, PDB code: 5xlk was solved by S.Y.Cho, W.S.Song, H.J.Hong, S.I.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.05
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	121.362, 121.362, 249.266, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 28.7

The binding sites of Zinc atom in the Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422 (pdb code 5xlk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422, PDB code: 5xlk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422


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 the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:82.9 occ:1.00 NE2 A:HIS266 2.8 76.4 1.0 CE1 A:HIS266 3.6 76.2 1.0 CD2 A:HIS266 3.8 75.3 1.0 CE B:LYS258 4.1 57.3 1.0 N B:LEU101 4.3 34.8 1.0 NE2 B:GLN226 4.3 42.6 1.0 NZ B:LYS258 4.4 60.0 1.0 OE1 B:GLN103 4.4 39.6 1.0 CB B:LEU101 4.5 34.0 1.0 CG B:LYS258 4.6 51.2 1.0 CD1 B:LEU101 4.7 39.2 1.0 ND1 A:HIS266 4.7 74.4 1.0 CD B:LYS258 4.7 54.0 1.0 CD A:PRO264 4.8 71.5 1.0 O A:PRO264 4.9 70.3 1.0 CG A:HIS266 4.9 74.9 1.0 CG A:PRO264 4.9 67.9 1.0 CA B:LEU101 5.0 32.7 1.0 O B:LEU101 5.0 32.0 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422


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 the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:83.4 occ:1.00 OD2 A:ASP205 2.1 50.5 1.0 CG A:ASP205 3.0 47.4 1.0 OD1 A:ASP205 3.2 49.2 1.0 CB A:ASP205 4.4 43.9 1.0 O A:ASP201 4.5 46.8 1.0 CB A:ASP201 4.7 52.4 1.0 C A:ASP201 4.8 47.9 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422


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 the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:91.4 occ:1.00 OD2 A:ASP227 2.1 48.8 1.0 CG A:ASP227 2.9 43.5 1.0 OD1 A:ASP227 3.0 46.1 1.0 CB A:ASP227 4.3 39.1 1.0 CB A:GLU189 4.4 44.1 1.0 ND2 A:ASN190 4.7 51.4 1.0 N A:GLU189 4.7 39.1 1.0 CB A:SER240 4.8 39.4 1.0 N A:ASN190 4.9 39.6 1.0 CG A:ASN190 4.9 46.1 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422


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 the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:79.0 occ:1.00 OD2 B:ASP227 2.1 52.5 1.0 CG B:ASP227 2.9 46.3 1.0 OD1 B:ASP227 3.1 49.2 1.0 NZ B:LYS238 4.2 53.2 1.0 CB B:ASP227 4.4 41.0 1.0 CB B:SER240 4.6 42.9 1.0 CB B:GLU189 4.6 47.0 1.0 ND2 B:ASN190 4.8 54.3 1.0 CE B:LYS238 4.8 53.4 1.0 N B:SER240 4.9 39.3 1.0 N B:GLU189 4.9 41.7 1.0 CA B:SER240 5.0 39.2 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422


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 the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:84.7 occ:1.00 NE2 B:HIS266 2.6 85.0 1.0 CD2 B:HIS266 3.5 83.6 1.0 CE1 B:HIS266 3.5 84.7 1.0 O B:PRO264 4.3 76.2 1.0 CD B:PRO264 4.5 77.2 1.0 ND1 B:HIS266 4.7 82.5 1.0 CG B:PRO264 4.7 72.9 1.0 CG B:HIS266 4.7 82.8 1.0 CA B:GLU263 4.7 87.7 1.0 N B:PRO264 4.9 74.7 1.0 O B:ASP262 5.0 0.0 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422


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 the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:87.2 occ:1.00 OD2 B:ASP205 2.4 53.7 1.0 CG B:ASP205 3.2 50.1 1.0 OD1 B:ASP205 3.3 51.9 1.0 O B:ASP201 4.3 49.3 1.0 CB B:ASP201 4.6 55.8 1.0 CB B:ASP205 4.6 45.7 1.0 C B:ASP201 4.8 50.1 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422


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 the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:44.4 occ:0.50 OD2 C:ASP205 2.0 48.9 1.0 OD2 C:ASP201 2.0 50.0 1.0 OD1 C:ASP201 2.5 48.0 1.0 CG C:ASP201 2.6 48.7 1.0 CG C:ASP205 2.7 45.8 1.0 OD1 C:ASP205 2.7 47.8 1.0 CB C:ASP201 4.1 47.7 1.0 O C:ASP201 4.1 43.8 1.0 CB C:ASP205 4.1 42.4 1.0 C C:ASP201 4.6 44.1 1.0 CA C:ASP201 4.9 44.7 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422


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 the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:70.7 occ:1.00 OD2 C:ASP227 2.0 51.1 1.0 CG C:ASP227 2.8 46.0 1.0 OD1 C:ASP227 3.0 48.8 1.0 CB C:ASP227 4.3 41.8 1.0 CB C:SER240 4.4 43.1 1.0 CB C:GLU189 4.6 50.1 1.0 N C:SER240 4.7 40.0 1.0 N C:GLU189 4.7 44.8 1.0 CA C:SER240 4.8 40.3 1.0 CE C:LYS238 5.0 47.1 1.0 C C:ARG239 5.0 38.1 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422


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 the Flagellar Cap Protein Flid D2-D3 Domains From Serratia Marcescens in Space Group I422 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:87.2 occ:1.00 NE2 C:HIS266 2.5 93.3 1.0 CE1 C:HIS266 3.4 93.6 1.0 CD2 C:HIS266 3.4 92.0 1.0 O C:PRO264 4.2 83.9 1.0 CD C:PRO264 4.3 83.2 1.0 CG C:PRO264 4.4 79.5 1.0 ND1 C:HIS266 4.5 91.8 1.0 CG C:HIS266 4.6 91.8 1.0 CA C:GLU263 4.7 93.3 1.0 N C:PRO264 4.8 81.0 1.0 O C:ASP262 5.0 0.9 1.0 C C:GLU263 5.0 85.1 1.0

S.Y.Cho, W.S.Song, H.J.Hong, G.S.Lee, S.G.Kang, H.J.Ko, P.H.Kim, S.I.Yoon. Tetrameric Structure of the Flagellar Cap Protein Flid From Serratia Marcescens. Biochem. Biophys. Res. V. 489 63 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28527888
DOI: 10.1016/J.BBRC.2017.05.093