Zinc in PDB 1xaf: Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T

The structure of Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T, PDB code: 1xaf was solved by Y.Kim, N.Maltseva, I.Dementieva, F.Collart, A.Joachimiak, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.05 / 2.01
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.874, 50.583, 55.347, 90.32, 96.32, 90.40
R / Rfree (%)	17.9 / 25.2

The binding sites of Zinc atom in the Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T (pdb code 1xaf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T, PDB code: 1xaf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T


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 Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:14.9 occ:1.00 OXT A:ACT512 2.0 15.6 1.0 NE2 A:HIS124 2.1 16.8 1.0 SG A:CYS107 2.1 12.3 1.0 NE2 A:HIS71 2.2 16.8 1.0 C A:ACT512 2.9 17.2 1.0 CE1 A:HIS124 3.0 16.3 1.0 CE1 A:HIS71 3.0 15.4 1.0 CD2 A:HIS71 3.1 16.5 1.0 CB A:CYS107 3.1 9.1 1.0 O A:ACT512 3.2 16.2 1.0 CD2 A:HIS124 3.2 16.3 1.0 O A:HOH580 3.9 26.5 1.0 ND1 A:HIS71 4.0 16.9 1.0 O A:HOH537 4.1 25.8 1.0 CG A:HIS71 4.1 16.8 1.0 ND1 A:HIS124 4.1 18.2 1.0 CG A:HIS124 4.3 13.7 1.0 CH3 A:ACT512 4.3 17.4 1.0 O B:HOH605 4.4 26.6 1.0 CA A:CYS107 4.4 9.0 1.0 N A:CYS107 4.6 9.2 1.0 O B:HOH682 4.7 38.3 1.0 CA A:GLY126 4.8 16.1 1.0 O B:HOH702 4.8 42.2 1.0 O A:HOH573 4.9 29.4 1.0 N A:GLY126 5.0 16.5 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T


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 Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:25.2 occ:1.00 NE2 A:HIS46 2.0 20.3 1.0 CD2 A:HIS46 2.9 18.4 1.0 CE1 A:HIS46 3.0 21.5 1.0 O A:HOH671 3.9 28.4 1.0 CG A:HIS46 4.1 18.3 1.0 ND1 A:HIS46 4.1 18.1 1.0 O A:VAL26 4.8 17.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T


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 Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:26.2 occ:1.00 OG1 A:THR219 2.0 19.1 1.0 O A:ACT514 2.1 20.7 1.0 SG A:CYS216 2.2 15.7 1.0 OXT A:ACT514 2.5 17.9 1.0 C A:ACT514 2.7 20.1 1.0 CB A:CYS216 3.0 12.8 1.0 O A:HOH538 3.0 31.3 1.0 CB A:THR219 3.2 19.1 1.0 N A:THR219 3.8 17.8 1.0 CA A:THR219 4.0 19.1 1.0 CH3 A:ACT514 4.1 19.5 1.0 CB A:ALA161 4.2 18.2 1.0 CG2 A:THR219 4.3 19.3 1.0 CA A:CYS216 4.4 14.0 1.0 CB A:ARG160 4.6 18.6 1.0 CA A:GLY158 4.7 12.0 1.0 N A:GLY158 4.7 12.4 1.0 N A:ALA161 4.7 19.2 1.0 C A:TYR218 4.9 17.3 1.0 C A:CYS216 4.9 13.7 1.0 CB A:TYR218 5.0 16.7 1.0 O A:HOH672 5.0 37.4 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T


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 Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:49.7 occ:1.00 NE2 A:HIS186 2.2 39.7 1.0 CE1 A:HIS186 2.4 40.0 1.0 O A:HOH646 2.6 35.8 1.0 CD2 A:HIS186 3.6 40.5 1.0 ND1 A:HIS186 3.6 40.7 1.0 CG A:HIS186 4.2 38.8 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T


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 Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:47.7 occ:1.00 NE2 A:HIS39 2.0 27.4 1.0 NE2 B:HIS186 2.0 36.6 1.0 CE1 A:HIS39 2.5 26.4 1.0 O B:HOH562 2.6 41.3 1.0 O B:HOH657 2.7 38.9 1.0 CE1 B:HIS186 3.0 36.9 1.0 CD2 B:HIS186 3.1 34.9 1.0 CD2 A:HIS39 3.4 23.7 1.0 ND1 A:HIS39 3.7 23.1 1.0 ND1 B:HIS186 4.1 36.9 1.0 CG A:HIS39 4.2 21.7 1.0 CG B:HIS186 4.2 34.9 1.0 CB A:ALA38 4.7 17.8 1.0 O A:HOH691 4.7 39.5 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T


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 Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:14.3 occ:1.00 OXT B:ACT513 2.0 16.8 1.0 SG B:CYS107 2.1 15.6 1.0 NE2 B:HIS124 2.1 16.3 1.0 NE2 B:HIS71 2.2 15.7 1.0 CE1 B:HIS124 2.9 16.8 1.0 C B:ACT513 2.9 17.5 1.0 CD2 B:HIS71 3.0 15.3 1.0 CB B:CYS107 3.0 12.7 1.0 CE1 B:HIS71 3.1 16.6 1.0 O B:ACT513 3.1 17.6 1.0 CD2 B:HIS124 3.3 15.6 1.0 O B:HOH571 4.0 35.6 1.0 O B:HOH667 4.0 33.3 1.0 ND1 B:HIS71 4.1 14.6 1.0 CG B:HIS71 4.1 16.4 1.0 ND1 B:HIS124 4.1 16.6 1.0 CH3 B:ACT513 4.3 17.7 1.0 CG B:HIS124 4.3 16.1 1.0 CA B:CYS107 4.4 11.3 1.0 O B:HOH669 4.6 37.4 1.0 N B:CYS107 4.7 10.7 1.0 CA B:GLY126 4.8 19.1 1.0 O B:HOH557 5.0 29.6 1.0 N B:GLY126 5.0 18.4 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T


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 Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn506 b:29.5 occ:1.00 NE2 B:HIS46 2.1 17.2 1.0 CD2 B:HIS46 2.9 14.6 1.0 CE1 B:HIS46 3.1 14.8 1.0 O B:HOH660 4.1 32.5 1.0 O B:HOH618 4.1 22.4 1.0 CG B:HIS46 4.1 17.3 1.0 ND1 B:HIS46 4.2 15.0 1.0 CG1 B:VAL26 4.8 16.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T


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 Protein of Unknown Function Yfih From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn507 b:26.8 occ:1.00 OG1 B:THR219 2.0 18.8 1.0 O B:ACT515 2.1 31.6 1.0 O B:ACT516 2.1 24.3 1.0 SG B:CYS216 2.2 12.0 1.0 OXT B:ACT516 2.6 22.5 1.0 C B:ACT516 2.7 23.5 1.0 CB B:CYS216 3.0 11.9 1.0 C B:ACT515 3.1 31.6 1.0 OXT B:ACT515 3.1 31.5 1.0 CB B:THR219 3.3 17.8 1.0 N B:THR219 3.8 16.4 1.0 CA B:THR219 4.1 17.8 1.0 CB B:ALA161 4.2 18.9 1.0 CH3 B:ACT516 4.2 23.4 1.0 CG2 B:THR219 4.4 19.0 1.0 CA B:CYS216 4.5 12.2 1.0 CH3 B:ACT515 4.5 31.0 1.0 CB B:ARG160 4.5 18.3 1.0 N B:ALA161 4.6 18.5 1.0 N B:GLY158 4.7 11.5 1.0 CA B:GLY158 4.7 11.9 1.0 CB B:TYR218 4.8 14.7 1.0 C B:TYR218 4.9 15.4 1.0 C B:CYS216 5.0 12.4 1.0 C B:ARG160 5.0 18.7 1.0 N B:ARG160 5.0 17.3 1.0 C B:GLY158 5.0 13.3 1.0

Y.Kim, N.Maltseva, I.Dementieva, F.Collart, D.Holzle, A.Joachimiak. Crystal Structure of Hypothetical Protein Yfih From Shigella Flexneri at 2 A Resolution. Proteins V. 63 1097 2006.
ISSN: ISSN 0887-3585
PubMed: 16498617
DOI: 10.1002/PROT.20589