Zinc in PDB 5fnp: High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe

All present enzymatic activity of High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe:
1.7.2.5;

The structure of High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe, PDB code: 5fnp was solved by F.-C.Lo, C.-C.Hsieh, M.Maestre-Reyna, C.-Y.Chen, T.-P.Ko, Y.-C.Horng, Y.-C.Lai, Y.-W.Chiang, C.-M.Chou, C.-H.Chiang, W.-N.Huang, W.-F.Liaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.87 / 1.80
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	98.454, 98.454, 126.138, 90.00, 90.00, 90.00
R / Rfree (%)	18.594 / 21.26

The structure of High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe (pdb code 5fnp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe, PDB code: 5fnp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1221 b:33.0 occ:1.00 OE2 A:GLU133 1.9 30.2 1.0 O A:O2118 2.0 28.3 1.0 NE2 A:HIS129 2.1 29.1 1.0 NE2 A:HIS160 2.2 27.2 1.0 OE1 A:GLU208 2.2 29.6 1.0 CD A:GLU133 2.8 31.2 1.0 CE1 A:HIS129 3.0 30.4 1.0 CD2 A:HIS129 3.1 29.7 1.0 OE1 A:GLU133 3.1 29.4 1.0 CE1 A:HIS160 3.1 28.1 1.0 CD2 A:HIS160 3.1 28.8 1.0 ZN A:ZN1222 3.1 30.5 1.0 CD A:GLU208 3.3 28.8 1.0 OE2 A:GLU208 3.7 28.9 1.0 ND1 A:HIS129 4.2 29.1 1.0 CG A:GLU133 4.2 30.2 1.0 CG A:HIS129 4.2 29.1 1.0 ND1 A:HIS160 4.2 25.9 1.0 NE2 A:HIS204 4.3 30.3 1.0 CG A:HIS160 4.3 26.7 1.0 CG A:GLU208 4.6 27.7 1.0 CZ A:PHE213 4.7 29.4 1.0 CE1 A:HIS204 4.8 29.7 1.0 CB A:MET156 4.8 32.9 1.0 CB A:GLU208 4.9 27.8 1.0

Zinc binding site 2 out of 4 in the High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1222 b:30.5 occ:1.00 O A:O2118 2.0 28.3 1.0 OE2 A:GLU208 2.0 28.9 1.0 NE2 A:HIS204 2.1 30.3 1.0 NE2 A:HIS84 2.2 27.4 1.0 OE1 A:GLU133 2.2 29.4 1.0 CD A:GLU208 2.8 28.8 1.0 CE1 A:HIS204 3.0 29.7 1.0 OE1 A:GLU208 3.0 29.6 1.0 CE1 A:HIS84 3.1 28.9 1.0 ZN A:ZN1221 3.1 33.0 1.0 CD2 A:HIS204 3.2 28.8 1.0 CD A:GLU133 3.2 31.2 1.0 CD2 A:HIS84 3.2 28.4 1.0 OE2 A:GLU133 3.5 30.2 1.0 CG2 A:ILE79 3.9 29.0 1.0 ND1 A:HIS204 4.1 28.1 1.0 ND1 A:HIS84 4.2 29.3 1.0 CZ A:PHE138 4.2 30.6 1.0 CG A:GLU208 4.2 27.7 1.0 CG A:HIS204 4.2 28.8 1.0 CG A:HIS84 4.3 27.5 1.0 NE2 A:HIS129 4.5 29.1 1.0 CG A:GLU133 4.5 30.2 1.0 CG A:MET130 4.6 28.9 1.0 CD2 A:HIS129 4.7 29.7 1.0 CE2 A:PHE138 4.8 30.6 1.0 CB A:GLU133 4.9 29.5 1.0 NE2 A:HIS160 5.0 27.2 1.0

Zinc binding site 3 out of 4 in the High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1221 b:38.2 occ:1.00 OE2 B:GLU133 2.0 35.5 1.0 O B:O2097 2.0 34.6 1.0 NE2 B:HIS129 2.0 35.2 1.0 NE2 B:HIS160 2.1 32.8 1.0 OE1 B:GLU208 2.2 31.4 1.0 CD B:GLU133 2.8 34.9 1.0 CE1 B:HIS129 3.0 37.6 1.0 CD2 B:HIS129 3.0 36.6 1.0 CE1 B:HIS160 3.1 34.5 1.0 OE1 B:GLU133 3.1 34.7 1.0 CD2 B:HIS160 3.1 34.3 1.0 ZN B:ZN1222 3.1 34.6 1.0 CD B:GLU208 3.2 32.7 1.0 OE2 B:GLU208 3.6 32.1 1.0 ND1 B:HIS129 4.1 36.9 1.0 CG B:HIS129 4.2 35.6 1.0 ND1 B:HIS160 4.2 33.7 1.0 CG B:GLU133 4.2 34.0 1.0 NE2 B:HIS204 4.3 31.3 1.0 CG B:HIS160 4.3 33.4 1.0 CG B:GLU208 4.6 32.6 1.0 CZ B:PHE213 4.7 35.2 1.0 CE1 B:HIS204 4.8 32.2 1.0 CB B:MET156 4.8 37.2 1.0 CB B:GLU208 4.9 33.3 1.0

Zinc binding site 4 out of 4 in the High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High Resolution Zn Containing Iron Sulfur Cluster Repair Protein Ytfe within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1222 b:34.6 occ:1.00 O B:O2097 1.9 34.6 1.0 OE2 B:GLU208 2.0 32.1 1.0 NE2 B:HIS204 2.1 31.3 1.0 OE1 B:GLU133 2.2 34.7 1.0 NE2 B:HIS84 2.2 33.5 1.0 CD B:GLU208 2.8 32.7 1.0 CE1 B:HIS204 3.0 32.2 1.0 OE1 B:GLU208 3.0 31.4 1.0 CE1 B:HIS84 3.1 33.5 1.0 ZN B:ZN1221 3.1 38.2 1.0 CD2 B:HIS204 3.2 30.8 1.0 CD B:GLU133 3.2 34.9 1.0 CD2 B:HIS84 3.2 33.9 1.0 OE2 B:GLU133 3.5 35.5 1.0 CG2 B:ILE79 3.9 33.2 1.0 ND1 B:HIS204 4.1 31.1 1.0 CG B:HIS204 4.2 30.5 1.0 CG B:GLU208 4.2 32.6 1.0 ND1 B:HIS84 4.2 33.6 1.0 CZ B:PHE138 4.3 34.2 1.0 CG B:HIS84 4.3 34.0 1.0 NE2 B:HIS129 4.5 35.2 1.0 CG B:GLU133 4.5 34.0 1.0 CD2 B:HIS129 4.6 36.6 1.0 CG B:MET130 4.6 34.5 1.0 CE2 B:PHE138 4.8 34.7 1.0 CB B:GLU133 4.9 31.6 1.0 NE2 B:HIS160 5.0 32.8 1.0

F.-C.Lo, C.-C.Hsieh, M.Maestre-Reyna, C.-Y.Chen, T.-P.Ko, Y.-C.Horng, Y.-C.Lai, Y.-W.Chiang, C.-M.Chou, C.-H.Chiang, W.-N.Huang, W.-F.Liaw. Crystal Structure of the Repair of Iron Centers Protein Ytfe and Its Interaction with No Chemistry V. 22 9768 2016.
ISSN: ISSN 0947-6539
PubMed: 27246459
DOI: 10.1002/CHEM.201600990