Manganese in PDB 7be8: Escherichia Coli Ytfe (Mn)

The structure of Escherichia Coli Ytfe (Mn), PDB code: 7be8 was solved by L.S.O.Silva, P.M.Matias, C.V.Romao, L.M.Saraiva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.18 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.145, 50.119, 88.238, 90, 100.3, 90
R / Rfree (%)	23.9 / 28.7

The binding sites of Manganese atom in the Escherichia Coli Ytfe (Mn) (pdb code 7be8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Escherichia Coli Ytfe (Mn), PDB code: 7be8:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Escherichia Coli Ytfe (Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Escherichia Coli Ytfe (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:26.9 occ:1.00 O A:O303 1.9 35.7 1.0 OE2 A:GLU208 2.0 21.3 1.0 NE2 A:HIS204 2.2 24.0 1.0 OE1 A:GLU133 2.2 23.6 1.0 NE2 A:HIS84 2.2 26.2 1.0 HE1 A:HIS204 2.7 30.9 1.0 CE1 A:HIS204 2.7 25.2 1.0 CD A:GLU208 3.0 16.6 1.0 CE1 A:HIS84 3.1 25.5 1.0 MN A:MN302 3.1 39.0 1.0 CD A:GLU133 3.1 28.1 1.0 HE1 A:HIS84 3.2 31.2 1.0 CD2 A:HIS84 3.2 29.6 1.0 HG21 A:ILE79 3.3 24.5 1.0 CD2 A:HIS204 3.4 26.9 1.0 OE2 A:GLU133 3.4 35.1 1.0 OE1 A:GLU208 3.4 28.9 1.0 HD2 A:HIS84 3.4 36.1 1.0 HZ A:PHE138 3.6 23.6 1.0 HG2 A:MET130 3.6 32.7 1.0 HD2 A:HIS204 3.8 32.9 1.0 HG23 A:ILE79 3.8 24.5 1.0 CG2 A:ILE79 3.8 19.9 1.0 HG22 A:ILE79 3.9 24.5 1.0 ND1 A:HIS204 4.0 31.2 1.0 ND1 A:HIS84 4.2 26.6 1.0 HD2 A:HIS129 4.3 34.3 1.0 CG A:HIS204 4.3 23.0 1.0 CG A:HIS84 4.3 24.8 1.0 CZ A:PHE138 4.3 19.2 1.0 CG A:GLU208 4.3 21.3 1.0 NE2 A:HIS129 4.4 35.4 1.0 HA A:MET130 4.4 26.1 1.0 HE2 A:PHE138 4.5 36.9 1.0 HB2 A:GLU133 4.5 35.1 1.0 CG A:GLU133 4.5 27.2 1.0 HG3 A:GLU208 4.5 26.1 1.0 HG2 A:GLU208 4.5 26.1 1.0 HB3 A:GLU133 4.5 35.1 1.0 CG A:MET130 4.6 26.8 1.0 HD13 A:ILE79 4.6 31.1 1.0 HD1 A:HIS204 4.7 38.1 1.0 CD2 A:HIS129 4.7 28.1 1.0 CB A:GLU133 4.8 28.8 1.0 CE2 A:PHE138 4.8 30.2 1.0 HD1 A:HIS84 5.0 32.5 1.0

Manganese binding site 2 out of 4 in the Escherichia Coli Ytfe (Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Escherichia Coli Ytfe (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:39.0 occ:1.00 OE1 A:GLU208 2.1 28.9 1.0 OE2 A:GLU133 2.1 35.1 1.0 O A:O303 2.1 35.7 1.0 NE2 A:HIS160 2.1 26.5 1.0 NE2 A:HIS129 2.2 35.4 1.0 CD A:GLU208 3.0 16.6 1.0 CD A:GLU133 3.0 28.1 1.0 CE1 A:HIS160 3.1 24.8 1.0 CE1 A:HIS129 3.1 31.4 1.0 MN A:MN301 3.1 26.9 1.0 CD2 A:HIS160 3.1 25.9 1.0 OE2 A:GLU208 3.2 21.3 1.0 HE1 A:HIS129 3.2 38.3 1.0 HE1 A:HIS160 3.2 30.3 1.0 CD2 A:HIS129 3.3 28.1 1.0 OE1 A:GLU133 3.3 23.6 1.0 HD2 A:HIS160 3.3 31.7 1.0 HD2 A:HIS129 3.5 34.3 1.0 HZ A:PHE213 4.1 30.2 1.0 ND1 A:HIS160 4.2 26.6 1.0 NE2 A:HIS204 4.2 24.0 1.0 HB3 A:MET156 4.2 28.2 1.0 CG A:HIS160 4.3 31.0 1.0 ND1 A:HIS129 4.3 30.5 1.0 CG A:GLU133 4.3 27.2 1.0 HG3 A:GLU133 4.3 33.2 1.0 HG12 A:ILE205 4.4 35.2 1.0 CG A:HIS129 4.4 28.6 1.0 CG A:GLU208 4.4 21.3 1.0 HE1 A:HIS204 4.5 30.9 1.0 CE1 A:HIS204 4.5 25.2 1.0 HB2 A:GLU208 4.5 31.8 1.0 HB3 A:GLU208 4.6 31.8 1.0 HG2 A:GLU133 4.7 33.2 1.0 HA A:ILE205 4.8 27.0 1.0 CB A:GLU208 4.8 26.0 1.0 CZ A:PHE213 4.8 24.6 1.0 HG2 A:GLU208 4.9 26.1 1.0 HG3 A:GLU208 4.9 26.1 1.0 CD2 A:HIS204 4.9 26.9 1.0 HD1 A:HIS160 5.0 32.5 1.0 HE2 A:PHE213 5.0 35.2 1.0

Manganese binding site 3 out of 4 in the Escherichia Coli Ytfe (Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Escherichia Coli Ytfe (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:38.8 occ:1.00 O B:O303 1.9 52.9 1.0 OE2 B:GLU208 2.0 41.0 1.0 OE1 B:GLU133 2.1 44.5 1.0 NE2 B:HIS204 2.1 34.9 1.0 NE2 B:HIS84 2.2 34.5 1.0 HE1 B:HIS204 2.5 39.4 1.0 CE1 B:HIS204 2.6 32.4 1.0 CD B:GLU208 3.0 40.2 1.0 CE1 B:HIS84 3.0 32.9 1.0 CD B:GLU133 3.1 45.7 1.0 HE1 B:HIS84 3.1 40.0 1.0 MN B:MN302 3.1 51.3 1.0 CD2 B:HIS84 3.3 35.2 1.0 HG21 B:ILE79 3.3 40.3 1.0 OE1 B:GLU208 3.3 37.6 1.0 OE2 B:GLU133 3.4 41.4 1.0 CD2 B:HIS204 3.4 45.9 1.0 HZ B:PHE138 3.5 39.2 1.0 HD2 B:HIS84 3.5 42.9 1.0 HG2 B:MET130 3.6 52.2 1.0 HG22 B:ILE79 3.8 40.3 1.0 HD2 B:HIS204 3.8 55.7 1.0 CG2 B:ILE79 3.8 33.1 1.0 HG23 B:ILE79 3.9 40.3 1.0 ND1 B:HIS204 3.9 41.1 1.0 HD2 B:HIS129 4.2 44.7 1.0 ND1 B:HIS84 4.2 34.8 1.0 CZ B:PHE138 4.3 32.1 1.0 CG B:HIS204 4.3 39.9 1.0 CG B:GLU208 4.3 39.9 1.0 CG B:HIS84 4.3 39.2 1.0 HE2 B:PHE138 4.4 47.7 1.0 CG B:GLU133 4.5 45.4 1.0 HB2 B:GLU133 4.5 44.9 1.0 NE2 B:HIS129 4.5 40.5 1.0 HG3 B:GLU208 4.5 48.5 1.0 HA B:MET130 4.5 48.6 1.0 HG2 B:GLU208 4.5 48.5 1.0 HB3 B:GLU133 4.5 44.9 1.0 CG B:MET130 4.5 43.0 1.0 HD1 B:HIS204 4.6 49.9 1.0 CD2 B:HIS129 4.7 36.8 1.0 HD13 B:ILE79 4.7 43.0 1.0 CE2 B:PHE138 4.7 39.2 1.0 CB B:GLU133 4.7 36.9 1.0 HD1 B:HIS84 4.9 42.4 1.0 HG3 B:MET130 5.0 52.2 1.0 HG2 B:GLU133 5.0 55.0 1.0 HG3 B:GLU133 5.0 55.0 1.0

Manganese binding site 4 out of 4 in the Escherichia Coli Ytfe (Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Escherichia Coli Ytfe (Mn) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:51.3 occ:1.00 OE2 B:GLU133 2.1 41.4 1.0 O B:O303 2.1 52.9 1.0 OE1 B:GLU208 2.1 37.6 1.0 NE2 B:HIS160 2.2 43.9 1.0 NE2 B:HIS129 2.2 40.5 1.0 CD B:GLU133 3.0 45.7 1.0 CD B:GLU208 3.0 40.2 1.0 CD2 B:HIS160 3.1 47.7 1.0 CE1 B:HIS129 3.1 40.7 1.0 MN B:MN301 3.1 38.8 1.0 CE1 B:HIS160 3.2 45.9 1.0 CD2 B:HIS129 3.2 36.8 1.0 OE1 B:GLU133 3.3 44.5 1.0 OE2 B:GLU208 3.3 41.0 1.0 HD2 B:HIS160 3.3 57.8 1.0 HE1 B:HIS129 3.3 49.4 1.0 HE1 B:HIS160 3.3 55.7 1.0 HD2 B:HIS129 3.4 44.7 1.0 HZ B:PHE213 4.1 42.0 1.0 HB3 B:MET156 4.2 45.7 1.0 NE2 B:HIS204 4.2 34.9 1.0 HG12 B:ILE205 4.3 62.2 1.0 ND1 B:HIS160 4.3 46.8 1.0 ND1 B:HIS129 4.3 42.5 1.0 CG B:GLU133 4.3 45.4 1.0 CG B:HIS160 4.3 48.9 1.0 HG3 B:GLU133 4.3 55.0 1.0 CG B:HIS129 4.3 39.8 1.0 HE1 B:HIS204 4.4 39.4 1.0 CG B:GLU208 4.4 39.9 1.0 CE1 B:HIS204 4.5 32.4 1.0 HB2 B:GLU208 4.6 55.5 1.0 HB3 B:GLU208 4.6 55.5 1.0 HG2 B:GLU133 4.7 55.0 1.0 HA B:ILE205 4.8 50.4 1.0 CB B:GLU208 4.8 45.7 1.0 CZ B:PHE213 4.9 34.5 1.0 HG3 B:GLU208 4.9 48.5 1.0 HE2 B:PHE213 5.0 56.7 1.0 CD2 B:HIS204 5.0 45.9 1.0 HG2 B:GLU208 5.0 48.5 1.0

L.S.O.Silva, P.M.Matias, C.V.Romao, L.M.Saraiva. Repair of Iron Center Proteins-A Different Class of Hemerythrin-Like Proteins. Molecules V. 27 2022.
ISSN: ESSN 1420-3049
PubMed: 35807291
DOI: 10.3390/MOLECULES27134051