Manganese in PDB 7oyi: Escherichia Coli YTFE_E159L(Mn)

The structure of Escherichia Coli YTFE_E159L(Mn), PDB code: 7oyi was solved by L.S.O.Silva, P.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)	53.39 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.824, 49.671, 88.091, 90, 100.48, 90
R / Rfree (%)	18.1 / 20.5

The structure of Escherichia Coli YTFE_E159L(Mn) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Escherichia Coli YTFE_E159L(Mn) (pdb code 7oyi). 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_E159L(Mn), PDB code: 7oyi:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Escherichia Coli YTFE_E159L(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_E159L(Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:20.6 occ:1.00 OE2 A:GLU208 2.1 18.6 1.0 NE2 A:HIS84 2.2 19.7 1.0 OE1 A:GLU133 2.2 18.3 1.0 NE2 A:HIS204 2.3 19.5 1.0 O A:O303 2.5 26.1 1.0 CD A:GLU208 3.0 17.9 1.0 CE1 A:HIS84 3.1 21.9 1.0 CE1 A:HIS204 3.1 21.1 1.0 CD A:GLU133 3.1 18.7 1.0 HE1 A:HIS204 3.2 25.4 1.0 HE1 A:HIS84 3.2 26.4 1.0 CD2 A:HIS84 3.2 17.6 1.0 OE1 A:GLU208 3.2 16.0 1.0 MN A:MN302 3.2 22.6 1.0 HG22 A:ILE79 3.3 23.8 1.0 HZ A:PHE138 3.4 23.8 1.0 CD2 A:HIS204 3.4 21.6 1.0 OE2 A:GLU133 3.4 22.1 1.0 HD2 A:HIS84 3.4 21.1 1.0 HG2 A:MET130 3.6 24.7 1.0 HD2 A:HIS204 3.6 25.9 1.0 CG2 A:ILE79 3.8 19.8 1.0 HG23 A:ILE79 3.8 23.8 1.0 HG21 A:ILE79 3.9 23.8 1.0 CZ A:PHE138 4.2 19.8 1.0 ND1 A:HIS84 4.2 20.8 1.0 ND1 A:HIS204 4.3 19.6 1.0 CG A:GLU208 4.3 18.4 1.0 CG A:HIS84 4.3 20.5 1.0 HD2 A:HIS129 4.3 26.7 1.0 HE2 A:PHE138 4.4 26.1 1.0 CG A:HIS204 4.4 16.5 1.0 HA A:MET130 4.4 24.9 1.0 HG3 A:GLU208 4.5 22.1 1.0 HD12 A:ILE79 4.5 23.4 1.0 HB2 A:GLU133 4.5 22.8 1.0 CG A:GLU133 4.5 21.7 1.0 CG A:MET130 4.6 20.6 1.0 HG2 A:GLU208 4.6 22.1 1.0 NE2 A:HIS129 4.6 19.8 1.0 HB3 A:GLU133 4.6 22.8 1.0 CE2 A:PHE138 4.7 21.8 1.0 CD2 A:HIS129 4.8 22.2 1.0 CB A:GLU133 4.8 18.9 1.0 HG3 A:GLU133 4.9 26.1 1.0 HD1 A:HIS84 5.0 25.0 1.0

Manganese binding site 2 out of 4 in the Escherichia Coli YTFE_E159L(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_E159L(Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:22.6 occ:1.00 OE2 A:GLU133 2.0 22.1 1.0 NE2 A:HIS160 2.2 24.1 1.0 OE1 A:GLU208 2.2 16.0 1.0 NE2 A:HIS129 2.2 19.8 1.0 O A:O303 2.5 26.1 1.0 CD A:GLU133 2.9 18.7 1.0 CE1 A:HIS160 3.1 20.1 1.0 CE1 A:HIS129 3.1 22.7 1.0 CD A:GLU208 3.2 17.9 1.0 CD2 A:HIS160 3.2 19.9 1.0 CD2 A:HIS129 3.2 22.2 1.0 MN A:MN301 3.2 20.6 1.0 OE1 A:GLU133 3.3 18.3 1.0 HE1 A:HIS129 3.3 27.3 1.0 HE1 A:HIS160 3.3 24.2 1.0 HD2 A:HIS160 3.4 23.9 1.0 HD2 A:HIS129 3.4 26.7 1.0 OE2 A:GLU208 3.5 18.6 1.0 HZ A:PHE213 3.9 35.4 1.0 HB3 A:MET156 4.0 25.1 1.0 CG A:GLU133 4.2 21.7 1.0 ND1 A:HIS160 4.3 22.5 1.0 ND1 A:HIS129 4.3 23.5 1.0 HG3 A:GLU133 4.3 26.1 1.0 CG A:HIS160 4.3 20.9 1.0 CG A:HIS129 4.4 20.6 1.0 HG12 A:ILE205 4.5 25.5 1.0 NE2 A:HIS204 4.5 19.5 1.0 HG2 A:GLU133 4.5 26.1 1.0 CG A:GLU208 4.5 18.4 1.0 HB2 A:GLU208 4.6 21.9 1.0 HB3 A:GLU208 4.7 21.9 1.0 CZ A:PHE213 4.7 29.4 1.0 HE2 A:PHE213 4.7 29.2 1.0 CB A:GLU208 4.9 18.2 1.0 HA A:ILE205 4.9 23.3 1.0 CB A:MET156 5.0 20.9 1.0

Manganese binding site 3 out of 4 in the Escherichia Coli YTFE_E159L(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_E159L(Mn) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:34.8 occ:1.00 OE2 B:GLU208 2.1 43.1 1.0 OE1 B:GLU133 2.1 37.9 1.0 NE2 B:HIS204 2.2 42.9 1.0 NE2 B:HIS84 2.2 39.4 1.0 O B:O303 2.5 34.6 1.0 HE1 B:HIS204 2.8 48.3 1.0 CE1 B:HIS204 2.8 40.2 1.0 CD B:GLU208 3.0 46.1 1.0 CE1 B:HIS84 3.1 35.9 1.0 CD B:GLU133 3.1 37.5 1.0 HE1 B:HIS84 3.2 43.1 1.0 MN B:MN302 3.2 38.3 1.0 CD2 B:HIS84 3.3 37.3 1.0 HG22 B:ILE79 3.3 49.4 1.0 OE1 B:GLU208 3.3 40.0 1.0 OE2 B:GLU133 3.4 39.1 1.0 CD2 B:HIS204 3.4 39.9 1.0 HZ B:PHE138 3.4 45.5 1.0 HD2 B:HIS84 3.5 44.8 1.0 HG2 B:MET130 3.5 50.9 1.0 HD2 B:HIS204 3.7 48.0 1.0 HG23 B:ILE79 3.8 49.4 1.0 CG2 B:ILE79 3.8 41.1 1.0 HG21 B:ILE79 3.9 49.4 1.0 ND1 B:HIS204 4.0 38.1 1.0 HD2 B:HIS129 4.2 53.7 1.0 CZ B:PHE138 4.2 37.9 1.0 ND1 B:HIS84 4.2 40.2 1.0 CG B:HIS204 4.3 40.6 1.0 HA B:MET130 4.3 44.2 1.0 CG B:HIS84 4.3 35.7 1.0 HE2 B:PHE138 4.4 39.4 1.0 CG B:GLU208 4.4 42.5 1.0 CG B:GLU133 4.4 42.8 1.0 HB2 B:GLU133 4.5 45.8 1.0 CG B:MET130 4.5 42.4 1.0 HG3 B:GLU208 4.5 51.0 1.0 HB3 B:GLU133 4.6 45.8 1.0 HG2 B:GLU208 4.6 51.0 1.0 NE2 B:HIS129 4.6 44.3 1.0 CD2 B:HIS129 4.7 44.8 1.0 CE2 B:PHE138 4.7 32.8 1.0 HD1 B:HIS204 4.7 45.7 1.0 CB B:GLU133 4.8 38.1 1.0 HG3 B:GLU133 4.9 51.3 1.0 HG3 B:MET130 4.9 50.9 1.0 HD1 B:HIS84 5.0 48.3 1.0

Manganese binding site 4 out of 4 in the Escherichia Coli YTFE_E159L(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_E159L(Mn) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:38.3 occ:1.00 OE2 B:GLU133 2.1 39.1 1.0 OE1 B:GLU208 2.1 40.0 1.0 NE2 B:HIS129 2.2 44.3 1.0 NE2 B:HIS160 2.2 48.2 1.0 O B:O303 2.5 34.6 1.0 CD B:GLU133 2.9 37.5 1.0 CD2 B:HIS129 3.1 44.8 1.0 CE1 B:HIS160 3.1 45.0 1.0 CD B:GLU208 3.1 46.1 1.0 HD2 B:HIS129 3.2 53.7 1.0 OE1 B:GLU133 3.2 37.9 1.0 CD2 B:HIS160 3.2 39.7 1.0 CE1 B:HIS129 3.2 44.1 1.0 HE1 B:HIS160 3.2 54.0 1.0 MN B:MN301 3.2 34.8 1.0 OE2 B:GLU208 3.4 43.1 1.0 HD2 B:HIS160 3.4 47.6 1.0 HE1 B:HIS129 3.5 53.0 1.0 HZ B:PHE213 3.8 50.6 1.0 HB3 B:MET156 4.1 51.0 1.0 CG B:GLU133 4.2 42.8 1.0 ND1 B:HIS160 4.2 48.4 1.0 CG B:HIS129 4.3 39.7 1.0 HG3 B:GLU133 4.3 51.3 1.0 ND1 B:HIS129 4.3 43.7 1.0 CG B:HIS160 4.3 42.7 1.0 NE2 B:HIS204 4.4 42.9 1.0 HG2 B:GLU133 4.5 51.3 1.0 HG12 B:ILE205 4.5 56.8 1.0 CG B:GLU208 4.5 42.5 1.0 HB2 B:GLU208 4.6 53.0 1.0 HB3 B:GLU208 4.6 53.0 1.0 CZ B:PHE213 4.6 42.1 1.0 HE2 B:PHE213 4.6 55.6 1.0 HE1 B:HIS204 4.8 48.3 1.0 CE1 B:HIS204 4.8 40.2 1.0 CB B:GLU208 4.8 44.1 1.0 HA B:ILE205 4.9 49.3 1.0 HG2 B:GLU208 5.0 51.0 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