Manganese in PDB 5u55: PSF4 in Complex with MN2+ and (S)-2-Hpp

All present enzymatic activity of PSF4 in Complex with MN2+ and (S)-2-Hpp:
1.11.1.23;

The structure of PSF4 in Complex with MN2+ and (S)-2-Hpp, PDB code: 5u55 was solved by J.R.Chekan, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.11 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.290, 111.005, 128.887, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.3

The binding sites of Manganese atom in the PSF4 in Complex with MN2+ and (S)-2-Hpp (pdb code 5u55). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the PSF4 in Complex with MN2+ and (S)-2-Hpp, PDB code: 5u55:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the PSF4 in Complex with MN2+ and (S)-2-Hpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of PSF4 in Complex with MN2+ and (S)-2-Hpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:37.7 occ:1.00 O A:HOH419 2.0 37.9 1.0 O6 A:S0H302 2.1 37.9 1.0 OE1 A:GLU132 2.2 38.8 1.0 O13 A:S0H302 2.2 33.3 1.0 NE2 A:HIS171 2.3 29.3 1.0 NE2 A:HIS128 2.3 44.1 1.0 CD A:GLU132 3.0 36.5 1.0 CE1 A:HIS171 3.1 32.0 1.0 OE2 A:GLU132 3.2 39.1 1.0 CE1 A:HIS128 3.2 42.4 1.0 C3 A:S0H302 3.3 35.5 1.0 P1 A:S0H302 3.3 36.8 1.0 CD2 A:HIS128 3.3 47.1 1.0 CD2 A:HIS171 3.4 33.9 1.0 C2 A:S0H302 3.6 36.7 1.0 ND2 A:ASN125 3.9 37.0 1.0 O14 A:S0H302 4.0 31.1 1.0 OD1 A:ASN188 4.1 40.9 1.0 ND1 A:HIS171 4.3 33.2 1.0 ND1 A:HIS128 4.4 45.4 1.0 CG A:GLU132 4.4 36.7 1.0 C1 A:S0H302 4.4 36.3 1.0 CG A:HIS128 4.5 43.1 1.0 CG A:HIS171 4.5 34.5 1.0 O15 A:S0H302 4.6 34.6 1.0 NZ D:LYS21 4.7 51.7 1.0 ND2 A:ASN188 4.8 45.8 1.0 CG A:ASN188 4.9 37.6 1.0 CB A:GLU132 4.9 35.1 1.0

Manganese binding site 2 out of 4 in the PSF4 in Complex with MN2+ and (S)-2-Hpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of PSF4 in Complex with MN2+ and (S)-2-Hpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:42.4 occ:1.00 O6 B:S0H302 2.0 44.0 1.0 O15 B:S0H302 2.1 46.8 1.0 NE2 B:HIS171 2.2 31.6 1.0 OE1 B:GLU132 2.2 51.1 1.0 O B:HOH407 2.3 28.4 1.0 NE2 B:HIS128 2.4 61.4 1.0 CE1 B:HIS171 3.0 32.4 1.0 CD B:GLU132 3.1 47.0 1.0 C3 B:S0H302 3.2 46.2 1.0 P1 B:S0H302 3.2 47.0 1.0 CE1 B:HIS128 3.2 55.1 1.0 OE2 B:GLU132 3.3 52.7 1.0 CD2 B:HIS171 3.3 34.0 1.0 CD2 B:HIS128 3.4 62.2 1.0 C2 B:S0H302 3.4 50.0 1.0 ND2 B:ASN125 3.9 52.9 1.0 O13 B:S0H302 4.0 41.4 1.0 ND1 B:HIS171 4.2 36.1 1.0 OD1 B:ASN188 4.3 42.9 1.0 C1 B:S0H302 4.3 49.4 1.0 CG B:HIS171 4.4 36.6 1.0 ND1 B:HIS128 4.4 54.8 1.0 O14 B:S0H302 4.5 43.5 1.0 CG B:HIS128 4.5 62.0 1.0 CG B:GLU132 4.5 44.0 1.0 NZ C:LYS21 4.6 65.2 1.0 CB B:GLU132 4.9 37.0 1.0

Manganese binding site 3 out of 4 in the PSF4 in Complex with MN2+ and (S)-2-Hpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of PSF4 in Complex with MN2+ and (S)-2-Hpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:36.2 occ:1.00 O6 C:S0H302 1.8 38.6 1.0 O13 C:S0H302 2.1 31.9 1.0 OE1 C:GLU132 2.2 33.9 1.0 NE2 C:HIS128 2.3 38.1 1.0 O C:HOH425 2.3 38.2 1.0 NE2 C:HIS171 2.4 35.1 1.0 CD C:GLU132 3.0 35.1 1.0 C3 C:S0H302 3.1 37.0 1.0 OE2 C:GLU132 3.2 33.9 1.0 CE1 C:HIS171 3.2 34.5 1.0 CE1 C:HIS128 3.2 40.3 1.0 P1 C:S0H302 3.3 36.7 1.0 CD2 C:HIS128 3.3 38.0 1.0 C2 C:S0H302 3.5 35.9 1.0 CD2 C:HIS171 3.6 34.5 1.0 ND2 C:ASN125 4.0 36.7 1.0 OD1 C:ASN188 4.1 39.1 1.0 C1 C:S0H302 4.2 38.7 1.0 O15 C:S0H302 4.2 34.1 1.0 ND1 C:HIS128 4.4 36.6 1.0 ND1 C:HIS171 4.4 35.1 1.0 CG C:GLU132 4.4 33.1 1.0 CG C:HIS128 4.5 37.6 1.0 O14 C:S0H302 4.5 37.0 1.0 NZ B:LYS21 4.5 41.8 1.0 CG C:HIS171 4.6 34.3 1.0 ND2 C:ASN188 4.7 41.2 1.0 CG C:ASN188 4.8 35.7 1.0 CB C:GLU132 4.9 33.1 1.0

Manganese binding site 4 out of 4 in the PSF4 in Complex with MN2+ and (S)-2-Hpp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of PSF4 in Complex with MN2+ and (S)-2-Hpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:49.4 occ:1.00 O14 D:S0H302 2.0 45.0 1.0 O6 D:S0H302 2.0 36.4 1.0 OE2 D:GLU132 2.2 42.4 1.0 NE2 D:HIS128 2.4 47.6 1.0 NE2 D:HIS171 2.4 45.7 1.0 CD D:GLU132 3.1 40.8 1.0 C3 D:S0H302 3.2 38.7 1.0 CE1 D:HIS171 3.2 41.3 1.0 P1 D:S0H302 3.3 45.2 1.0 OE1 D:GLU132 3.3 46.1 1.0 CE1 D:HIS128 3.3 51.4 1.0 CD2 D:HIS128 3.3 48.3 1.0 CD2 D:HIS171 3.6 37.4 1.0 C2 D:S0H302 3.6 38.6 1.0 ND2 D:ASN125 3.8 71.8 1.0 O15 D:S0H302 4.1 49.5 1.0 OD1 D:ASN188 4.1 41.2 1.0 C1 D:S0H302 4.3 40.6 1.0 ND1 D:HIS171 4.4 38.5 1.0 ND1 D:HIS128 4.4 55.2 1.0 O13 D:S0H302 4.5 41.0 1.0 CG D:GLU132 4.5 42.7 1.0 CG D:HIS128 4.5 54.7 1.0 CG D:HIS171 4.6 37.4 1.0 ND2 D:ASN188 4.7 48.0 1.0 NZ A:LYS21 4.7 51.8 1.0 CG D:ASN188 4.8 39.1 1.0

P.Olivares, E.C.Ulrich, J.R.Chekan, W.A.Van Der Donk, S.K.Nair. Characterization of Two Late-Stage Enzymes Involved in Fosfomycin Biosynthesis in Pseudomonads. Acs Chem. Biol. V. 12 456 2017.
ISSN: ESSN 1554-8937
PubMed: 27977135
DOI: 10.1021/ACSCHEMBIO.6B00939