Manganese in PDB 5u5d: PSF4 in Complex with MN2+ and (R)-2-Hpp

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

The structure of PSF4 in Complex with MN2+ and (R)-2-Hpp, PDB code: 5u5d 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)	84.12 / 2.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.464, 111.287, 128.499, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25

The binding sites of Manganese atom in the PSF4 in Complex with MN2+ and (R)-2-Hpp (pdb code 5u5d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the PSF4 in Complex with MN2+ and (R)-2-Hpp, PDB code: 5u5d:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the PSF4 in Complex with MN2+ and (R)-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 (R)-2-Hpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:37.8 occ:1.00 O13 A:TB6302 2.2 36.5 1.0 OE1 A:GLU132 2.3 36.3 1.0 O A:HOH446 2.3 39.0 1.0 NE2 A:HIS128 2.3 40.7 1.0 NE2 A:HIS171 2.5 35.7 1.0 O10 A:TB6302 2.5 35.2 1.0 CD A:GLU132 3.0 33.7 1.0 CE1 A:HIS171 3.1 33.3 1.0 C2 A:TB6302 3.1 37.4 1.0 OE2 A:GLU132 3.1 35.9 1.0 CE1 A:HIS128 3.2 39.0 1.0 P7 A:TB6302 3.3 36.4 1.0 CD2 A:HIS128 3.3 38.8 1.0 C6 A:TB6302 3.5 36.5 1.0 CD2 A:HIS171 3.7 37.6 1.0 ND2 A:ASN125 3.9 41.8 1.0 OD1 A:ASN188 4.1 41.5 1.0 O12 A:TB6302 4.3 36.5 1.0 O14 A:TB6302 4.3 39.2 1.0 ND1 A:HIS171 4.3 35.6 1.0 ND1 A:HIS128 4.3 43.2 1.0 CG A:HIS128 4.4 40.4 1.0 CG A:GLU132 4.5 31.0 1.0 C1 A:TB6302 4.5 42.3 1.0 CG A:HIS171 4.7 35.6 1.0 ND2 A:ASN188 4.9 47.3 1.0 CG A:ASN188 4.9 37.0 1.0 CB A:GLU132 5.0 31.4 1.0

Manganese binding site 2 out of 3 in the PSF4 in Complex with MN2+ and (R)-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 (R)-2-Hpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:92.4 occ:1.00 O12 B:TB6302 2.4 89.0 1.0 NE2 B:HIS128 2.4 88.7 1.0 OE1 B:GLU132 2.5 48.7 1.0 NE2 B:HIS171 2.5 48.2 1.0 O10 B:TB6302 2.6 64.4 1.0 C2 B:TB6302 3.1 75.8 1.0 P7 B:TB6302 3.1 82.3 1.0 OE2 B:GLU132 3.2 50.2 1.0 CD B:GLU132 3.2 46.5 1.0 CE1 B:HIS171 3.2 45.4 1.0 O13 B:TB6302 3.3 66.9 1.0 CE1 B:HIS128 3.4 88.8 1.0 CD2 B:HIS128 3.4 87.3 1.0 C6 B:TB6302 3.5 83.8 1.0 CD2 B:HIS171 3.7 42.9 1.0 ND2 B:ASN125 3.9 70.6 1.0 OD1 B:ASN188 4.1 38.3 1.0 NZ D:LYS21 4.4 82.9 1.0 ND1 B:HIS171 4.4 43.9 1.0 ND1 B:HIS128 4.5 95.1 1.0 C1 B:TB6302 4.5 79.6 1.0 CG B:HIS128 4.5 89.6 1.0 O14 B:TB6302 4.6 82.1 1.0 CG B:GLU132 4.6 45.5 1.0 CG B:HIS171 4.7 43.0 1.0 ND2 B:ASN188 4.8 51.2 1.0 CG B:ASN188 4.9 39.2 1.0

Manganese binding site 3 out of 3 in the PSF4 in Complex with MN2+ and (R)-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 (R)-2-Hpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:69.9 occ:1.00 O10 D:TB6302 1.9 61.0 1.0 O13 D:TB6302 2.2 56.9 1.0 NE2 D:HIS128 2.5 68.7 1.0 OE1 D:GLU132 2.6 43.6 1.0 NE2 D:HIS171 2.7 37.4 1.0 C2 D:TB6302 3.0 59.5 1.0 OE2 D:GLU132 3.1 40.9 1.0 CD D:GLU132 3.2 38.6 1.0 P7 D:TB6302 3.3 61.0 1.0 CE1 D:HIS171 3.4 38.7 1.0 CD2 D:HIS128 3.4 71.3 1.0 C6 D:TB6302 3.5 59.2 1.0 CE1 D:HIS128 3.5 71.6 1.0 CD2 D:HIS171 3.9 33.3 1.0 ND2 D:ASN125 3.9 78.3 1.0 OD1 D:ASN188 4.2 46.2 1.0 C1 D:TB6302 4.2 65.6 1.0 O12 D:TB6302 4.3 62.2 1.0 O14 D:TB6302 4.3 60.1 1.0 NZ B:LYS21 4.6 63.8 1.0 CG D:HIS128 4.6 73.8 1.0 ND1 D:HIS171 4.6 36.9 1.0 ND1 D:HIS128 4.6 73.8 1.0 CG D:GLU132 4.7 38.5 1.0 ND2 D:ASN188 4.8 46.8 1.0 CG D:HIS171 4.9 35.1 1.0 CG D:ASN188 4.9 39.8 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