Manganese in PDB 4j25: Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H)

The structure of Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H), PDB code: 4j25 was solved by J.S.Scotti, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.13 / 1.97
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.330, 62.160, 132.830, 91.84, 94.70, 90.08
R / Rfree (%)	21.2 / 25.7

The binding sites of Manganese atom in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) (pdb code 4j25). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H), PDB code: 4j25:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:21.3 occ:1.00 NE2 A:HIS183 2.1 13.7 1.0 O2' A:OGA402 2.1 24.2 1.0 OD1 A:ASP126 2.2 15.3 1.0 O2 A:OGA402 2.2 24.2 1.0 NE2 A:HIS124 2.2 19.5 1.0 O A:HOH503 2.2 14.9 1.0 C2 A:OGA402 2.7 26.3 1.0 C1 A:OGA402 2.8 26.8 1.0 CE1 A:HIS183 3.0 13.7 1.0 CE1 A:HIS124 3.0 20.1 1.0 CG A:ASP126 3.1 16.9 1.0 CD2 A:HIS183 3.2 14.0 1.0 CD2 A:HIS124 3.2 20.1 1.0 OD2 A:ASP126 3.3 17.6 1.0 O1 A:OGA402 4.0 25.8 1.0 N1 A:OGA402 4.1 27.6 1.0 ND1 A:HIS183 4.1 13.9 1.0 ND1 A:HIS124 4.2 21.1 1.0 CG A:HIS183 4.2 14.1 1.0 CG A:HIS124 4.3 21.3 1.0 CB A:ASP126 4.5 18.7 1.0 CE2 A:TYR121 4.7 31.6 1.0 C4 A:OGA402 4.7 27.4 1.0 CZ A:PHE176 4.9 15.4 1.0 CA A:ASP126 4.9 19.9 1.0 CZ A:TYR121 5.0 32.9 1.0

Manganese binding site 2 out of 8 in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:19.6 occ:1.00 O2 B:OGA402 2.1 24.0 1.0 NE2 B:HIS183 2.1 17.6 1.0 OD1 B:ASP126 2.2 19.7 1.0 NE2 B:HIS124 2.2 20.7 1.0 O B:HOH518 2.3 21.9 1.0 O2' B:OGA402 2.3 24.8 1.0 C2 B:OGA402 2.8 27.0 1.0 C1 B:OGA402 2.8 27.1 1.0 CE1 B:HIS183 3.1 16.4 1.0 CG B:ASP126 3.1 21.1 1.0 CE1 B:HIS124 3.1 20.7 1.0 CD2 B:HIS183 3.2 16.0 1.0 CD2 B:HIS124 3.2 20.3 1.0 OD2 B:ASP126 3.4 22.3 1.0 O1 B:OGA402 4.1 25.5 1.0 N1 B:OGA402 4.1 27.3 1.0 ND1 B:HIS183 4.2 14.5 1.0 ND1 B:HIS124 4.2 22.3 1.0 CG B:HIS183 4.3 14.5 1.0 CG B:HIS124 4.3 21.8 1.0 CB B:ASP126 4.5 23.3 1.0 CE1 B:TYR121 4.7 31.6 1.0 C4 B:OGA402 4.8 26.9 1.0 CZ B:PHE176 4.9 14.5 1.0 CA B:ASP126 4.9 26.7 1.0 N B:ASP126 5.0 25.5 1.0

Manganese binding site 3 out of 8 in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:20.1 occ:1.00 OD1 C:ASP126 2.1 21.8 1.0 NE2 C:HIS124 2.2 23.2 1.0 O2 C:OGA402 2.2 26.0 1.0 O2' C:OGA402 2.2 26.4 1.0 NE2 C:HIS183 2.2 19.8 1.0 O C:HOH508 2.3 23.5 1.0 C2 C:OGA402 2.8 26.1 1.0 C1 C:OGA402 2.8 27.8 1.0 CE1 C:HIS124 2.9 21.2 1.0 CG C:ASP126 3.1 23.4 1.0 CE1 C:HIS183 3.1 19.6 1.0 CD2 C:HIS183 3.3 18.9 1.0 CD2 C:HIS124 3.3 22.8 1.0 OD2 C:ASP126 3.3 25.5 1.0 O1 C:OGA402 4.0 29.8 1.0 O C:HOH588 4.0 38.2 1.0 N1 C:OGA402 4.1 27.1 1.0 ND1 C:HIS124 4.1 22.5 1.0 ND1 C:HIS183 4.3 18.4 1.0 CG C:HIS124 4.3 23.3 1.0 CG C:HIS183 4.4 17.7 1.0 CB C:ASP126 4.5 23.5 1.0 CE2 C:TYR121 4.7 30.0 1.0 C4 C:OGA402 4.7 25.6 1.0 CA C:ASP126 4.8 26.7 1.0 CZ2 C:TRP198 4.9 25.4 1.0 CZ C:PHE176 4.9 17.0 1.0 N C:ASP126 5.0 26.5 1.0 CZ C:TYR121 5.0 32.8 1.0

Manganese binding site 4 out of 8 in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:17.6 occ:1.00 OD1 D:ASP126 2.2 19.5 1.0 NE2 D:HIS183 2.2 17.0 1.0 O2' D:OGA402 2.2 26.6 1.0 O D:HOH505 2.3 18.7 1.0 O2 D:OGA402 2.3 25.9 1.0 NE2 D:HIS124 2.3 20.1 1.0 C2 D:OGA402 2.8 27.4 1.0 C1 D:OGA402 2.9 28.6 1.0 CG D:ASP126 3.1 21.3 1.0 CE1 D:HIS183 3.1 17.2 1.0 CD2 D:HIS183 3.2 17.3 1.0 CE1 D:HIS124 3.2 20.1 1.0 CD2 D:HIS124 3.3 21.8 1.0 OD2 D:ASP126 3.3 21.0 1.0 N1 D:OGA402 4.1 28.4 1.0 O1 D:OGA402 4.1 30.1 1.0 ND1 D:HIS183 4.2 18.3 1.0 CG D:HIS183 4.3 18.9 1.0 ND1 D:HIS124 4.3 20.8 1.0 CG D:HIS124 4.4 21.4 1.0 CB D:ASP126 4.5 21.3 1.0 C4 D:OGA402 4.6 28.0 1.0 O D:HOH520 4.7 32.5 1.0 CE2 D:TYR121 4.7 33.3 1.0 CA D:ASP126 4.9 21.6 1.0 CZ D:PHE176 4.9 14.7 1.0 CZ2 D:TRP198 5.0 19.2 1.0

Manganese binding site 5 out of 8 in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn401 b:20.1 occ:1.00 O2 E:OGA402 2.1 23.7 1.0 O2' E:OGA402 2.2 26.1 1.0 NE2 E:HIS183 2.2 20.2 1.0 OD1 E:ASP126 2.2 23.9 1.0 NE2 E:HIS124 2.2 24.9 1.0 O E:HOH509 2.3 21.4 1.0 C2 E:OGA402 2.8 25.6 1.0 C1 E:OGA402 2.8 26.5 1.0 CE1 E:HIS124 3.1 23.0 1.0 CG E:ASP126 3.1 23.7 1.0 CE1 E:HIS183 3.1 20.7 1.0 CD2 E:HIS183 3.2 19.8 1.0 CD2 E:HIS124 3.3 24.8 1.0 OD2 E:ASP126 3.3 23.5 1.0 O1 E:OGA402 4.0 28.7 1.0 N1 E:OGA402 4.1 24.9 1.0 O E:HOH504 4.2 27.5 1.0 ND1 E:HIS183 4.2 20.7 1.0 ND1 E:HIS124 4.2 21.6 1.0 O E:HOH516 4.2 33.2 1.0 CG E:HIS183 4.3 20.1 1.0 CG E:HIS124 4.4 23.3 1.0 CB E:ASP126 4.5 25.6 1.0 CZ2 E:TRP198 4.6 23.1 1.0 C4 E:OGA402 4.7 25.3 1.0 CE2 E:TYR121 4.8 24.3 1.0 O E:HOH530 4.8 29.2 1.0 CA E:ASP126 4.9 28.1 1.0 CZ E:TYR121 5.0 24.9 1.0

Manganese binding site 6 out of 8 in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn401 b:29.1 occ:1.00 O1 F:OGA402 2.1 30.8 1.0 NE2 F:HIS183 2.1 29.3 1.0 OD1 F:ASP126 2.2 34.8 1.0 O2' F:OGA402 2.2 29.9 1.0 O F:HOH506 2.3 25.3 1.0 NE2 F:HIS124 2.3 33.4 1.0 C1 F:OGA402 2.8 31.1 1.0 C2 F:OGA402 2.8 28.8 1.0 CE1 F:HIS183 2.9 30.2 1.0 CG F:ASP126 3.1 36.7 1.0 CD2 F:HIS183 3.2 28.1 1.0 CD2 F:HIS124 3.2 34.4 1.0 CE1 F:HIS124 3.3 33.4 1.0 OD2 F:ASP126 3.4 34.5 1.0 O2 F:OGA402 4.0 31.3 1.0 ND1 F:HIS183 4.1 29.8 1.0 N1 F:OGA402 4.1 28.6 1.0 CG F:HIS183 4.3 28.5 1.0 ND1 F:HIS124 4.4 34.4 1.0 CG F:HIS124 4.4 35.1 1.0 CB F:ASP126 4.5 38.8 1.0 CE2 F:TYR121 4.7 38.4 1.0 C4 F:OGA402 4.8 28.4 1.0 CZ2 F:TRP198 4.9 36.3 1.0 CA F:ASP126 4.9 40.5 1.0 CZ F:PHE176 4.9 30.1 1.0

Manganese binding site 7 out of 8 in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn401 b:25.5 occ:1.00 NE2 G:HIS124 2.1 29.6 1.0 NE2 G:HIS183 2.2 29.8 1.0 O G:HOH505 2.2 36.5 1.0 OD1 G:ASP126 2.2 28.7 1.0 O1 G:OGA402 2.4 31.2 1.0 O2' G:OGA402 2.4 30.9 1.0 CE1 G:HIS124 3.0 29.9 1.0 C2 G:OGA402 3.0 31.5 1.0 CD2 G:HIS183 3.1 30.2 1.0 C1 G:OGA402 3.1 32.1 1.0 CG G:ASP126 3.1 28.7 1.0 CE1 G:HIS183 3.1 28.6 1.0 CD2 G:HIS124 3.2 28.8 1.0 OD2 G:ASP126 3.4 30.8 1.0 ND1 G:HIS124 4.1 28.6 1.0 CG G:HIS124 4.2 27.9 1.0 ND1 G:HIS183 4.2 28.1 1.0 CG G:HIS183 4.3 29.4 1.0 N1 G:OGA402 4.3 30.5 1.0 O2 G:OGA402 4.3 32.1 1.0 O G:HOH509 4.3 29.3 1.0 CB G:ASP126 4.5 27.5 1.0 CE2 G:TYR121 4.6 33.4 1.0 CZ2 G:TRP198 4.8 30.7 1.0 CA G:ASP126 4.8 28.9 1.0 CZ G:TYR121 4.9 32.8 1.0 C4 G:OGA402 4.9 30.3 1.0 CZ G:PHE176 5.0 30.5 1.0

Manganese binding site 8 out of 8 in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn401 b:19.8 occ:1.00 O H:HOH502 2.1 26.7 1.0 NE2 H:HIS183 2.1 22.1 1.0 OD1 H:ASP126 2.2 20.4 1.0 NE2 H:HIS124 2.2 21.3 1.0 O2' H:OGA402 2.3 29.0 1.0 O1 H:OGA402 2.3 27.7 1.0 C2 H:OGA402 2.9 29.5 1.0 C1 H:OGA402 2.9 29.8 1.0 CD2 H:HIS183 3.1 22.2 1.0 CG H:ASP126 3.1 21.4 1.0 CE1 H:HIS124 3.1 22.9 1.0 CE1 H:HIS183 3.1 20.9 1.0 CD2 H:HIS124 3.2 22.8 1.0 OD2 H:ASP126 3.3 22.3 1.0 N1 H:OGA402 4.2 30.8 1.0 O2 H:OGA402 4.2 32.1 1.0 ND1 H:HIS183 4.2 21.8 1.0 ND1 H:HIS124 4.2 23.3 1.0 CG H:HIS183 4.2 23.5 1.0 CG H:HIS124 4.3 24.1 1.0 CB H:ASP126 4.5 23.1 1.0 CE2 H:TYR121 4.7 27.9 1.0 CZ2 H:TRP198 4.8 25.1 1.0 C4 H:OGA402 4.8 29.4 1.0 CA H:ASP126 4.9 25.6 1.0 CZ H:TYR121 4.9 29.1 1.0 OH H:TYR121 5.0 29.4 1.0

J.S.Scotti, I.K.H.Leung, W.Ge, M.A.Bentley, J.Paps, H.B.Kramer, J.Lee, W.Aik, H.Choi, S.M.Paulsen, L.A.H.Bowman, N.D.Loik, S.Horita, C.H.Ho, N.J.Kershaw, C.M.Tang, T.D.W.Claridge, G.M.Preston, M.A.Mcdonough, C.J.Schofield. Human Oxygen Sensing May Have Origins in Prokaryotic Elongation Factor Tu Prolyl-Hydroxylation Proc.Natl.Acad.Sci.Usa V. 111 13331 2014.
ISSN: ISSN 0027-8424
PubMed: 25197067
DOI: 10.1073/PNAS.1409916111