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Manganese in PDB 4iw3: Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) in Complex with Elongation Factor Tu (Ef-Tu)

Protein crystallography data

The structure of Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) in Complex with Elongation Factor Tu (Ef-Tu), PDB code: 4iw3 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) 29.56 / 2.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 200.704, 200.704, 74.833, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / 21.8

Other elements in 4iw3:

The structure of Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) in Complex with Elongation Factor Tu (Ef-Tu) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) in Complex with Elongation Factor Tu (Ef-Tu) (pdb code 4iw3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) in Complex with Elongation Factor Tu (Ef-Tu), PDB code: 4iw3:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4iw3

Go back to Manganese Binding Sites List in 4iw3
Manganese binding site 1 out of 2 in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) in Complex with Elongation Factor Tu (Ef-Tu)


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) in Complex with Elongation Factor Tu (Ef-Tu) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:39.5
occ:1.00
O A:HOH563 2.1 30.3 1.0
O2 A:OGA402 2.1 27.0 1.0
NE2 A:HIS183 2.1 23.1 1.0
OD1 A:ASP126 2.2 24.0 1.0
O2' A:OGA402 2.2 36.9 1.0
NE2 A:HIS124 2.2 21.1 1.0
C2 A:OGA402 2.8 33.2 1.0
C1 A:OGA402 2.8 41.7 1.0
CE1 A:HIS183 3.1 25.6 1.0
CG A:ASP126 3.1 37.4 1.0
CE1 A:HIS124 3.2 21.5 1.0
CD2 A:HIS183 3.2 21.7 1.0
CD2 A:HIS124 3.2 23.9 1.0
OD2 A:ASP126 3.4 20.9 1.0
O1 A:OGA402 4.0 46.8 1.0
N1 A:OGA402 4.0 43.2 1.0
ND1 A:HIS183 4.2 19.9 1.0
ND1 A:HIS124 4.3 23.6 1.0
CG A:HIS183 4.3 25.9 1.0
CG B:PRO54 4.3 37.9 1.0
CG A:HIS124 4.3 27.6 1.0
CE2 A:TYR121 4.4 25.6 1.0
CB A:ASP126 4.5 20.5 1.0
C4 A:OGA402 4.7 49.2 1.0
CD2 A:TYR121 4.8 35.2 1.0
CD B:PRO54 4.8 38.5 1.0
CZ A:PHE176 4.9 17.1 1.0
CA A:ASP126 4.9 23.9 1.0
CZ A:TYR121 4.9 32.2 1.0

Manganese binding site 2 out of 2 in 4iw3

Go back to Manganese Binding Sites List in 4iw3
Manganese binding site 2 out of 2 in the Crystal Structure of A Pseudomonas Putida Prolyl-4-Hydroxylase (P4H) in Complex with Elongation Factor Tu (Ef-Tu)


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) in Complex with Elongation Factor Tu (Ef-Tu) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn401

b:16.7
occ:1.00
NE2 J:HIS183 2.1 31.1 1.0
O2 J:OGA402 2.2 22.0 1.0
NE2 J:HIS124 2.2 25.2 1.0
OD1 J:ASP126 2.2 25.0 1.0
O2' J:OGA402 2.3 14.3 1.0
O J:HOH532 2.3 32.2 1.0
C2 J:OGA402 2.8 32.9 1.0
C1 J:OGA402 2.8 39.8 1.0
CE1 J:HIS124 2.9 31.7 1.0
CG J:ASP126 3.1 34.7 1.0
CE1 J:HIS183 3.1 36.4 1.0
CD2 J:HIS183 3.1 25.3 1.0
OD2 J:ASP126 3.2 27.6 1.0
CD2 J:HIS124 3.4 26.5 1.0
CG K:PRO54 3.9 47.5 1.0
O1 J:OGA402 4.1 45.4 1.0
N1 J:OGA402 4.1 27.9 1.0
ND1 J:HIS124 4.2 30.2 1.0
ND1 J:HIS183 4.2 29.5 1.0
CG J:HIS183 4.2 28.1 1.0
CG J:HIS124 4.4 34.9 1.0
CE2 J:TYR121 4.4 28.8 1.0
CB J:ASP126 4.5 23.1 1.0
CD K:PRO54 4.5 40.7 1.0
CZ2 J:TRP198 4.7 28.2 1.0
CD2 J:TYR121 4.8 36.4 1.0
CA J:ASP126 4.8 28.3 1.0
C4 J:OGA402 4.9 39.2 1.0
NE1 J:TRP198 4.9 37.4 1.0
CZ J:TYR121 5.0 30.4 1.0

Reference:

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
Page generated: Tue Dec 15 04:22:53 2020

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