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Magnesium 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:

Manganese (Mn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4iw3

Go back to Magnesium Binding Sites List in 4iw3
Magnesium 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 Magnesium with other atoms in the Mg 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
B:Mg502

b:60.4
occ:1.00
OG1 B:THR26 2.0 69.4 1.0
O B:HOH616 2.1 48.3 1.0
O1B B:GDP501 2.4 69.1 1.0
O B:CYS82 3.3 65.5 1.0
CB B:THR26 3.3 80.5 1.0
O3B B:GDP501 3.4 58.7 1.0
PB B:GDP501 3.5 71.7 1.0
NZ B:LYS25 3.7 98.5 1.0
OD1 B:ASP81 3.8 63.8 1.0
N B:THR26 3.8 84.4 1.0
OD2 B:ASP81 3.9 81.8 1.0
CA B:THR26 4.1 89.8 1.0
O2B B:GDP501 4.2 54.6 1.0
O B:PRO83 4.2 78.0 1.0
CG B:ASP81 4.2 77.1 1.0
C B:CYS82 4.3 66.8 1.0
CG2 B:THR26 4.4 80.6 1.0
CA B:PRO83 4.4 65.5 1.0
CB B:LYS25 4.5 71.7 1.0
O2A B:GDP501 4.7 82.3 1.0
N B:PRO83 4.7 71.1 1.0
O3A B:GDP501 4.8 0.5 1.0
C B:PRO83 4.8 71.5 1.0
C B:LYS25 4.9 75.6 1.0

Magnesium binding site 2 out of 2 in 4iw3

Go back to Magnesium Binding Sites List in 4iw3
Magnesium 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 Magnesium with other atoms in the Mg 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
K:Mg401

b:48.3
occ:1.00
OG1 K:THR26 2.0 69.0 1.0
O K:HOH525 2.1 45.4 1.0
O K:HOH536 2.1 56.3 1.0
O K:HOH537 2.1 51.8 1.0
O1B K:GDP402 2.5 54.9 1.0
O K:CYS82 3.1 89.1 1.0
CB K:THR26 3.4 64.7 1.0
OD2 K:ASP81 3.5 77.4 1.0
PB K:GDP402 3.6 56.9 1.0
O3B K:GDP402 3.7 41.3 1.0
OD1 K:ASP81 3.9 88.2 1.0
C K:CYS82 4.0 69.5 1.0
CA K:PRO83 4.1 63.7 1.0
CG K:ASP81 4.1 83.2 1.0
O K:PRO83 4.1 62.8 1.0
N K:THR26 4.2 71.0 1.0
CA K:THR26 4.2 68.7 1.0
CG2 K:THR26 4.3 60.3 1.0
N K:PRO83 4.4 64.3 1.0
CE K:LYS25 4.5 54.3 1.0
O2B K:GDP402 4.5 39.1 1.0
C K:PRO83 4.6 66.7 1.0
O2A K:GDP402 4.7 66.2 1.0
CB K:LYS25 4.9 55.4 1.0
O3A K:GDP402 4.9 0.5 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: Fri Aug 16 17:03:05 2024

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