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Sodium in PDB 4u0p: The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine

Enzymatic activity of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine

All present enzymatic activity of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine:
2.8.1.8;

Protein crystallography data

The structure of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine, PDB code: 4u0p was solved by J.E.Harmer, M.J.Hiscox, J.Sandy, P.C.Dinis, P.L.Roach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.89 / 1.62
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 71.090, 161.130, 59.470, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.7

Other elements in 4u0p:

The structure of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine (pdb code 4u0p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine, PDB code: 4u0p:

Sodium binding site 1 out of 1 in 4u0p

Go back to Sodium Binding Sites List in 4u0p
Sodium binding site 1 out of 1 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:45.7
occ:1.00
OG B:SER283 2.4 29.2 1.0
O B:HOH569 2.4 55.4 1.0
O B:HOH570 2.6 42.3 1.0
H B:SER283 3.0 34.6 1.0
HB2 B:SER282 3.3 36.5 1.0
HB3 B:SER283 3.4 36.0 1.0
HG21 B:ILE36 3.4 42.6 1.0
HG21 B:THR55 3.5 30.2 1.0
CB B:SER283 3.5 30.0 1.0
FE4 B:SF4302 3.5 29.2 1.0
N B:SER283 3.7 28.9 1.0
HB3 B:ARG281 3.7 39.2 1.0
S1 B:SF4302 3.7 29.6 1.0
H B:SER282 4.0 35.5 1.0
OG1 B:THR55 4.1 26.5 1.0
CB B:SER282 4.2 30.4 1.0
HB2 B:SER283 4.2 36.0 1.0
HB2 B:ARG281 4.2 39.2 1.0
HD22 B:LEU138 4.2 40.8 1.0
CA B:SER283 4.2 27.1 1.0
N B:SER282 4.3 29.5 1.0
CG2 B:ILE36 4.3 35.5 1.0
O B:HOH552 4.3 42.7 1.0
HG22 B:ILE36 4.3 42.6 1.0
CG2 B:THR55 4.3 25.2 1.0
HB B:THR55 4.4 32.6 1.0
CB B:ARG281 4.4 32.7 1.0
O B:HOH553 4.5 37.5 1.0
HD23 B:LEU138 4.5 40.8 1.0
HB B:ILE36 4.5 35.8 1.0
C B:SER282 4.5 32.5 1.0
HD21 B:LEU138 4.5 40.8 1.0
HG1 B:THR55 4.5 31.8 1.0
CA B:SER282 4.5 30.2 1.0
CB B:THR55 4.6 27.2 1.0
CD2 B:LEU138 4.6 34.0 1.0
HG13 B:ILE36 4.7 38.5 1.0
HB3 B:SER282 4.7 36.5 1.0
HG23 B:THR55 4.8 30.2 1.0
HA B:SER283 4.9 32.6 1.0
CB B:ILE36 4.9 29.8 1.0
C B:ARG281 4.9 28.7 1.0
OG B:SER282 4.9 39.4 1.0
HG22 B:THR55 5.0 30.2 1.0
HG23 B:ILE36 5.0 42.6 1.0

Reference:

J.E.Harmer, M.J.Hiscox, P.C.Dinis, S.J.Fox, A.Iliopoulos, J.E.Hussey, J.Sandy, F.T.Van Beek, J.W.Essex, P.L.Roach. Structures of Lipoyl Synthase Reveal A Compact Active Site For Controlling Sequential Sulfur Insertion Reactions. Biochem.J. V. 464 123 2014.
ISSN: ESSN 1470-8728
PubMed: 25100160
DOI: 10.1042/BJ20140895
Page generated: Tue Dec 15 07:39:08 2020

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