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Sodium in PDB 6c9u: Crystal Structure of [KS3][AT3] Didomain From Module 3 of 6- Deoxyerthronolide B Synthase in Complex with Antibody Fragment (Fab)

Enzymatic activity of Crystal Structure of [KS3][AT3] Didomain From Module 3 of 6- Deoxyerthronolide B Synthase in Complex with Antibody Fragment (Fab)

All present enzymatic activity of Crystal Structure of [KS3][AT3] Didomain From Module 3 of 6- Deoxyerthronolide B Synthase in Complex with Antibody Fragment (Fab):
2.3.1.94;

Protein crystallography data

The structure of Crystal Structure of [KS3][AT3] Didomain From Module 3 of 6- Deoxyerthronolide B Synthase in Complex with Antibody Fragment (Fab), PDB code: 6c9u was solved by L.N.Deis, X.Li, I.I.Mathews, C.Khosla, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.08 / 2.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.768, 139.684, 102.580, 90.00, 97.05, 90.00
R / Rfree (%) 16.6 / 21

Other elements in 6c9u:

The structure of Crystal Structure of [KS3][AT3] Didomain From Module 3 of 6- Deoxyerthronolide B Synthase in Complex with Antibody Fragment (Fab) also contains other interesting chemical elements:

Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of [KS3][AT3] Didomain From Module 3 of 6- Deoxyerthronolide B Synthase in Complex with Antibody Fragment (Fab) (pdb code 6c9u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of [KS3][AT3] Didomain From Module 3 of 6- Deoxyerthronolide B Synthase in Complex with Antibody Fragment (Fab), PDB code: 6c9u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6c9u

Go back to Sodium Binding Sites List in 6c9u
Sodium binding site 1 out of 2 in the Crystal Structure of [KS3][AT3] Didomain From Module 3 of 6- Deoxyerthronolide B Synthase in Complex with Antibody Fragment (Fab)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of [KS3][AT3] Didomain From Module 3 of 6- Deoxyerthronolide B Synthase in Complex with Antibody Fragment (Fab) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1002

b:55.2
occ:1.00
 OE2 A:GLU850 2.3 92.5 1.0
O A:GLU844 2.6 71.4 1.0
O A:ALA846 2.6 68.0 1.0
O A:VAL843 2.6 47.5 1.0
HA A:GLU844 2.9 81.1 1.0
CD A:GLU850 3.1 99.4 1.0
C A:GLU844 3.3 68.6 1.0
OE1 A:GLU850 3.3 92.8 1.0
O A:GLY848 3.5 81.2 1.0
CA A:GLU844 3.5 67.6 1.0
H A:ALA846 3.6 81.7 1.0
H A:GLY848 3.6 89.0 1.0
C A:VAL843 3.7 54.0 1.0
C A:ALA846 3.7 65.1 1.0
HA A:GLU850 3.8 90.0 1.0
N A:ALA846 3.9 68.1 1.0
O A:ALA849 3.9 72.4 1.0
N A:GLU844 4.1 54.2 1.0
HB3 A:ALA846 4.1 70.1 1.0
HG12 A:VAL843 4.2 54.1 1.0
N A:GLY848 4.3 74.2 1.0
CA A:ALA846 4.3 65.0 1.0
C A:GLY848 4.3 73.8 1.0
CG A:GLU850 4.3 84.2 1.0
N A:GLU845 4.4 69.7 1.0
HG2 A:GLU850 4.4 0.1 1.0
C A:GLU845 4.5 65.5 1.0
C A:ALA849 4.6 76.7 1.0
CA A:GLU850 4.6 75.0 1.0
OE2 A:GLU844 4.7 97.6 1.0
CD A:GLU844 4.7 97.0 1.0
HA A:ASP847 4.7 78.6 1.0
HG13 A:VAL843 4.7 54.1 1.0
CB A:ALA846 4.8 58.4 1.0
N A:ASP847 4.8 70.7 1.0
HG3 A:GLU844 4.8 95.4 1.0
CA A:GLY848 4.9 69.2 1.0
CB A:GLU844 4.9 65.2 1.0
CG1 A:VAL843 4.9 45.1 1.0
OE1 A:GLU844 4.9 93.2 1.0
CA A:GLU845 5.0 72.9 1.0
N A:GLU850 5.0 67.2 1.0
H A:GLU844 5.0 65.1 1.0

Sodium binding site 2 out of 2 in 6c9u

Go back to Sodium Binding Sites List in 6c9u
Sodium binding site 2 out of 2 in the Crystal Structure of [KS3][AT3] Didomain From Module 3 of 6- Deoxyerthronolide B Synthase in Complex with Antibody Fragment (Fab)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of [KS3][AT3] Didomain From Module 3 of 6- Deoxyerthronolide B Synthase in Complex with Antibody Fragment (Fab) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1003

b:20.7
occ:1.00
 O A:HOH1489 2.3 38.5 1.0
O A:ALA545 2.4 25.1 1.0
O A:VAL548 2.5 29.6 1.0
O A:HOH1287 2.6 38.9 1.0
O A:ALA543 2.6 30.2 1.0
O A:HOH1377 2.9 48.2 1.0
HA A:ASP546 3.4 49.5 1.0
C A:ALA545 3.5 40.0 1.0
HB1 A:ALA543 3.6 39.8 1.0
C A:ALA543 3.7 39.7 1.0
C A:VAL548 3.7 28.0 1.0
H A:VAL548 3.8 31.2 1.0
HG12 A:VAL549 3.9 43.2 1.0
O A:THR544 4.1 37.4 1.0
HB A:VAL548 4.1 32.2 1.0
HA A:VAL549 4.1 29.2 1.0
CA A:ASP546 4.1 41.2 1.0
C A:THR544 4.1 39.1 1.0
N A:ASP546 4.2 28.4 1.0
CB A:ALA543 4.3 33.2 1.0
O A:ASP546 4.3 29.5 1.0
C A:ASP546 4.3 35.3 1.0
N A:ALA545 4.4 33.6 1.0
HA A:THR544 4.4 46.2 1.0
HB3 A:ALA543 4.4 39.8 1.0
N A:VAL548 4.4 26.0 1.0
CA A:VAL548 4.5 29.9 1.0
CA A:ALA543 4.5 31.0 1.0
N A:THR544 4.6 35.5 1.0
CA A:ALA545 4.6 36.4 1.0
HG13 A:VAL549 4.6 43.2 1.0
CG1 A:VAL549 4.6 36.0 1.0
CA A:THR544 4.6 38.5 1.0
N A:VAL549 4.7 18.7 1.0
HA A:ALA543 4.7 37.2 1.0
CB A:VAL548 4.7 26.8 1.0
H A:ALA545 4.8 40.3 1.0
CA A:VAL549 4.8 24.3 1.0
O A:HOH1371 4.9 31.9 1.0
HG12 A:VAL548 4.9 33.2 1.0

Reference:

X.Li, N.Sevillano, F.La Greca, L.Deis, Y.C.Liu, M.C.Deller, I.I.Mathews, T.Matsui, D.E.Cane, C.S.Craik, C.Khosla. Structure-Function Analysis of the Extended Conformation of A Polyketide Synthase Module. J. Am. Chem. Soc. V. 140 6518 2018.
ISSN: ESSN 1520-5126
PubMed: 29762030
DOI: 10.1021/JACS.8B02100
Page generated: Tue Dec 15 12:02:00 2020

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