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Sodium in PDB 6g8b: E. Coli Aminopeptidase N Solved By Native Sad From A Dataset Collected in 60 Second with Jungfrau Detector

Enzymatic activity of E. Coli Aminopeptidase N Solved By Native Sad From A Dataset Collected in 60 Second with Jungfrau Detector

All present enzymatic activity of E. Coli Aminopeptidase N Solved By Native Sad From A Dataset Collected in 60 Second with Jungfrau Detector:
3.4.11.2;

Protein crystallography data

The structure of E. Coli Aminopeptidase N Solved By Native Sad From A Dataset Collected in 60 Second with Jungfrau Detector, PDB code: 6g8b was solved by F.Leonarski, V.Olieric, S.Redford, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.79 / 2.37
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 122.109, 122.109, 172.021, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 20.6

Other elements in 6g8b:

The structure of E. Coli Aminopeptidase N Solved By Native Sad From A Dataset Collected in 60 Second with Jungfrau Detector also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli Aminopeptidase N Solved By Native Sad From A Dataset Collected in 60 Second with Jungfrau Detector (pdb code 6g8b). 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 E. Coli Aminopeptidase N Solved By Native Sad From A Dataset Collected in 60 Second with Jungfrau Detector, PDB code: 6g8b:

Sodium binding site 1 out of 1 in 6g8b

Go back to Sodium Binding Sites List in 6g8b
Sodium binding site 1 out of 1 in the E. Coli Aminopeptidase N Solved By Native Sad From A Dataset Collected in 60 Second with Jungfrau Detector


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli Aminopeptidase N Solved By Native Sad From A Dataset Collected in 60 Second with Jungfrau Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1002

b:27.8
occ:1.00
 O A:GLY335 2.3 15.7 1.0
O A:HOH1636 2.4 30.1 1.0
O A:HOH1612 2.4 27.4 1.0
O A:SER332 2.4 20.8 1.0
O A:HOH1594 2.6 20.0 1.0
O A:ASP333 2.9 14.8 1.0
HA A:ASP333 3.3 16.7 1.0
C A:ASP333 3.4 10.4 1.0
C A:GLY335 3.5 18.9 1.0
C A:SER332 3.6 13.3 1.0
H A:ARG337 3.6 18.7 1.0
CA A:ASP333 3.8 14.0 1.0
HB2 A:ARG337 3.9 22.1 1.0
N A:GLY335 4.0 13.6 1.0
H A:GLY335 4.0 16.2 1.0
HA A:SER336 4.0 18.4 1.0
N A:ARG337 4.1 15.6 1.0
N A:ASP333 4.2 12.0 1.0
O A:HOH1424 4.2 27.9 1.0
N A:LEU334 4.2 13.2 1.0
CA A:GLY335 4.3 10.3 1.0
C A:LEU334 4.3 16.0 1.0
N A:SER336 4.4 17.8 1.0
O A:HOH1371 4.4 31.6 1.0
O A:HOH1668 4.5 29.4 1.0
CA A:SER336 4.6 15.4 1.0
HA2 A:GLY335 4.7 12.3 1.0
O A:HOH1712 4.7 37.3 1.0
CB A:ARG337 4.7 18.4 1.0
HA A:SER332 4.7 25.1 1.0
C A:SER336 4.7 10.8 1.0
O A:LEU334 4.7 16.2 1.0
CA A:LEU334 4.7 12.7 1.0
CA A:SER332 4.8 20.9 1.0
H A:LEU334 4.8 15.8 1.0
HB3 A:ARG337 4.8 22.1 1.0
HA A:LEU334 4.8 15.2 1.0
CA A:ARG337 4.9 17.6 1.0
HE A:ARG337 5.0 16.6 1.0

Reference:

F.Leonarski, S.Redford, A.Mozzanica, C.Lopez-Cuenca, E.Panepucci, K.Nass, D.Ozerov, L.Vera, V.Olieric, D.Buntschu, R.Schneider, G.Tinti, E.Froejdh, K.Diederichs, O.Bunk, B.Schmitt, M.Wang. Fast and Accurate Data Collection For Macromolecular Crystallography Using the Jungfrau Detector. Nat. Methods V. 15 799 2018.
ISSN: ESSN 1548-7105
PubMed: 30275593
DOI: 10.1038/S41592-018-0143-7
Page generated: Tue Dec 15 12:16:51 2020

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