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Sodium in PDB 6g8a: Lysozyme Solved By Native Sad From A Dataset Collected in 5 Seconds at 1 A Wavelength with Jungfrau Detector

Enzymatic activity of Lysozyme Solved By Native Sad From A Dataset Collected in 5 Seconds at 1 A Wavelength with Jungfrau Detector

All present enzymatic activity of Lysozyme Solved By Native Sad From A Dataset Collected in 5 Seconds at 1 A Wavelength with Jungfrau Detector:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Solved By Native Sad From A Dataset Collected in 5 Seconds at 1 A Wavelength with Jungfrau Detector, PDB code: 6g8a was solved by F.Leonarski, V.Olieric, L.Vera, S.Redford, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.26 / 1.14
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.903, 78.903, 36.941, 90.00, 90.00, 90.00
R / Rfree (%) 11.2 / 13

Other elements in 6g8a:

The structure of Lysozyme Solved By Native Sad From A Dataset Collected in 5 Seconds at 1 A Wavelength with Jungfrau Detector also contains other interesting chemical elements:

Chlorine (Cl) 17 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Lysozyme Solved By Native Sad From A Dataset Collected in 5 Seconds at 1 A Wavelength with Jungfrau Detector (pdb code 6g8a). 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 Lysozyme Solved By Native Sad From A Dataset Collected in 5 Seconds at 1 A Wavelength with Jungfrau Detector, PDB code: 6g8a:

Sodium binding site 1 out of 1 in 6g8a

Go back to Sodium Binding Sites List in 6g8a
Sodium binding site 1 out of 1 in the Lysozyme Solved By Native Sad From A Dataset Collected in 5 Seconds at 1 A Wavelength 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 Lysozyme Solved By Native Sad From A Dataset Collected in 5 Seconds at 1 A Wavelength with Jungfrau Detector within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na218

b:9.0
occ:1.00
O C:SER60 2.4 8.9 1.0
O C:CYS64 2.4 7.7 1.0
O C:HOH389 2.4 11.2 1.0
O C:ARG73 2.4 11.0 1.0
O C:HOH364 2.5 8.5 1.0
OG C:SER72 2.5 11.5 1.0
HB2 C:SER72 2.9 14.0 1.0
HA C:ASN65 3.0 9.5 1.0
CB C:SER72 3.2 11.7 1.0
C C:ARG73 3.5 11.3 1.0
C C:CYS64 3.5 7.5 1.0
HB2 C:SER60 3.5 8.6 1.0
C C:SER60 3.5 7.8 1.0
HB C:THR69 3.8 10.4 1.0
HA C:SER60 3.8 8.2 1.0
HB3 C:SER72 3.9 14.0 1.0
H C:ARG73 3.9 14.8 1.0
CA C:ASN65 3.9 7.9 1.0
N C:ARG73 3.9 12.3 1.0
H C:CYS64 3.9 8.7 1.0
HB2 C:ASN74 3.9 13.0 1.0
H C:ASP66 3.9 8.4 1.0
CA C:SER60 4.1 6.8 1.0
N C:ASN65 4.1 7.6 1.0
HA C:ASN74 4.1 12.7 1.0
C C:SER72 4.2 12.7 1.0
CB C:SER60 4.2 7.2 1.0
CA C:ARG73 4.3 12.6 1.0
CA C:SER72 4.3 12.3 1.0
N C:ASN74 4.4 11.6 1.0
N C:CYS64 4.5 7.2 1.0
HA C:ARG61 4.5 12.4 1.0
O C:ARG61 4.5 12.4 1.0
C C:ARG61 4.5 10.4 1.0
O C:HOH374 4.6 27.8 0.8
N C:ARG61 4.6 8.3 1.0
CA C:ASN74 4.6 10.6 1.0
N C:ASP66 4.6 7.0 1.0
CA C:CYS64 4.6 7.2 1.0
HB2 C:ASN65 4.6 10.3 1.0
OD1 C:ASN65 4.6 9.8 1.0
CL C:CL207 4.7 11.2 1.0
HA C:ARG73 4.7 15.1 1.0
CB C:ASN74 4.7 10.8 1.0
CB C:THR69 4.7 8.7 1.0
O C:SER72 4.8 14.7 1.0
CA C:ARG61 4.8 10.4 1.0
C C:ASN65 4.8 6.6 1.0
CB C:ASN65 4.8 8.6 1.0
H C:TRP63 4.8 9.8 1.0
HA C:SER72 4.9 14.7 1.0
HB3 C:SER60 4.9 8.6 1.0
HG21 C:THR69 4.9 11.3 1.0
N C:TRP62 4.9 9.0 1.0
H C:ASN65 4.9 9.1 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 Oct 8 08:57:55 2024

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