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Sodium in PDB 5njq: Mix-and-Diffuse Serial Synchrotron Crystallography: Structure of N,N', N''-Triacetylchitotriose Bound to Lysozyme with 1S Time-Delay, Phased with 4ET8

Enzymatic activity of Mix-and-Diffuse Serial Synchrotron Crystallography: Structure of N,N', N''-Triacetylchitotriose Bound to Lysozyme with 1S Time-Delay, Phased with 4ET8

All present enzymatic activity of Mix-and-Diffuse Serial Synchrotron Crystallography: Structure of N,N', N''-Triacetylchitotriose Bound to Lysozyme with 1S Time-Delay, Phased with 4ET8:
3.2.1.17;

Protein crystallography data

The structure of Mix-and-Diffuse Serial Synchrotron Crystallography: Structure of N,N', N''-Triacetylchitotriose Bound to Lysozyme with 1S Time-Delay, Phased with 4ET8, PDB code: 5njq was solved by D.Oberthuer, A.Meents, K.R.Beyerlein, H.N.Chapman, J.Lieseke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.68 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.610, 79.610, 38.300, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20

Other elements in 5njq:

The structure of Mix-and-Diffuse Serial Synchrotron Crystallography: Structure of N,N', N''-Triacetylchitotriose Bound to Lysozyme with 1S Time-Delay, Phased with 4ET8 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Mix-and-Diffuse Serial Synchrotron Crystallography: Structure of N,N', N''-Triacetylchitotriose Bound to Lysozyme with 1S Time-Delay, Phased with 4ET8 (pdb code 5njq). 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 Mix-and-Diffuse Serial Synchrotron Crystallography: Structure of N,N', N''-Triacetylchitotriose Bound to Lysozyme with 1S Time-Delay, Phased with 4ET8, PDB code: 5njq:

Sodium binding site 1 out of 1 in 5njq

Go back to Sodium Binding Sites List in 5njq
Sodium binding site 1 out of 1 in the Mix-and-Diffuse Serial Synchrotron Crystallography: Structure of N,N', N''-Triacetylchitotriose Bound to Lysozyme with 1S Time-Delay, Phased with 4ET8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mix-and-Diffuse Serial Synchrotron Crystallography: Structure of N,N', N''-Triacetylchitotriose Bound to Lysozyme with 1S Time-Delay, Phased with 4ET8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:36.8
occ:1.00
 O A:SER60 2.4 31.1 1.0
O A:CYS64 2.4 29.2 1.0
OG A:SER72 2.5 46.6 1.0
O A:HOH370 2.5 43.6 1.0
O A:ARG73 2.6 43.2 1.0
O A:HOH339 2.8 34.9 1.0
HB2 A:SER72 2.8 54.2 1.0
HA A:ASN65 3.1 35.8 1.0
CB A:SER72 3.2 45.1 1.0
HG A:SER72 3.2 56.0 1.0
C A:CYS64 3.5 27.1 1.0
C A:ARG73 3.5 45.8 1.0
C A:SER60 3.6 27.2 1.0
HB3 A:SER72 3.9 54.2 1.0
N A:ARG73 3.9 35.9 1.0
HB A:THR69 3.9 45.7 1.0
H A:CYS64 3.9 30.1 1.0
HB2 A:SER60 3.9 35.9 1.0
H A:ARG73 3.9 43.0 1.0
C A:SER72 4.0 50.6 1.0
HB2 A:ASN74 4.0 39.2 1.0
CA A:ASN65 4.0 29.9 1.0
HA A:SER60 4.0 30.8 1.0
HA A:ASN74 4.0 42.6 1.0
N A:ASN65 4.2 29.3 1.0
CA A:SER72 4.2 50.2 1.0
CA A:SER60 4.3 25.6 1.0
CA A:ARG73 4.3 46.5 1.0
HA A:ARG61 4.3 38.5 1.0
H A:ASP66 4.3 35.8 1.0
N A:ASN74 4.4 41.7 1.0
C A:ARG61 4.4 35.0 1.0
O A:ARG61 4.4 36.8 1.0
N A:CYS64 4.4 25.0 1.0
O A:SER72 4.4 41.9 1.0
HB2 A:ASN65 4.5 40.6 1.0
CA A:ASN74 4.5 35.5 1.0
N A:ARG61 4.6 27.3 1.0
CB A:SER60 4.6 29.9 1.0
CA A:CYS64 4.6 28.6 1.0
CA A:ARG61 4.7 32.1 1.0
CB A:ASN74 4.7 32.6 1.0
N A:TRP62 4.7 29.3 1.0
HA A:ARG73 4.8 55.8 1.0
H A:TRP63 4.8 33.6 1.0
CB A:THR69 4.8 38.1 1.0
CB A:ASN65 4.8 33.8 1.0
HG21 A:THR69 4.8 43.2 1.0
HA A:SER72 4.8 60.3 1.0
OD1 A:ASN65 4.9 41.8 1.0
O A:THR69 4.9 41.3 1.0
H A:SER72 4.9 55.3 1.0
N A:ASP66 5.0 29.8 1.0
H A:TRP62 5.0 35.2 1.0
O A:HOH369 5.0 41.2 1.0
N A:TRP63 5.0 28.0 1.0
H A:ASN65 5.0 35.2 1.0

Reference:

K.R.Beyerlein, D.Dierksmeyer, V.Mariani, M.Kuhn, I.Sarrou, A.Ottaviano, S.Awel, J.Knoska, S.Fuglerud, O.Jonsson, S.Stern, M.O.Wiedorn, O.Yefanov, L.Adriano, R.Bean, A.Burkhardt, P.Fischer, M.Heymann, D.A.Horke, K.E.J.Jungnickel, E.Kovaleva, O.Lorbeer, M.Metz, J.Meyer, A.Morgan, K.Pande, S.Panneerselvam, C.Seuring, A.Tolstikova, J.Lieske, S.Aplin, M.Roessle, T.A.White, H.N.Chapman, A.Meents, D.Oberthuer. Mix-and-Diffuse Serial Synchrotron Crystallography. Iucrj V. 4 769 2017.
ISSN: ESSN 2052-2525
PubMed: 29123679
DOI: 10.1107/S2052252517013124
Page generated: Mon Oct 7 23:00:27 2024

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