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Sodium in PDB 5d5c: In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme at 100 K

Enzymatic activity of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme at 100 K

All present enzymatic activity of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme at 100 K:
3.2.1.17;

Protein crystallography data

The structure of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme at 100 K, PDB code: 5d5c was solved by C.-Y.Huang, V.Olieric, K.Diederichs, M.Wang, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.55 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.090, 79.090, 38.290, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.2

Other elements in 5d5c:

The structure of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme at 100 K also contains other interesting chemical elements:

Bromine (Br) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme at 100 K (pdb code 5d5c). 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 In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme at 100 K, PDB code: 5d5c:

Sodium binding site 1 out of 1 in 5d5c

Go back to Sodium Binding Sites List in 5d5c
Sodium binding site 1 out of 1 in the In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme at 100 K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of In Meso in Situ Serial X-Ray Crystallography Structure of Lysozyme at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:18.3
occ:0.80
 O A:SER60 2.4 19.4 1.0
O A:HOH380 2.4 20.8 1.0
O A:CYS64 2.4 22.1 1.0
O A:HOH341 2.4 19.5 1.0
OG A:SER72 2.4 24.0 1.0
O A:ARG73 2.6 23.7 1.0
CB A:SER72 3.2 24.2 1.0
C A:CYS64 3.5 20.0 1.0
C A:SER60 3.5 19.8 1.0
C A:ARG73 3.7 25.6 1.0
CA A:ASN65 3.9 21.6 1.0
N A:ARG73 4.0 23.1 1.0
C A:SER72 4.1 27.3 1.0
CA A:SER60 4.1 17.3 1.0
N A:ASN65 4.2 19.2 1.0
CB A:SER60 4.3 17.7 1.0
O A:HOH369 4.3 29.4 0.8
CA A:SER72 4.3 27.0 1.0
CA A:ARG73 4.4 25.1 1.0
N A:CYS64 4.5 19.8 1.0
O A:SER72 4.5 25.4 1.0
N A:ASN74 4.6 21.8 1.0
N A:ARG61 4.6 19.0 1.0
N A:ASP66 4.6 19.5 1.0
CA A:CYS64 4.7 19.8 1.0
CB A:ASN65 4.7 22.6 1.0
C A:ARG61 4.7 25.0 1.0
BR A:BR205 4.7 33.7 0.5
O A:ARG61 4.7 24.4 1.0
CB A:THR69 4.7 19.7 1.0
OD1 A:ASN65 4.7 24.9 1.0
CA A:ASN74 4.8 22.3 1.0
C A:ASN65 4.8 20.3 1.0
CB A:ASN74 4.9 21.2 1.0
CA A:ARG61 4.9 23.5 1.0
OG A:SER60 5.0 15.9 1.0

Reference:

C.Y.Huang, V.Olieric, P.Ma, N.Howe, L.Vogeley, X.Liu, R.Warshamanage, T.Weinert, E.Panepucci, B.Kobilka, K.Diederichs, M.Wang, M.Caffrey. In Meso in Situ Serial X-Ray Crystallography of Soluble and Membrane Proteins at Cryogenic Temperatures. Acta Crystallogr D Struct V. 72 93 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894538
DOI: 10.1107/S2059798315021683
Page generated: Mon Oct 7 20:29:14 2024

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