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Sodium in PDB 4n8z: In Situ Lysozyme Crystallized on A Mitegen Micromesh with Benzamidine Ligand

Enzymatic activity of In Situ Lysozyme Crystallized on A Mitegen Micromesh with Benzamidine Ligand

All present enzymatic activity of In Situ Lysozyme Crystallized on A Mitegen Micromesh with Benzamidine Ligand:
3.2.1.17;

Protein crystallography data

The structure of In Situ Lysozyme Crystallized on A Mitegen Micromesh with Benzamidine Ligand, PDB code: 4n8z was solved by X.Yin, A.Scalia, L.Leroy, C.M.Cuttitta, G.M.Polizzo, D.L.Ericson, C.G.Roessler, O.Campos, R.Agarwal, M.Allaire, A.M.Orville, R.Jackimowicz, M.Y.Ma, R.M.Sweet, A.S.Soares, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.76 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.150, 79.150, 36.280, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 25.1

Other elements in 4n8z:

The structure of In Situ Lysozyme Crystallized on A Mitegen Micromesh with Benzamidine Ligand also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the In Situ Lysozyme Crystallized on A Mitegen Micromesh with Benzamidine Ligand (pdb code 4n8z). 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 Situ Lysozyme Crystallized on A Mitegen Micromesh with Benzamidine Ligand, PDB code: 4n8z:

Sodium binding site 1 out of 1 in 4n8z

Go back to Sodium Binding Sites List in 4n8z
Sodium binding site 1 out of 1 in the In Situ Lysozyme Crystallized on A Mitegen Micromesh with Benzamidine Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of In Situ Lysozyme Crystallized on A Mitegen Micromesh with Benzamidine Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:17.2
occ:1.00
 O A:SER60 2.3 18.3 1.0
O A:ARG73 2.4 20.2 1.0
O A:CYS64 2.4 15.3 1.0
O A:HOH336 2.4 21.7 1.0
OG A:SER72 2.5 19.6 1.0
O A:HOH311 2.6 15.4 1.0
CB A:SER72 3.4 19.8 1.0
C A:CYS64 3.5 14.2 1.0
C A:SER60 3.5 16.4 1.0
C A:ARG73 3.5 20.3 1.0
CA A:ASN65 3.9 16.4 1.0
N A:ARG73 3.9 21.2 1.0
CA A:SER60 4.0 14.9 1.0
N A:ASN65 4.1 15.7 1.0
C A:SER72 4.1 20.9 1.0
CA A:ARG73 4.2 21.3 1.0
CB A:SER60 4.2 14.2 1.0
CA A:SER72 4.4 20.6 1.0
O A:ARG61 4.4 14.9 0.5
N A:ASN74 4.4 17.5 1.0
N A:CYS64 4.5 15.1 1.0
N A:ASP66 4.6 14.5 1.0
C A:ARG61 4.6 15.2 0.5
N A:ARG61 4.6 15.5 0.5
C A:ARG61 4.6 16.4 0.5
N A:TRP62 4.6 18.9 0.5
CA A:CYS64 4.6 15.6 1.0
O A:SER72 4.6 22.4 1.0
N A:ARG61 4.6 15.7 0.5
O A:ARG61 4.7 15.9 0.5
CA A:ASN74 4.7 18.8 1.0
CL A:CL206 4.7 22.4 1.0
CA A:ARG61 4.7 16.2 0.5
CB A:THR69 4.7 17.7 1.0
OD1 A:ASN65 4.7 18.9 1.0
CB A:ASN65 4.8 17.0 1.0
O A:HOH382 4.8 30.7 1.0
C A:ASN65 4.8 14.4 1.0
CB A:ASN74 4.8 20.0 1.0
CA A:ARG61 4.9 17.6 0.5
OG A:SER60 5.0 14.8 1.0

Reference:

X.Yin, A.Scalia, L.Leroy, C.M.Cuttitta, G.M.Polizzo, D.L.Ericson, C.G.Roessler, O.Campos, M.Y.Ma, R.Agarwal, R.Jackimowicz, M.Allaire, A.M.Orville, R.M.Sweet, A.S.Soares. Hitting the Target: Fragment Screening with Acoustic in Situ Co-Crystallization of Proteins Plus Fragment Libraries on Pin-Mounted Data-Collection Micromeshes. Acta Crystallogr.,Sect.D V. 70 1177 2014.
ISSN: ISSN 0907-4449
PubMed: 24816088
DOI: 10.1107/S1399004713034603
Page generated: Sun Aug 17 20:44:39 2025

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