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Sodium in PDB 9fud: Serial Microseconds Crystallography at ID29 Using Fixed-Target (Si Chip): Lysozyme - Without Ligand Glcnac (Apo)

Enzymatic activity of Serial Microseconds Crystallography at ID29 Using Fixed-Target (Si Chip): Lysozyme - Without Ligand Glcnac (Apo)

All present enzymatic activity of Serial Microseconds Crystallography at ID29 Using Fixed-Target (Si Chip): Lysozyme - Without Ligand Glcnac (Apo):
3.2.1.17;

Protein crystallography data

The structure of Serial Microseconds Crystallography at ID29 Using Fixed-Target (Si Chip): Lysozyme - Without Ligand Glcnac (Apo), PDB code: 9fud was solved by J.Orlans, S.L.Rose, S.Basu, D.De Sanctis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.65 / 2.05
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.7, 78.7, 37.86, 90, 90, 90
R / Rfree (%) 21.6 / 25.2

Other elements in 9fud:

The structure of Serial Microseconds Crystallography at ID29 Using Fixed-Target (Si Chip): Lysozyme - Without Ligand Glcnac (Apo) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Serial Microseconds Crystallography at ID29 Using Fixed-Target (Si Chip): Lysozyme - Without Ligand Glcnac (Apo) (pdb code 9fud). 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 Serial Microseconds Crystallography at ID29 Using Fixed-Target (Si Chip): Lysozyme - Without Ligand Glcnac (Apo), PDB code: 9fud:

Sodium binding site 1 out of 1 in 9fud

Go back to Sodium Binding Sites List in 9fud
Sodium binding site 1 out of 1 in the Serial Microseconds Crystallography at ID29 Using Fixed-Target (Si Chip): Lysozyme - Without Ligand Glcnac (Apo)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Serial Microseconds Crystallography at ID29 Using Fixed-Target (Si Chip): Lysozyme - Without Ligand Glcnac (Apo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:49.9
occ:1.00
 O A:CYS64 2.2 48.2 1.0
O A:SER60 2.3 49.1 1.0
O A:ARG73 2.4 50.7 1.0
O A:HOH320 2.6 49.2 1.0
OG A:SER72 2.7 51.3 1.0
O A:HOH329 2.7 50.3 1.0
C A:CYS64 3.3 47.1 1.0
C A:ARG73 3.4 50.4 1.0
CB A:SER72 3.4 51.3 1.0
C A:SER60 3.5 48.1 1.0
N A:ARG73 3.8 52.1 1.0
CA A:ASN65 3.9 49.2 1.0
N A:ASN65 4.0 47.2 1.0
C A:SER72 4.1 53.0 1.0
N A:CYS64 4.2 46.5 1.0
CA A:SER60 4.2 46.8 1.0
CA A:ARG73 4.2 51.9 1.0
N A:ASN74 4.3 50.2 1.0
CA A:CYS64 4.4 47.3 1.0
C A:ARG61 4.4 49.2 1.0
CA A:SER72 4.4 52.6 1.0
CA A:ASN74 4.5 49.1 1.0
N A:ARG61 4.5 47.8 1.0
CB A:SER60 4.5 47.6 1.0
N A:TRP62 4.5 48.9 1.0
CA A:ARG61 4.6 49.1 1.0
O A:ARG61 4.6 50.7 1.0
O A:SER72 4.7 53.5 1.0
CB A:ASN74 4.7 49.4 1.0
CB A:ASN65 4.7 48.4 1.0
N A:TRP63 4.8 47.8 1.0
CB A:THR69 4.9 51.0 1.0
N A:ASP66 4.9 47.7 1.0
C A:TRP62 4.9 47.3 1.0
CL A:CL204 4.9 54.6 1.0
C A:ASN65 4.9 46.9 1.0

Reference:

J.Orlans, S.L.Rose, G.Ferguson, M.Oscarsson, A.Homs Puron, A.Beteva, S.Debionne, P.Theveneau, N.Coquelle, J.Kieffer, P.Busca, J.Sinoir, V.Armijo, M.Lopez Marrero, F.Felisaz, G.Papp, H.Gonzalez, H.Caserotto, F.Dobias, J.Gigmes, G.Lebon, S.Basu, D.De Sanctis. Advancing Macromolecular Structure Determination with Microsecond X-Ray Pulses at A 4TH Generation Synchrotron. Commun Chem V. 8 6 2025.
ISSN: ESSN 2399-3669
PubMed: 39775172
DOI: 10.1038/S42004-024-01404-Y
Page generated: Sat Feb 8 23:54:17 2025

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