Sodium in PDB 8wzf: Dark State Sfx Structure of Hen Egg White Lysozyme Microcrystals Immobilized with A Mn Carbonyl Complex at Rt.

The structure of Dark State Sfx Structure of Hen Egg White Lysozyme Microcrystals Immobilized with A Mn Carbonyl Complex at Rt., PDB code: 8wzf was solved by B.Maity, M.Shoji, F.Luo, T.Nakane, S.Abe, S.Owada, J.Kang, K.Tono, R.Tanaka, T.T.Thuc, M.Kojima, Y.Hishikawa, J.Tanaka, J.Tian, H.Noya, Y.Nakasuji, A.Asanuma, X.Yao, S.Iwata, Y.Shigeta, E.Nango, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.49 / 1.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	81, 81, 37.7, 90, 90, 90
R / Rfree (%)	19.3 / 22.6

The structure of Dark State Sfx Structure of Hen Egg White Lysozyme Microcrystals Immobilized with A Mn Carbonyl Complex at Rt. also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Manganese	(Mn)	1 atom

The binding sites of Sodium atom in the Dark State Sfx Structure of Hen Egg White Lysozyme Microcrystals Immobilized with A Mn Carbonyl Complex at Rt. (pdb code 8wzf). 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 Dark State Sfx Structure of Hen Egg White Lysozyme Microcrystals Immobilized with A Mn Carbonyl Complex at Rt., PDB code: 8wzf:

Sodium binding site 1 out of 1 in the Dark State Sfx Structure of Hen Egg White Lysozyme Microcrystals Immobilized with A Mn Carbonyl Complex at Rt.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dark State Sfx Structure of Hen Egg White Lysozyme Microcrystals Immobilized with A Mn Carbonyl Complex at Rt. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:23.1 occ:1.00 O A:SER60 2.3 21.1 1.0 OG A:SER72 2.4 29.0 1.0 O A:HOH357 2.4 22.1 1.0 O A:HOH363 2.4 25.0 1.0 O A:CYS64 2.5 17.2 1.0 O A:ARG73 2.5 26.9 1.0 CB A:SER72 3.3 24.2 1.0 C A:SER60 3.5 18.4 1.0 C A:CYS64 3.5 15.7 1.0 C A:ARG73 3.6 25.9 1.0 CA A:ASN65 3.9 18.3 1.0 N A:ARG73 4.0 25.8 1.0 C A:SER72 4.1 32.1 1.0 N A:ASN65 4.1 16.0 1.0 CA A:SER60 4.2 16.0 1.0 CA A:SER72 4.3 29.3 1.0 CB A:SER60 4.4 14.9 1.0 CA A:ARG73 4.4 26.1 1.0 N A:CYS64 4.4 16.3 1.0 N A:ASN74 4.5 22.9 1.0 C A:ARG61 4.5 22.7 1.0 N A:ARG61 4.5 17.1 1.0 O A:ARG61 4.5 23.2 1.0 O A:SER72 4.6 30.4 1.0 CA A:CYS64 4.6 15.9 1.0 CA A:ASN74 4.6 19.9 1.0 O A:HOH369 4.6 22.8 1.0 CA A:ARG61 4.6 21.7 1.0 OD1 A:ASN65 4.7 26.8 1.0 CB A:THR69 4.7 16.9 1.0 CB A:ASN65 4.7 18.7 1.0 N A:ASP66 4.7 16.2 1.0 CB A:ASN74 4.8 19.3 1.0 N A:TRP62 4.8 20.6 1.0 O A:THR69 4.9 24.0 1.0 C A:ASN65 4.9 16.4 1.0

B.Maity, M.Shoji, F.Luo, T.Nakane, S.Abe, S.Owada, J.Kang, K.Tono, R.Tanaka, T.T.Pham, M.Kojima, Y.Hishikawa, J.Tanaka, J.Tian, M.Nagama, T.Suzuki, H.Noya, Y.Nakasuji, A.Asanuma, X.Yao, S.Iwata, Y.Shigeta, E.Nango, T.Ueno. Real-Time Observation of A Metal Complex-Driven Reaction Intermediate Using A Porous Protein Crystal and Serial Femtosecond Crystallography. Nat Commun V. 15 5518 2024.
ISSN: ESSN 2041-1723
PubMed: 38951539
DOI: 10.1038/S41467-024-49814-9