Sodium in PDB 8wzr: Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 100 Ns After Photoexcitation at Rt.

The structure of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 100 Ns After Photoexcitation at Rt., PDB code: 8wzr 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)	31.69 / 1.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.7, 81.7, 37.9, 90, 90, 90
R / Rfree (%)	19.4 / 19.7

The structure of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 100 Ns After Photoexcitation at Rt. also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 100 Ns After Photoexcitation at Rt. (pdb code 8wzr). 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 Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 100 Ns After Photoexcitation at Rt., PDB code: 8wzr:

Sodium binding site 1 out of 1 in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 100 Ns After Photoexcitation at Rt.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 100 Ns After Photoexcitation at Rt. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:37.5 occ:1.00 O A:HOH350 2.3 34.5 1.0 O A:HOH349 2.4 33.4 1.0 O A:ARG73 2.4 39.1 1.0 OG A:SER72 2.5 41.8 1.0 O A:CYS64 2.5 28.5 1.0 O A:SER60 2.5 31.2 1.0 CB A:SER72 3.3 35.9 1.0 C A:CYS64 3.5 24.8 1.0 C A:ARG73 3.5 34.8 1.0 C A:SER60 3.7 29.6 1.0 CA A:ASN65 3.8 28.6 1.0 N A:ARG73 4.0 37.5 1.0 N A:ASN65 4.1 27.2 1.0 C A:SER72 4.1 43.2 1.0 CA A:SER72 4.3 40.9 1.0 CA A:ARG73 4.4 37.8 1.0 N A:ASN74 4.4 34.5 1.0 CA A:SER60 4.4 27.4 1.0 N A:CYS64 4.5 25.7 1.0 CA A:ASN74 4.6 30.4 1.0 CB A:ASN65 4.6 28.8 1.0 O A:SER72 4.6 40.9 1.0 CA A:CYS64 4.6 26.2 1.0 OD1 A:ASN65 4.6 39.0 1.0 C A:ARG61 4.6 35.9 1.0 O A:ARG61 4.6 34.1 1.0 CB A:SER60 4.6 24.9 1.0 O A:HOH357 4.7 33.5 1.0 CB A:ASN74 4.7 28.8 1.0 N A:ASP66 4.7 27.0 1.0 N A:ARG61 4.7 27.9 1.0 CA A:ARG61 4.8 32.0 1.0 C A:ASN65 4.8 27.3 1.0 CB A:THR69 4.9 28.2 1.0 O A:THR69 4.9 34.0 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