Sodium in PDB 8wzv: Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation with 40 Microjoules Laser Intensity at Rt.

Enzymatic activity of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation with 40 Microjoules Laser Intensity at Rt.

All present enzymatic activity of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation with 40 Microjoules Laser Intensity at Rt.:
3.2.1.17;

Protein crystallography data

The structure of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation with 40 Microjoules Laser Intensity at Rt., PDB code: 8wzv 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) 28.57 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.8, 80.8, 37.6, 90, 90, 90
R / Rfree (%) 19 / 19.1

Other elements in 8wzv:

The structure of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation with 40 Microjoules Laser Intensity at Rt. also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation with 40 Microjoules Laser Intensity at Rt. (pdb code 8wzv). 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, 1 Microsecond After Photoexcitation with 40 Microjoules Laser Intensity at Rt., PDB code: 8wzv:

Sodium binding site 1 out of 1 in 8wzv

Go back to Sodium Binding Sites List in 8wzv
Sodium binding site 1 out of 1 in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation with 40 Microjoules Laser Intensity 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, 1 Microsecond After Photoexcitation with 40 Microjoules Laser Intensity at Rt. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:38.1
occ:1.00
 OG A:SER72 2.3 44.1 1.0
O A:SER60 2.3 33.4 1.0
O A:CYS64 2.4 30.2 1.0
O A:HOH333 2.4 40.5 1.0
O A:HOH329 2.5 34.9 1.0
O A:ARG73 2.5 41.2 1.0
CB A:SER72 3.1 39.8 1.0
C A:CYS64 3.4 26.4 1.0
C A:ARG73 3.5 39.9 1.0
C A:SER60 3.5 29.3 1.0
N A:ARG73 3.8 41.0 1.0
CA A:ASN65 3.8 30.0 1.0
C A:SER72 3.9 47.1 1.0
N A:ASN65 4.1 29.5 1.0
CA A:SER72 4.1 46.2 1.0
CA A:SER60 4.2 26.3 1.0
CA A:ARG73 4.3 42.1 1.0
N A:ASN74 4.4 38.3 1.0
O A:ARG61 4.4 38.5 1.0
C A:ARG61 4.4 38.1 1.0
N A:CYS64 4.4 28.9 1.0
O A:SER72 4.5 43.2 1.0
CB A:SER60 4.5 27.5 1.0
N A:ARG61 4.5 29.4 1.0
CA A:ASN74 4.6 35.0 1.0
O A:HOH357 4.6 39.6 1.0
CA A:CYS64 4.6 29.7 1.0
CA A:ARG61 4.6 35.7 1.0
CB A:ASN65 4.6 30.5 1.0
OD1 A:ASN65 4.7 41.4 1.0
CB A:ASN74 4.7 33.6 1.0
N A:ASP66 4.8 30.0 1.0
CB A:THR69 4.8 32.7 1.0
C A:ASN65 4.9 28.2 1.0
N A:TRP62 4.9 34.9 1.0
O A:THR69 4.9 37.2 1.0

Reference:

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
Page generated: Wed Oct 9 14:20:19 2024

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