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Sodium in PDB 8wzt: Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation at Rt.

Enzymatic activity of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation 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 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 at Rt., PDB code: 8wzt 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 (%) 19.3 / 21.2

Other elements in 8wzt:

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

Manganese (Mn) 1 atom
Chlorine (Cl) 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 at Rt. (pdb code 8wzt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation at Rt., PDB code: 8wzt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8wzt

Go back to Sodium Binding Sites List in 8wzt
Sodium binding site 1 out of 2 in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond 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, 1 Microsecond After Photoexcitation at Rt. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:37.8
occ:1.00
 OG A:SER72 2.3 44.0 1.0
O A:SER60 2.4 34.4 1.0
O A:HOH348 2.4 38.0 1.0
O A:HOH350 2.4 33.7 1.0
O A:ARG73 2.5 43.6 1.0
O A:CYS64 2.6 28.6 1.0
CB A:SER72 3.2 41.6 1.0
C A:SER60 3.6 29.4 1.0
C A:CYS64 3.6 24.7 1.0
C A:ARG73 3.6 37.6 1.0
N A:ARG73 3.9 39.6 1.0
CA A:ASN65 4.0 29.4 1.0
C A:SER72 4.0 44.3 1.0
N A:ASN65 4.2 27.6 1.0
CA A:SER72 4.2 43.9 1.0
CA A:SER60 4.3 26.9 1.0
CA A:ARG73 4.4 37.8 1.0
O A:ARG61 4.4 34.3 1.0
C A:ARG61 4.5 35.9 1.0
N A:ASN74 4.5 37.6 1.0
N A:CYS64 4.5 26.8 1.0
N A:ARG61 4.6 28.1 1.0
O A:SER72 4.6 43.3 1.0
CB A:SER60 4.6 25.4 1.0
CA A:ARG61 4.6 34.0 1.0
CA A:ASN74 4.7 32.4 1.0
CA A:CYS64 4.7 27.1 1.0
O A:HOH359 4.7 34.7 1.0
OD1 A:ASN65 4.7 41.6 1.0
CB A:ASN65 4.8 30.0 1.0
CB A:THR69 4.8 29.7 1.0
N A:ASP66 4.8 27.6 1.0
CB A:ASN74 4.8 30.9 1.0
O A:THR69 4.9 34.6 1.0
N A:TRP62 4.9 32.9 1.0
C A:ASN65 4.9 28.3 1.0

Sodium binding site 2 out of 2 in 8wzt

Go back to Sodium Binding Sites List in 8wzt
Sodium binding site 2 out of 2 in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation at Rt.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 1 Microsecond After Photoexcitation at Rt. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:49.1
occ:1.00
 O A:HOH322 2.4 42.0 1.0
OE1 A:GLU35 2.6 30.6 1.0
CD A:GLU35 3.7 32.5 1.0
O A:HOH304 3.7 43.6 1.0
OE2 A:GLU35 4.1 33.8 1.0
O A:GLU35 4.4 27.3 1.0
O A:HOH315 4.5 45.3 1.0
CG A:GLN57 4.6 23.6 1.0
CA A:GLU35 4.6 21.4 1.0
OE1 A:GLN57 4.7 28.4 1.0
CB A:GLN57 4.7 26.5 1.0
OD2 A:ASP52 4.8 41.7 1.0
CG1 A:VAL109 4.8 29.6 0.4
CG A:GLU35 4.9 28.2 1.0
CB A:GLU35 5.0 25.6 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 14:19:57 2024

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