Sodium in PDB 8wzg: Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 Ns After Photoexcitation at Rt.

Enzymatic activity of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 Ns After Photoexcitation at Rt.

All present enzymatic activity of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 Ns 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, 10 Ns After Photoexcitation at Rt., PDB code: 8wzg 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 (%) 18.6 / 20.1

Other elements in 8wzg:

The structure of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 Ns After Photoexcitation 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, 10 Ns After Photoexcitation at Rt. (pdb code 8wzg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 Ns After Photoexcitation at Rt., PDB code: 8wzg:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8wzg

Go back to Sodium Binding Sites List in 8wzg
Sodium binding site 1 out of 4 in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 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, 10 Ns After Photoexcitation at Rt. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:26.4
occ:1.00
 O A:SER60 2.3 22.8 1.0
O A:ARG73 2.4 28.1 1.0
OG A:SER72 2.4 29.4 1.0
O A:CYS64 2.4 18.9 1.0
O A:HOH349 2.5 22.8 1.0
O A:HOH362 2.5 28.0 1.0
CB A:SER72 3.2 27.9 1.0
C A:SER60 3.5 19.9 1.0
C A:CYS64 3.5 15.9 1.0
C A:ARG73 3.5 26.4 1.0
CA A:ASN65 3.9 19.8 1.0
N A:ARG73 3.9 29.6 1.0
C A:SER72 4.1 34.6 1.0
N A:ASN65 4.1 18.2 1.0
CA A:SER60 4.2 16.7 1.0
CA A:SER72 4.3 32.3 1.0
CA A:ARG73 4.3 28.0 1.0
N A:ASN74 4.4 23.9 1.0
C A:ARG61 4.4 25.1 1.0
N A:CYS64 4.4 18.2 1.0
CB A:SER60 4.4 16.1 1.0
O A:ARG61 4.4 25.8 1.0
N A:ARG61 4.5 19.5 1.0
CA A:ASN74 4.6 21.2 1.0
CA A:ARG61 4.6 22.9 1.0
O A:HOH342 4.6 43.6 1.0
CA A:CYS64 4.6 17.7 1.0
O A:SER72 4.6 31.8 1.0
O A:HOH372 4.7 25.4 1.0
CB A:THR69 4.7 19.8 1.0
CB A:ASN74 4.7 21.1 1.0
N A:ASP66 4.7 17.2 1.0
CB A:ASN65 4.8 19.3 1.0
OD1 A:ASN65 4.8 29.0 1.0
N A:TRP62 4.8 21.9 1.0
O A:THR69 4.9 25.3 1.0
C A:ASN65 4.9 17.0 1.0

Sodium binding site 2 out of 4 in 8wzg

Go back to Sodium Binding Sites List in 8wzg
Sodium binding site 2 out of 4 in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 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 2 of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 Ns After Photoexcitation at Rt. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:38.9
occ:1.00
 O A:HOH389 2.1 46.0 1.0
O A:HOH314 2.1 36.3 1.0
O A:HOH333 2.2 38.4 1.0
O A:HOH307 2.2 41.2 1.0
O A:HOH340 2.3 41.9 1.0
OD2 A:ASP52 2.5 32.8 1.0
CG A:ASP52 3.3 25.6 1.0
O A:HOH357 3.4 33.5 1.0
O A:HOH325 3.6 33.1 1.0
OD1 A:ASP52 3.6 22.8 1.0
NA A:NA204 3.9 38.4 1.0
O A:GLN57 4.2 19.2 1.0
CB A:ASP52 4.4 15.9 1.0
OE1 A:GLU35 4.5 22.7 1.0
ND2 A:ASN46 4.7 33.2 1.0
O A:HOH384 4.7 42.5 1.0
CB A:GLN57 4.8 16.9 1.0

Sodium binding site 3 out of 4 in 8wzg

Go back to Sodium Binding Sites List in 8wzg
Sodium binding site 3 out of 4 in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 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 3 of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 Ns After Photoexcitation at Rt. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:38.4
occ:1.00
 O A:HOH314 1.9 36.3 1.0
O A:HOH384 2.2 42.5 1.0
O A:HOH360 2.3 37.7 1.0
O A:HOH325 2.4 33.1 1.0
OE1 A:GLU35 2.5 22.7 1.0
O A:HOH337 3.0 31.3 1.0
CD A:GLU35 3.6 20.9 1.0
NA A:NA203 3.9 38.9 1.0
OE2 A:GLU35 4.1 23.2 1.0
O A:GLU35 4.3 18.6 1.0
CG A:GLN57 4.4 16.2 1.0
CA A:GLU35 4.4 13.2 1.0
O A:HOH389 4.5 46.0 1.0
O A:HOH333 4.5 38.4 1.0
CB A:GLN57 4.5 16.9 1.0
OE1 A:GLN57 4.5 19.5 1.0
OD2 A:ASP52 4.6 32.8 1.0
CG A:GLU35 4.8 18.1 1.0
CB A:GLU35 4.8 15.8 1.0
C A:GLU35 4.9 15.1 1.0
O A:HOH307 5.0 41.2 1.0
CD A:GLN57 5.0 16.2 1.0

Sodium binding site 4 out of 4 in 8wzg

Go back to Sodium Binding Sites List in 8wzg
Sodium binding site 4 out of 4 in the Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 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 4 of Sfx Structure of An Mn-Carbonyl Complex Immobilized in Hen Egg White Lysozyme Microcrystals, 10 Ns After Photoexcitation at Rt. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:46.8
occ:1.00
 OD2 A:ASP101 2.3 41.6 1.0
O A:HOH379 2.3 49.4 1.0
O A:HOH346 2.3 47.7 1.0
O A:HOH302 2.7 38.0 1.0
O A:HOH387 3.1 52.1 1.0
CG A:ASP101 3.3 41.6 1.0
OD1 A:ASP101 3.6 49.1 1.0
CB A:ASP101 4.6 33.9 1.0
O A:HOH313 4.9 40.7 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 14:19:38 2024

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