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

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy