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Sodium in PDB 7bcu: The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours.

Enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours.

All present enzymatic activity of The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours.:
3.2.1.17;

Protein crystallography data

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours., PDB code: 7bcu was solved by L.Chiniadis, P.Giastas, I.Bratsos, A.Papakyriakou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.02 / 0.98
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.419, 77.419, 37.643, 90, 90, 90
R / Rfree (%) 12.7 / 14.4

Other elements in 7bcu:

The structure of The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours. also contains other interesting chemical elements:

Chlorine (Cl) 21 atoms
Ruthenium (Ru) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours. (pdb code 7bcu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours., PDB code: 7bcu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7bcu

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Sodium binding site 1 out of 5 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na222

b:6.2
occ:0.87
 O A:SER60 2.4 7.2 1.0
O A:HOH403 2.4 9.1 1.0
O A:CYS64 2.4 6.2 1.0
O A:ARG73 2.4 7.9 1.0
OG A:SER72 2.5 9.6 1.0
O A:HOH371 2.5 7.3 1.0
CB A:SER72 3.3 10.0 1.0
C A:CYS64 3.5 5.8 1.0
C A:SER60 3.5 6.7 1.0
C A:ARG73 3.5 7.9 1.0
CA A:ASN65 4.0 6.5 1.0
N A:ARG73 4.0 9.4 1.0
CA A:SER60 4.0 6.2 1.0
C A:SER72 4.1 9.5 1.0
N A:ASN65 4.2 6.1 1.0
CB A:SER60 4.2 6.4 1.0
CA A:SER72 4.4 9.9 1.0
CA A:ARG73 4.4 9.1 1.0
N A:ASN74 4.4 7.8 1.0
N A:CYS64 4.4 5.8 1.0
O A:HOH381 4.5 11.5 1.0
O A:SER72 4.5 10.6 1.0
CA A:ASN74 4.5 7.3 1.0
CA A:CYS64 4.6 5.8 1.0
N A:ARG61 4.6 7.7 1.0
CB A:ASN74 4.6 7.7 1.0
C A:ARG61 4.6 8.3 1.0
OD1 A:ASN65 4.7 10.8 1.0
N A:ASP66 4.7 6.2 1.0
CB A:THR69 4.7 8.0 1.0
CL A:CL231 4.7 9.1 0.8
O A:ARG61 4.8 8.9 1.0
N A:TRP62 4.8 7.7 1.0
CB A:ASN65 4.9 7.9 1.0
O A:HOH420 4.9 21.3 1.0
C A:ASN65 4.9 6.3 1.0
CA A:ARG61 4.9 8.7 1.0
N A:TRP63 5.0 6.0 1.0
O A:THR69 5.0 8.8 1.0

Sodium binding site 2 out of 5 in 7bcu

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Sodium binding site 2 out of 5 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na223

b:42.6
occ:0.44
 O A:HOH343 2.0 33.5 1.0
O A:HOH367 2.8 26.2 1.0
O A:GLN57 2.8 7.4 1.0
O A:HOH313 2.9 12.6 1.0
OD2 A:ASP52 3.3 10.5 1.0
OE1 A:GLU35 3.4 8.1 1.0
CB A:GLN57 3.6 6.9 1.0
OE2 A:GLU35 3.7 8.0 1.0
O A:HOH429 3.7 37.8 1.0
CD A:GLU35 3.7 7.4 1.0
C A:GLN57 3.8 6.8 1.0
O A:HOH399 3.9 30.9 1.0
O A:HOH315 4.0 27.4 1.0
CG A:ASP52 4.0 8.0 1.0
CD1 A:TRP108 4.0 7.8 1.0
O A:LEU56 4.3 8.5 1.0
CA A:GLN57 4.3 6.6 1.0
OD1 A:ASP52 4.5 7.7 1.0
CL A:CL234 4.6 27.1 1.0
NE1 A:TRP108 4.7 8.1 1.0
O A:HOH360 4.7 10.4 1.0
CA A:TRP108 4.7 7.2 1.0
CB A:ASP52 4.8 6.9 1.0
O A:ALA107 4.8 9.6 1.0
CG A:GLU35 4.8 6.7 1.0
CG A:GLN57 4.8 6.6 1.0
CG A:TRP108 4.8 6.9 1.0
N A:VAL109 4.9 8.7 1.0
N A:ILE58 5.0 6.6 1.0

Sodium binding site 3 out of 5 in 7bcu

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Sodium binding site 3 out of 5 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na224

b:19.0
occ:0.81
 N A:ASP18 2.8 11.7 1.0
O A:LYS13 2.9 9.5 1.0
CB A:ASP18 3.1 14.3 1.0
CA A:GLY16 3.3 12.8 1.0
C A:GLY16 3.3 12.8 1.0
N A:LEU17 3.3 11.9 1.0
CL A:CL235 3.4 64.4 1.0
CA A:ASP18 3.4 12.6 1.0
CA A:LYS13 3.5 9.0 1.0
C A:LYS13 3.6 8.9 1.0
CG A:LYS13 3.7 12.7 1.0
N A:GLY16 3.7 12.1 1.0
O A:ASP18 3.8 12.8 1.0
C A:LEU17 3.9 11.4 1.0
O A:GLY16 3.9 13.8 1.0
C A:ASP18 4.1 12.0 1.0
CB A:LYS13 4.2 10.4 1.0
CA A:LEU17 4.2 11.3 1.0
O A:MET12 4.2 8.5 1.0
CG A:ASP18 4.5 16.3 1.0
N A:LYS13 4.6 8.2 1.0
OD2 A:ASP18 4.9 18.0 1.0
C A:MET12 4.9 8.1 1.0
CD A:LYS13 4.9 14.9 1.0
N A:ARG14 4.9 9.1 1.0
CE A:LYS13 4.9 17.6 1.0
O A:LEU17 4.9 11.8 1.0

Sodium binding site 4 out of 5 in 7bcu

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Sodium binding site 4 out of 5 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na225

b:39.9
occ:0.89
 O A:HOH423 2.4 18.6 1.0
C1 A:DMS216 2.7 10.2 0.8
CL A:CL217 3.3 9.9 0.8
C2 A:DMS202 3.8 10.7 0.7
C2 A:DMS216 3.8 9.9 0.8
S A:DMS216 3.9 9.0 0.8
O A:HOH413 4.2 30.9 1.0
NH2 A:ARG5 4.5 11.8 1.0
CL A:CL220 4.5 9.7 0.8
RU A:RU221 4.7 8.1 0.8

Sodium binding site 5 out of 5 in 7bcu

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Sodium binding site 5 out of 5 in the The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Adduct of Nami-A with Hen Egg White Lysozyme at 1.5 Hours. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na226

b:38.2
occ:0.90
 OD1 A:ASN19 2.6 22.4 1.0
CB A:ASN19 2.8 15.8 1.0
CG A:ASN19 3.0 20.4 1.0
CA A:ASN19 3.0 12.2 1.0
O A:GLY22 3.1 8.6 1.0
C A:GLY22 3.1 8.1 1.0
CA A:GLY22 3.4 9.0 1.0
O A:HOH356 3.6 15.4 1.0
N A:TYR23 3.7 7.1 1.0
O A:ASN19 3.8 11.2 1.0
C A:ASN19 3.8 10.6 1.0
N A:SER24 4.0 7.3 1.0
C A:TYR23 4.0 7.2 1.0
N A:ASN19 4.1 11.5 1.0
ND2 A:ASN19 4.1 21.9 1.0
N A:GLY22 4.3 9.2 1.0
CA A:TYR23 4.4 6.9 1.0
CA A:SER24 4.4 7.5 1.0
O A:HOH389 4.4 10.1 1.0
O A:TYR23 4.5 7.2 1.0
CB A:SER24 4.8 9.2 1.0

Reference:

L.Chiniadis, P.Giastas, I.Bratsos, A.Papakyriakou. Insights Into the Protein Ruthenation Mechanism By Antimetastatic Metallodrugs: High-Resolution X-Ray Structures of the Adduct Formed Between Hen Egg-White Lysozyme and Nami-A at Various Time Points. Inorg.Chem. V. 60 10729 2021.
ISSN: ISSN 0020-1669
PubMed: 34197115
DOI: 10.1021/ACS.INORGCHEM.1C01441
Page generated: Tue Oct 8 16:08:34 2024

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