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Chlorine in PDB 5on8: Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid)

Protein crystallography data

The structure of Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid), PDB code: 5on8 was solved by C.Cavazza, S.Menage, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.87 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.536, 94.092, 124.564, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.2

Other elements in 5on8:

The structure of Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid) also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid) (pdb code 5on8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid), PDB code: 5on8:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5on8

Go back to Chlorine Binding Sites List in 5on8
Chlorine binding site 1 out of 4 in the Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl612

b:50.1
occ:1.00
NZ A:LYS433 3.4 46.3 1.0
CA A:LEU430 3.5 17.2 1.0
N A:LEU430 3.6 17.6 1.0
CB A:LEU430 3.8 18.5 1.0
CE A:LYS433 3.8 37.3 1.0
C A:PRO429 4.0 18.1 1.0
O A:PRO429 4.2 18.7 1.0
CD1 A:LEU430 4.2 25.8 1.0
O A:HOH1088 4.2 26.0 1.0
CD A:LYS433 4.3 22.4 1.0
CB A:PRO429 4.4 18.7 1.0
CB A:LYS433 4.7 17.9 1.0
CG A:LEU430 4.7 19.8 1.0
C A:LEU430 4.8 19.1 1.0
CA A:PRO429 4.9 22.2 1.0

Chlorine binding site 2 out of 4 in 5on8

Go back to Chlorine Binding Sites List in 5on8
Chlorine binding site 2 out of 4 in the Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl613

b:72.6
occ:1.00
NH2 A:ARG386 2.7 56.6 1.0
O A:HOH974 3.0 42.4 1.0
OG A:SER415 3.3 40.4 1.0
CZ A:ARG386 3.7 49.4 1.0
CB A:SER415 3.9 31.7 1.0
NH1 A:ARG386 4.1 39.5 1.0
O A:HOH1080 4.1 38.4 1.0
NE A:ARG386 4.7 45.9 1.0
O A:HOH1061 4.8 34.7 1.0
NH1 A:ARG97 4.9 51.2 1.0

Chlorine binding site 3 out of 4 in 5on8

Go back to Chlorine Binding Sites List in 5on8
Chlorine binding site 3 out of 4 in the Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl621

b:46.3
occ:1.00
O A:HOH1185 2.9 40.2 1.0
CG2 A:THR23 3.3 27.9 0.5
CG2 A:THR23 3.4 26.3 0.5
NE2 A:GLN26 3.4 18.9 1.0
O A:HOH878 3.9 29.9 1.0
CB A:THR23 4.0 24.4 0.5
CD A:GLN26 4.4 23.0 1.0
CB A:THR23 4.4 25.0 0.5
OG1 A:THR23 4.4 26.8 0.5
OE1 A:GLN26 4.4 22.9 1.0
O A:HOH1271 4.7 43.3 1.0
CA A:THR23 4.9 23.3 0.5
CA A:THR23 4.9 23.3 0.5
O A:HOH814 5.0 36.9 1.0

Chlorine binding site 4 out of 4 in 5on8

Go back to Chlorine Binding Sites List in 5on8
Chlorine binding site 4 out of 4 in the Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Nika in Complex with Reduced Fe-L2 (N-(2-Hydroxy- 3-Methoxybenzyl)-N'-(2-Thiomethylbenzyl)- N,N'-Ethylenediamine Diacetic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl604

b:53.8
occ:1.00
O B:HOH706 2.9 43.1 1.0
CD B:ARG365 3.4 33.1 1.0
NH1 B:ARG365 3.9 38.8 1.0
NE B:ARG365 4.1 42.8 1.0
CZ B:ARG365 4.3 39.5 1.0
CG B:ARG365 4.7 27.5 1.0

Reference:

S.Lopez, L.Rondot, C.Lepretre, C.Marchi-Delapierre, S.Menage, C.Cavazza. Cross-Linked Artificial Enzyme Crystals As Heterogeneous Catalysts For Oxidation Reactions. J. Am. Chem. Soc. V. 139 17994 2017.
ISSN: ESSN 1520-5126
PubMed: 29148757
DOI: 10.1021/JACS.7B09343
Page generated: Sat Dec 12 12:13:00 2020

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