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Chlorine in PDB 5on1: Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-N'-(2-Thiomethylbenzyl)-N,N'-Ethylenediamine Diacetic Acid)

Protein crystallography data

The structure of Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-N'-(2-Thiomethylbenzyl)-N,N'-Ethylenediamine Diacetic Acid), PDB code: 5on1 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) 38.22 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.138, 94.896, 125.283, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.5

Other elements in 5on1:

The structure of Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-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 Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-N'-(2-Thiomethylbenzyl)-N,N'-Ethylenediamine Diacetic Acid) (pdb code 5on1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-N'-(2-Thiomethylbenzyl)-N,N'-Ethylenediamine Diacetic Acid), PDB code: 5on1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5on1

Go back to Chlorine Binding Sites List in 5on1
Chlorine binding site 1 out of 7 in the Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-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 Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-N'-(2-Thiomethylbenzyl)-N,N'-Ethylenediamine Diacetic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl610

b:58.1
occ:1.00
 NE2 A:GLN26 3.2 27.6 1.0
CG2 A:THR23 3.3 37.5 0.5
O A:HOH969 3.6 42.8 1.0
CG2 A:THR23 4.0 33.9 0.5
OG1 A:THR23 4.2 35.7 0.5
CD A:GLN26 4.2 33.7 1.0
CB A:THR23 4.3 34.3 0.5
OE1 A:GLN26 4.4 27.0 1.0
CB A:THR23 4.5 34.3 0.5
CA A:THR23 4.7 30.4 0.5
CA A:THR23 4.7 30.5 0.5
CA A:PRO24 4.8 23.3 1.0
O A:HOH1026 4.9 39.4 1.0
O A:ASN25 4.9 24.9 1.0
O A:PRO24 5.0 27.9 1.0

Chlorine binding site 2 out of 7 in 5on1

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Chlorine binding site 2 out of 7 in the Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-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 Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-N'-(2-Thiomethylbenzyl)-N,N'-Ethylenediamine Diacetic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl614

b:42.4
occ:1.00
 N A:TYR22 3.2 21.5 1.0
NE A:ARG97 3.3 49.8 1.0
NH2 A:ARG97 3.3 52.9 1.0
CD2 A:TYR22 3.7 22.8 1.0
CZ A:ARG97 3.8 61.5 1.0
CB A:TYR22 3.8 25.7 1.0
CB A:LEU21 3.8 24.8 1.0
CD2 A:LEU21 3.9 26.1 1.0
CA A:TYR22 4.0 23.0 1.0
CA A:LEU21 4.1 21.4 1.0
C A:LEU21 4.2 21.9 1.0
O A:THR23 4.2 32.3 0.5
O A:THR23 4.2 32.4 0.5
O A:HOH1062 4.2 39.2 1.0
CG A:TYR22 4.2 23.0 1.0
C A:TYR22 4.3 24.4 1.0
CG A:LEU21 4.3 22.0 1.0
CD A:ARG97 4.5 41.7 1.0
CG A:ARG97 4.5 29.4 1.0
N A:THR23 4.6 31.1 0.5
N A:THR23 4.6 31.1 0.5
CD1 A:LEU21 4.8 25.5 1.0
CE2 A:TYR22 4.8 23.8 1.0
O A:TYR22 4.9 24.8 1.0

Chlorine binding site 3 out of 7 in 5on1

Go back to Chlorine Binding Sites List in 5on1
Chlorine binding site 3 out of 7 in the Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-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 Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-N'-(2-Thiomethylbenzyl)-N,N'-Ethylenediamine Diacetic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl617

b:59.2
occ:1.00
 N A:ASN149 3.2 31.2 1.0
NZ A:LYS157 3.5 34.4 1.0
O A:HOH1119 3.6 57.5 1.0
CE A:LYS157 3.7 38.0 1.0
O A:HOH931 3.9 46.9 1.0
CA A:ASN149 4.0 33.3 1.0
CA A:LYS148 4.1 28.4 1.0
C A:LYS148 4.2 33.9 1.0
O A:HOH831 4.2 35.5 1.0
O A:PHE147 4.4 28.1 1.0
CB A:ASN149 4.7 42.7 1.0
CB A:LYS148 4.8 28.0 1.0

Chlorine binding site 4 out of 7 in 5on1

Go back to Chlorine Binding Sites List in 5on1
Chlorine binding site 4 out of 7 in the Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-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 Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-N'-(2-Thiomethylbenzyl)-N,N'-Ethylenediamine Diacetic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl619

b:54.8
occ:1.00
 N A:VAL46 3.2 26.1 1.0
CB A:SER45 3.7 33.3 1.0
CA A:SER45 3.7 30.5 1.0
CG2 A:VAL46 3.7 30.9 1.0
O A:VAL46 3.8 31.3 1.0
C A:SER45 3.9 25.9 1.0
CA A:VAL46 4.2 27.2 1.0
CB A:VAL46 4.4 23.6 1.0
NE2 A:GLN131 4.4 40.1 1.0
C A:VAL46 4.4 28.7 1.0
CG1 A:VAL46 4.7 32.2 1.0
OG A:SER45 4.8 32.2 1.0
CD1 A:LEU130 4.8 31.7 1.0

Chlorine binding site 5 out of 7 in 5on1

Go back to Chlorine Binding Sites List in 5on1
Chlorine binding site 5 out of 7 in the Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-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 5 of Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-N'-(2-Thiomethylbenzyl)-N,N'-Ethylenediamine Diacetic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl622

b:62.4
occ:1.00
 O A:HOH1114 2.9 56.5 1.0
N A:LYS115 3.4 32.4 1.0
CB A:LYS115 3.8 40.1 1.0
CB A:SER114 3.8 34.8 1.0
O A:HOH785 3.8 41.4 1.0
O A:HOH1143 4.0 45.2 1.0
CA A:SER114 4.2 28.7 1.0
CA A:LYS115 4.2 34.7 1.0
CG A:LYS115 4.2 49.7 1.0
C A:SER114 4.3 31.8 1.0
CD A:LYS115 4.4 54.0 1.0
OG A:SER114 4.6 30.9 1.0

Chlorine binding site 6 out of 7 in 5on1

Go back to Chlorine Binding Sites List in 5on1
Chlorine binding site 6 out of 7 in the Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-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 6 of Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-N'-(2-Thiomethylbenzyl)-N,N'-Ethylenediamine Diacetic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl607

b:50.9
occ:1.00
 N B:TYR22 3.4 29.2 1.0
O B:HOH950 3.6 42.9 1.0
NE B:ARG97 3.8 52.0 1.0
CD2 B:LEU21 3.8 29.9 1.0
CD2 B:TYR22 3.8 29.1 1.0
CB B:TYR22 3.9 31.5 1.0
CB B:LEU21 3.9 31.8 1.0
CA B:TYR22 4.1 28.2 1.0
NH2 B:ARG97 4.1 60.8 1.0
O B:THR23 4.1 41.2 1.0
CA B:LEU21 4.3 27.6 1.0
C B:LEU21 4.3 25.6 1.0
O B:HOH998 4.4 42.6 1.0
C B:TYR22 4.4 29.8 1.0
CG B:LEU21 4.4 32.4 1.0
CG B:TYR22 4.4 28.2 1.0
CZ B:ARG97 4.4 61.0 1.0
CG B:ARG97 4.6 38.7 1.0
N B:THR23 4.7 31.8 1.0
CD1 B:LEU21 4.7 32.2 1.0
CD B:ARG97 4.7 45.2 1.0
O B:TYR22 4.9 29.9 1.0
CE2 B:TYR22 4.9 31.4 1.0

Chlorine binding site 7 out of 7 in 5on1

Go back to Chlorine Binding Sites List in 5on1
Chlorine binding site 7 out of 7 in the Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-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 7 of Crystal Structure of Nika in Complex with Hydroxylated Fe-L1 (N-(2- Hydroxybenzyl)-N'-(2-Thiomethylbenzyl)-N,N'-Ethylenediamine Diacetic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl610

b:65.0
occ:1.00
 O B:HOH1060 2.3 59.6 1.0
O B:ARG180 2.9 43.2 1.0
OE2 B:GLU182 3.0 47.5 1.0
O B:HOH1011 3.7 51.9 1.0
CG B:GLU182 3.7 36.5 1.0
CD B:GLU182 3.8 49.0 1.0
CB B:VAL179 3.8 37.1 1.0
N B:ARG180 3.8 36.5 1.0
C B:ARG180 3.8 41.7 1.0
CA B:ARG180 4.2 33.9 1.0
CG2 B:VAL179 4.2 34.6 1.0
CB B:ARG180 4.3 42.9 1.0
O B:HOH949 4.3 55.0 1.0
C B:VAL179 4.3 34.4 1.0
O B:LYS192 4.3 37.0 1.0
CG B:LYS192 4.5 52.9 1.0
CA B:VAL179 4.6 32.0 1.0
O B:HOH931 4.6 41.8 1.0
CG1 B:VAL179 4.6 36.2 1.0
NE B:ARG180 4.9 51.8 1.0
OE1 B:GLU182 5.0 51.3 1.0
N B:GLU182 5.0 41.6 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: Fri Jul 26 14:35:19 2024

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