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Chlorine in PDB 7e47: Crystal Structure of Compound 6 Bound to Mif

Enzymatic activity of Crystal Structure of Compound 6 Bound to Mif

All present enzymatic activity of Crystal Structure of Compound 6 Bound to Mif:
5.3.2.1; 5.3.3.12;

Protein crystallography data

The structure of Crystal Structure of Compound 6 Bound to Mif, PDB code: 7e47 was solved by C.P.Fan, L.Yang, D.Y.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.11 / 1.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.388, 67.713, 88.224, 90, 90, 90
R / Rfree (%) 15.4 / 17.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Compound 6 Bound to Mif (pdb code 7e47). 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 Compound 6 Bound to Mif, PDB code: 7e47:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 7e47

Go back to Chlorine Binding Sites List in 7e47
Chlorine binding site 1 out of 7 in the Crystal Structure of Compound 6 Bound to Mif


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 Compound 6 Bound to Mif within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:18.3
occ:1.00
 O C:HOH329 3.0 18.1 1.0
N A:ASN102 3.1 13.6 1.0
ND2 A:ASN105 3.2 16.4 1.0
CG A:ASN102 3.7 21.8 1.0
CB A:ASN102 3.8 16.9 1.0
CA A:MET101 3.9 13.3 1.0
O A:HOH387 3.9 25.3 1.0
CB A:ASN105 3.9 14.2 1.0
C A:MET101 4.0 13.9 1.0
CG A:ASN105 4.0 15.6 1.0
ND2 A:ASN102 4.0 24.5 1.0
CA A:ASN102 4.1 14.5 1.0
O C:HOH406 4.1 22.6 1.0
CE A:MET101 4.1 17.1 1.0
OD1 A:ASN102 4.1 24.8 1.0
O A:ASP100 4.2 15.1 1.0
SD A:MET101 4.3 17.2 1.0
CB A:MET101 4.5 14.1 1.0
O C:HOH357 4.5 23.0 1.0
O A:HOH307 4.5 23.0 1.0
O A:ASN102 4.7 13.8 1.0
O C:HOH407 4.7 40.4 1.0
O A:HOH313 4.8 33.5 1.0
N A:MET101 4.9 13.5 1.0
C A:ASN102 4.9 14.1 1.0
O C:TYR98 4.9 14.4 1.0
C A:ASP100 5.0 14.2 1.0
O A:HOH396 5.0 23.8 1.0

Chlorine binding site 2 out of 7 in 7e47

Go back to Chlorine Binding Sites List in 7e47
Chlorine binding site 2 out of 7 in the Crystal Structure of Compound 6 Bound to Mif


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 Compound 6 Bound to Mif within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:26.7
occ:1.00
 N A:PRO1 3.2 15.0 1.0
N A:ILE64 3.2 14.2 1.0
CD A:PRO1 3.4 16.3 1.0
O A:HOH305 3.4 36.9 1.0
CA A:PRO1 3.6 14.1 1.0
CG A:PRO1 3.7 16.8 1.0
O A:HOH405 3.7 25.8 1.0
CG1 A:ILE64 3.8 15.9 1.0
CB A:ILE64 3.8 14.6 1.0
CA A:SER63 3.9 13.3 1.0
CD1 A:ILE64 4.0 17.4 1.0
C A:SER63 4.0 14.2 1.0
CA A:ILE64 4.1 14.6 1.0
OG A:SER63 4.2 15.8 1.0
CB A:PRO1 4.3 15.6 1.0
CE A:LYS32 4.3 24.3 1.0
NZ A:LYS32 4.5 28.1 1.0
CD A:LYS32 4.5 24.5 1.0
CB A:SER63 4.7 15.0 1.0
O A:ILE64 4.8 16.4 1.0
O A:HIS62 4.9 14.0 1.0
C A:ILE64 4.9 14.6 1.0
C A:PRO1 4.9 12.9 1.0

Chlorine binding site 3 out of 7 in 7e47

Go back to Chlorine Binding Sites List in 7e47
Chlorine binding site 3 out of 7 in the Crystal Structure of Compound 6 Bound to Mif


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 Compound 6 Bound to Mif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:17.5
occ:1.00
 O B:HOH376 3.1 33.8 1.0
O A:HOH326 3.1 16.5 1.0
N B:ASN102 3.1 15.3 1.0
ND2 B:ASN105 3.2 16.1 1.0
O B:HOH384 3.3 36.6 1.0
CG B:ASN102 3.8 22.4 1.0
CB B:ASN102 3.8 16.6 1.0
CA B:MET101 3.8 14.0 1.0
CB B:ASN105 3.9 14.1 1.0
CE B:MET101 3.9 17.9 1.0
C B:MET101 4.0 15.1 1.0
O B:HOH366 4.0 23.0 1.0
CG B:ASN105 4.0 15.7 1.0
ND2 B:ASN102 4.0 26.3 1.0
O A:HOH433 4.0 21.8 1.0
CA B:ASN102 4.1 15.0 1.0
OD1 B:ASN102 4.1 25.7 1.0
O B:ASP100 4.2 17.0 1.0
SD B:MET101 4.3 17.8 1.0
CB B:MET101 4.5 14.6 1.0
O B:HOH302 4.6 21.8 1.0
O B:ASN102 4.6 14.6 1.0
O A:HOH364 4.7 19.8 1.0
O A:HOH435 4.7 31.8 1.0
C B:ASN102 4.9 13.9 1.0
N B:MET101 4.9 14.1 1.0
O B:HOH305 4.9 36.0 1.0
O A:TYR98 5.0 13.4 1.0
C B:ASP100 5.0 15.7 1.0

Chlorine binding site 4 out of 7 in 7e47

Go back to Chlorine Binding Sites List in 7e47
Chlorine binding site 4 out of 7 in the Crystal Structure of Compound 6 Bound to Mif


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 Compound 6 Bound to Mif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:29.8
occ:1.00
 N B:PRO1 3.1 16.7 1.0
N B:ILE64 3.3 14.8 1.0
CD B:PRO1 3.3 19.0 1.0
O B:HOH313 3.5 30.9 1.0
O B:HOH374 3.7 25.1 1.0
CA B:PRO1 3.7 15.8 1.0
CG B:PRO1 3.7 18.4 1.0
CG1 B:ILE64 3.7 17.3 1.0
CB B:ILE64 3.8 16.3 1.0
CD1 B:ILE64 3.9 17.1 1.0
CA B:SER63 4.0 14.5 1.0
C B:SER63 4.1 14.8 1.0
CA B:ILE64 4.1 15.7 1.0
OG B:SER63 4.2 17.1 1.0
CB B:PRO1 4.3 16.9 1.0
CE B:LYS32 4.4 26.1 1.0
CD B:LYS32 4.6 26.8 1.0
NZ B:LYS32 4.7 26.7 1.0
CB B:SER63 4.7 15.2 1.0
O B:ILE64 4.8 18.1 1.0
O B:HIS62 4.9 15.9 1.0
C B:ILE64 4.9 16.3 1.0
C B:PRO1 5.0 15.3 1.0

Chlorine binding site 5 out of 7 in 7e47

Go back to Chlorine Binding Sites List in 7e47
Chlorine binding site 5 out of 7 in the Crystal Structure of Compound 6 Bound to Mif


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 Compound 6 Bound to Mif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:37.7
occ:1.00
 NE2 B:GLN71 3.2 26.8 1.0
N B:GLN71 3.3 22.7 1.0
N B:ALA70 3.5 24.3 1.0
C B:GLY68 3.5 20.8 1.0
CA B:GLY68 3.6 18.8 1.0
CG B:GLN71 3.6 23.4 1.0
N B:GLY69 3.6 22.4 1.0
CB B:GLN71 3.9 20.3 1.0
CD B:GLN71 3.9 24.9 1.0
O B:GLY68 4.0 20.2 1.0
CB B:ALA70 4.0 24.7 1.0
CA B:ALA70 4.1 24.2 1.0
C B:ALA70 4.2 23.4 1.0
CA B:GLN71 4.2 19.8 1.0
N B:GLY68 4.2 19.4 1.0
C B:GLY69 4.3 22.3 1.0
CA B:GLY69 4.4 23.1 1.0
C B:ILE67 4.9 20.2 1.0
O B:ILE67 5.0 23.4 1.0

Chlorine binding site 6 out of 7 in 7e47

Go back to Chlorine Binding Sites List in 7e47
Chlorine binding site 6 out of 7 in the Crystal Structure of Compound 6 Bound to Mif


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 Compound 6 Bound to Mif within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:20.1
occ:1.00
 O B:HOH323 3.0 16.0 1.0
N C:ASN102 3.1 16.4 1.0
ND2 C:ASN105 3.2 19.1 1.0
O C:HOH398 3.3 42.3 1.0
CB C:ASN102 3.7 20.2 1.0
CG C:ASN102 3.8 24.9 1.0
CA C:MET101 3.8 15.2 1.0
CB C:ASN105 3.9 16.6 1.0
C C:MET101 4.0 15.2 1.0
O C:HOH369 4.0 30.2 1.0
CG C:ASN105 4.0 18.1 1.0
CA C:ASN102 4.1 18.2 1.0
CE C:MET101 4.1 18.9 1.0
O B:HOH405 4.1 21.8 1.0
OD1 C:ASN102 4.1 28.7 1.0
ND2 C:ASN102 4.1 29.3 1.0
O C:ASP100 4.2 17.5 1.0
SD C:MET101 4.3 18.6 1.0
CB C:MET101 4.6 15.8 1.0
O B:HOH348 4.6 19.1 1.0
O C:ASN102 4.6 17.1 1.0
O B:HOH403 4.8 31.5 1.0
O C:HOH317 4.8 45.1 1.0
N C:MET101 4.8 15.5 1.0
C C:ASN102 4.9 18.1 1.0
C C:ASP100 5.0 15.2 1.0
O B:TYR98 5.0 15.3 1.0

Chlorine binding site 7 out of 7 in 7e47

Go back to Chlorine Binding Sites List in 7e47
Chlorine binding site 7 out of 7 in the Crystal Structure of Compound 6 Bound to Mif


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 Compound 6 Bound to Mif within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:31.6
occ:1.00
 OG C:SER63 2.9 22.3 1.0
N C:PRO1 3.1 16.9 1.0
CE C:LYS32 3.4 30.3 1.0
CA C:PRO1 3.5 15.8 1.0
C19 C:HWR203 3.5 17.2 1.0
CB C:SER63 3.6 18.6 1.0
CA C:SER63 3.6 15.1 1.0
N C:ILE64 3.7 15.5 1.0
CG C:LYS32 3.8 24.6 1.0
CD C:PRO1 3.9 18.3 1.0
C20 C:HWR203 4.0 18.3 1.0
CD C:LYS32 4.0 29.2 1.0
C22 C:HWR203 4.1 16.6 1.0
O6 C:HWR203 4.1 19.0 1.0
CB C:PRO1 4.2 17.9 1.0
C C:SER63 4.2 17.1 1.0
O5 C:HWR203 4.3 16.4 1.0
C15 C:HWR203 4.4 17.3 1.0
C18 C:HWR203 4.5 17.0 1.0
NZ C:LYS32 4.5 28.8 1.0
O C:ILE64 4.6 25.2 1.0
C16 C:HWR203 4.6 17.5 1.0
O C:HIS62 4.6 14.6 1.0
CG C:PRO1 4.6 19.3 1.0
C21 C:HWR203 4.7 15.3 1.0
C C:PRO1 4.8 15.4 1.0
CB C:LYS32 4.8 23.1 1.0
CA C:ILE64 4.8 16.8 1.0
C14 C:HWR203 4.9 17.4 1.0
N C:SER63 4.9 14.0 1.0
C C:ILE64 5.0 22.4 1.0

Reference:

L.Yang, D.Guo, C.Fan. Identification and Structure-Activity Relationships of Dietary Flavonoids As Human Macrophage Migration Inhibitory Factor (Mif) Inhibitors. J.Agric.Food Chem. V. 69 10138 2021.
ISSN: ESSN 1520-5118
PubMed: 34459191
DOI: 10.1021/ACS.JAFC.1C03367
Page generated: Mon Jul 29 20:23:17 2024

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