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Chlorine in PDB 7e4a: Crystal Structure of Mif Bound to Compound 13

Enzymatic activity of Crystal Structure of Mif Bound to Compound 13

All present enzymatic activity of Crystal Structure of Mif Bound to Compound 13:
5.3.2.1; 5.3.3.12;

Protein crystallography data

The structure of Crystal Structure of Mif Bound to Compound 13, PDB code: 7e4a was solved by C.P.Fa, D.Y.Guo, L.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.14 / 1.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.766, 68.4, 88.663, 90, 90, 90
R / Rfree (%) 17.6 / 20.7

Other elements in 7e4a:

The structure of Crystal Structure of Mif Bound to Compound 13 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Mif Bound to Compound 13 (pdb code 7e4a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Crystal Structure of Mif Bound to Compound 13, PDB code: 7e4a:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 7e4a

Go back to Chlorine Binding Sites List in 7e4a
Chlorine binding site 1 out of 11 in the Crystal Structure of Mif Bound to Compound 13


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 Mif Bound to Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:27.5
occ:1.00
 NE2 A:GLN71 3.3 17.2 1.0
N A:GLN71 3.3 15.1 1.0
N A:ALA70 3.4 16.1 1.0
CA A:GLY68 3.6 14.3 1.0
C A:GLY68 3.6 14.5 1.0
N A:GLY69 3.6 15.0 1.0
CG A:GLN71 3.6 15.8 1.0
CB A:ALA70 3.8 16.9 1.0
CB A:GLN71 3.9 14.7 1.0
CD A:GLN71 4.0 17.5 1.0
CA A:ALA70 4.0 15.8 1.0
C A:ALA70 4.1 16.0 1.0
O A:GLY68 4.2 14.8 1.0
C A:GLY69 4.2 15.3 1.0
CA A:GLN71 4.2 13.8 1.0
N A:GLY68 4.3 14.2 1.0
O A:HOH381 4.3 33.8 1.0
CA A:GLY69 4.4 15.4 1.0
C A:ILE67 4.9 14.1 1.0
O A:ILE67 4.9 14.4 1.0

Chlorine binding site 2 out of 11 in 7e4a

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Chlorine binding site 2 out of 11 in the Crystal Structure of Mif Bound to Compound 13


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 Mif Bound to Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:15.5
occ:1.00
 O C:HOH349 3.0 16.3 1.0
N A:ASN102 3.1 12.7 1.0
ND2 A:ASN105 3.2 11.6 1.0
O A:HOH416 3.3 30.6 1.0
CG A:ASN102 3.8 16.8 1.0
CB A:ASN102 3.8 14.6 1.0
O A:HOH383 3.8 21.1 1.0
CA A:MET101 3.8 11.4 1.0
CB A:ASN105 3.9 11.1 1.0
C A:MET101 4.0 12.1 1.0
CE A:MET101 4.0 13.9 1.0
CG A:ASN105 4.1 12.0 1.0
CA A:ASN102 4.1 12.6 1.0
OD1 A:ASN102 4.1 18.4 1.0
O C:HOH450 4.1 19.0 1.0
ND2 A:ASN102 4.1 17.6 1.0
O A:ASP100 4.2 13.4 1.0
SD A:MET101 4.3 16.6 1.0
CB A:MET101 4.5 12.1 1.0
O A:HOH306 4.5 20.7 1.0
O C:HOH373 4.6 16.1 1.0
O A:ASN102 4.7 11.8 1.0
O C:HOH451 4.7 32.9 1.0
N A:MET101 4.9 12.3 1.0
C A:ASN102 4.9 11.8 1.0
O A:HOH311 4.9 24.8 1.0
O C:TYR98 4.9 11.6 1.0
C A:ASP100 5.0 11.7 1.0

Chlorine binding site 3 out of 11 in 7e4a

Go back to Chlorine Binding Sites List in 7e4a
Chlorine binding site 3 out of 11 in the Crystal Structure of Mif Bound to Compound 13


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 Mif Bound to Compound 13 within 5.0Å range:

Chlorine binding site 4 out of 11 in 7e4a

Go back to Chlorine Binding Sites List in 7e4a
Chlorine binding site 4 out of 11 in the Crystal Structure of Mif Bound to Compound 13


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 Mif Bound to Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:25.1
occ:1.00
 O C:HOH328 2.9 32.6 1.0
N A:ILE64 3.1 10.8 1.0
N A:PRO1 3.2 14.3 1.0
CD A:PRO1 3.4 14.2 1.0
O A:HOH388 3.5 22.1 1.0
CA A:PRO1 3.6 13.3 1.0
CG A:PRO1 3.6 14.2 1.0
CG1 A:ILE64 3.7 10.8 1.0
CA A:SER63 3.8 10.9 1.0
CB A:ILE64 3.8 11.0 1.0
CD1 A:ILE64 3.9 11.1 1.0
C A:SER63 4.0 10.9 1.0
CA A:ILE64 4.1 12.1 1.0
OG A:SER63 4.2 13.3 1.0
CB A:PRO1 4.2 14.2 1.0
NZ A:LYS32 4.2 28.0 1.0
CE A:LYS32 4.4 26.7 1.0
CB A:SER63 4.6 12.8 1.0
CD A:LYS32 4.6 25.7 1.0
O A:HIS62 4.8 12.7 1.0
O A:ILE64 4.8 15.1 1.0
C A:ILE64 4.9 13.0 1.0
C A:PRO1 4.9 13.3 1.0
N A:SER63 4.9 11.2 1.0

Chlorine binding site 5 out of 11 in 7e4a

Go back to Chlorine Binding Sites List in 7e4a
Chlorine binding site 5 out of 11 in the Crystal Structure of Mif Bound to Compound 13


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 Mif Bound to Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:26.8
occ:1.00
 O B:HOH309 2.9 31.1 1.0
N B:PRO1 3.0 14.8 1.0
O B:HOH384 3.0 24.6 1.0
O A:HOH399 3.0 31.1 1.0
N B:ILE64 3.3 14.4 1.0
CD B:PRO1 3.5 14.7 1.0
CA B:PRO1 3.6 15.0 1.0
NZ B:LYS32 3.6 27.7 1.0
CG1 B:ILE64 3.7 15.2 1.0
CA B:SER63 3.9 14.5 1.0
CG B:PRO1 3.9 15.7 1.0
CB B:ILE64 3.9 14.7 1.0
CD1 B:ILE64 4.0 14.8 1.0
C B:SER63 4.1 14.4 1.0
CA B:ILE64 4.2 14.9 1.0
OG B:SER63 4.3 17.1 1.0
CB B:PRO1 4.4 15.8 1.0
CB B:SER63 4.7 16.1 1.0
O B:HIS62 4.8 14.5 1.0
C B:PRO1 4.8 14.9 1.0
O A:HOH379 4.8 34.7 1.0
CE B:LYS32 4.8 26.4 1.0
CD B:LYS32 4.9 25.1 1.0
OH A:TYR95 4.9 15.9 1.0
N B:SER63 5.0 13.6 1.0

Chlorine binding site 6 out of 11 in 7e4a

Go back to Chlorine Binding Sites List in 7e4a
Chlorine binding site 6 out of 11 in the Crystal Structure of Mif Bound to Compound 13


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 Mif Bound to Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:31.6
occ:1.00
 NE2 B:GLN71 3.2 23.2 1.0
N B:GLN71 3.3 20.4 1.0
N B:ALA70 3.5 21.1 1.0
C B:GLY68 3.5 19.1 1.0
CA B:GLY68 3.5 18.3 1.0
CG B:GLN71 3.5 20.0 1.0
N B:GLY69 3.6 20.0 1.0
CB B:GLN71 3.9 18.9 1.0
CD B:GLN71 3.9 22.3 1.0
O B:GLY68 4.0 19.3 1.0
CB B:ALA70 4.0 20.1 1.0
CA B:ALA70 4.1 20.9 1.0
C B:ALA70 4.2 21.7 1.0
CA B:GLN71 4.2 18.8 1.0
N B:GLY68 4.2 17.7 1.0
C B:GLY69 4.3 20.5 1.0
CA B:GLY69 4.4 19.3 1.0
C B:ILE67 4.9 17.6 1.0
O B:ILE67 4.9 18.8 1.0

Chlorine binding site 7 out of 11 in 7e4a

Go back to Chlorine Binding Sites List in 7e4a
Chlorine binding site 7 out of 11 in the Crystal Structure of Mif Bound to Compound 13


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 Mif Bound to Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:16.8
occ:1.00
 N1 A:HWL205 3.0 16.6 1.0
O4 A:HWL205 3.4 16.9 1.0
C17 A:HWL205 3.4 17.2 1.0
C7 A:HWL205 3.6 16.0 1.0
C8 A:HWL205 3.6 16.5 1.0
C24 A:HWL205 3.7 17.6 1.0
C23 A:HWL205 3.7 17.8 1.0
C20 A:HWL205 3.7 18.4 1.0
C19 A:HWL205 3.8 16.7 1.0
C18 A:HWL205 3.8 16.1 1.0
C21 A:HWL205 3.8 20.2 1.0
O3 A:HWL205 4.0 18.1 1.0
C22 A:HWL205 4.3 19.6 1.0
C6 A:HWL205 4.5 16.3 1.0
C9 A:HWL205 4.7 17.1 1.0

Chlorine binding site 8 out of 11 in 7e4a

Go back to Chlorine Binding Sites List in 7e4a
Chlorine binding site 8 out of 11 in the Crystal Structure of Mif Bound to Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Mif Bound to Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:30.6
occ:1.00
 O B:HOH371 3.0 20.6 1.0
N B:LEU19 3.4 17.2 1.0
N B:PHE18 3.5 18.4 1.0
N B:GLY17 3.5 25.1 1.0
CG B:LEU19 3.8 21.0 1.0
O B:PRO15 3.8 25.9 1.0
CB B:LEU19 3.9 18.5 1.0
C B:GLY17 4.0 19.7 1.0
CA B:GLY17 4.1 22.9 1.0
CA B:PHE18 4.2 17.4 1.0
CA B:LEU19 4.3 17.2 1.0
C B:PHE18 4.3 16.6 1.0
C B:ASP16 4.4 28.6 1.0
CB B:PHE18 4.4 18.9 1.0
CD1 B:LEU19 4.4 21.2 1.0
CA B:ASP16 4.5 29.8 1.0
CD1 A:LEU46 4.7 20.7 1.0
C B:PRO15 4.9 25.7 1.0
O B:GLY17 4.9 18.6 1.0
CD2 B:LEU19 5.0 21.4 1.0

Chlorine binding site 9 out of 11 in 7e4a

Go back to Chlorine Binding Sites List in 7e4a
Chlorine binding site 9 out of 11 in the Crystal Structure of Mif Bound to Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Mif Bound to Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:23.6
occ:1.00
 O C:HOH432 3.0 29.8 1.0
NE2 C:GLN71 3.2 15.9 1.0
N C:GLN71 3.3 12.9 1.0
N C:ALA70 3.4 14.4 1.0
C C:GLY68 3.5 13.2 1.0
CA C:GLY68 3.5 13.2 1.0
N C:GLY69 3.6 13.4 1.0
CG C:GLN71 3.6 14.8 1.0
O C:HOH400 3.8 29.3 1.0
CB C:ALA70 3.9 15.1 1.0
CD C:GLN71 3.9 15.9 1.0
CB C:GLN71 3.9 14.3 1.0
O C:GLY68 4.0 13.7 1.0
CA C:ALA70 4.0 13.6 1.0
C C:ALA70 4.1 13.5 1.0
N C:GLY68 4.2 12.2 1.0
C C:GLY69 4.2 13.8 1.0
CA C:GLN71 4.3 13.7 1.0
CA C:GLY69 4.4 14.1 1.0
O C:HOH399 4.5 30.1 1.0
C C:ILE67 4.9 13.3 1.0
O C:ILE67 5.0 16.3 1.0

Chlorine binding site 10 out of 11 in 7e4a

Go back to Chlorine Binding Sites List in 7e4a
Chlorine binding site 10 out of 11 in the Crystal Structure of Mif Bound to Compound 13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Mif Bound to Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:24.4
occ:1.00
 N C:PRO1 3.1 13.1 1.0
N C:ILE64 3.2 12.0 1.0
O B:HOH329 3.4 19.4 1.0
OH B:TYR95 3.4 18.7 1.0
CA C:PRO1 3.5 12.8 1.0
CD C:PRO1 3.6 14.3 1.0
CG1 C:ILE64 3.6 12.9 1.0
C15 C:HWL204 3.7 30.9 1.0
CA C:SER63 3.7 11.4 1.0
C14 C:HWL204 3.8 30.6 1.0
CD1 C:ILE64 3.9 13.5 1.0
CG C:PRO1 3.9 14.9 1.0
C C:SER63 3.9 10.9 1.0
CB C:ILE64 4.1 12.0 1.0
CA C:ILE64 4.2 11.9 1.0
CB C:PRO1 4.4 13.6 1.0
O C:HIS62 4.4 12.6 1.0
O C:HOH305 4.4 20.1 1.0
CZ B:TYR95 4.5 17.5 1.0
OG C:SER63 4.6 13.4 1.0
N C:SER63 4.6 11.3 1.0
NZ C:LYS32 4.7 24.1 1.0
CB C:SER63 4.7 12.4 1.0
C C:PRO1 4.7 12.5 1.0
C C:HIS62 4.9 11.6 1.0
CG1 C:VAL106 5.0 15.6 1.0
C16 C:HWL204 5.0 29.9 1.0
CG2 C:VAL106 5.0 13.3 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 20:23:35 2024

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