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Chlorine in PDB 3dji: Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi

Enzymatic activity of Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi

All present enzymatic activity of Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi:
5.3.2.1;

Protein crystallography data

The structure of Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi, PDB code: 3dji was solved by G.V.Crichlow, E.Lolis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.68 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.974, 60.899, 77.806, 90.00, 93.28, 90.00
R / Rfree (%) 20.9 / 24.7

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi (pdb code 3dji). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 15 binding sites of Chlorine where determined in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi, PDB code: 3dji:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 15 in 3dji

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Chlorine binding site 1 out of 15 in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi


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 Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:46.0
occ:1.00
 N A:ALA70 3.4 34.5 1.0
N A:GLY69 3.5 32.8 1.0
N A:GLN71 3.5 34.9 1.0
CG A:GLN71 3.5 37.2 1.0
NE2 A:GLN71 3.6 40.5 1.0
C A:GLY68 3.7 34.2 1.0
CA A:GLY68 3.8 33.1 1.0
CB A:GLN71 4.0 36.0 1.0
CD A:GLN71 4.1 38.5 1.0
CA A:ALA70 4.2 35.0 1.0
CB A:ALA70 4.2 35.0 1.0
C A:GLY69 4.2 33.9 1.0
CA A:GLY69 4.2 34.1 1.0
C A:ALA70 4.4 35.2 1.0
O A:GLY68 4.4 33.3 1.0
CA A:GLN71 4.4 34.9 1.0
N A:GLY68 4.6 33.4 1.0

Chlorine binding site 2 out of 15 in 3dji

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Chlorine binding site 2 out of 15 in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi


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 Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:33.2
occ:1.00
 O C:HOH312 3.0 25.9 1.0
ND2 A:ASN105 3.2 25.8 1.0
O A:HOH754 3.2 46.0 1.0
N A:ASN102 3.2 29.2 1.0
ND2 A:ASN102 3.5 40.3 1.0
CG A:ASN102 3.8 38.0 1.0
O A:HOH755 3.8 46.0 1.0
CA A:MET101 3.8 26.8 1.0
O A:HOH734 3.9 38.6 1.0
CB A:ASN105 4.0 23.5 1.0
C A:MET101 4.0 27.6 1.0
CG A:ASN105 4.0 26.4 1.0
CB A:ASN102 4.1 34.2 1.0
CE A:MET101 4.1 29.1 1.0
O A:ASP100 4.2 28.5 1.0
CA A:ASN102 4.2 30.6 1.0
OD1 A:ASN102 4.4 43.4 1.0
SD A:MET101 4.5 32.1 1.0
CB A:MET101 4.5 26.5 1.0
O A:HOH756 4.6 47.8 1.0
O C:HOH342 4.7 35.8 1.0
O A:ASN102 4.7 30.2 1.0
N A:MET101 4.8 24.7 1.0
O A:HOH758 4.9 48.6 1.0
C A:ASP100 4.9 26.6 1.0
O C:TYR98 4.9 25.5 1.0

Chlorine binding site 3 out of 15 in 3dji

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Chlorine binding site 3 out of 15 in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi


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 Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:34.5
occ:1.00
 NE A:ARG11 3.1 35.1 1.0
O A:HOH722 3.2 33.7 1.0
O A:HOH713 3.3 28.6 1.0
CD A:ARG11 3.9 34.6 1.0
NH1 A:ARG11 3.9 38.8 1.0
CZ A:ARG11 3.9 37.8 1.0
CD1 C:LEU46 4.1 26.1 1.0
CD2 C:LEU46 4.6 27.9 1.0
CG A:ARG11 4.6 33.2 1.0
CB C:LEU46 4.6 22.8 1.0
CG C:LEU46 4.7 27.2 1.0
O A:HOH735 4.8 38.7 1.0

Chlorine binding site 4 out of 15 in 3dji

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Chlorine binding site 4 out of 15 in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi


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 Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:65.7
occ:1.00
 NE2 B:GLN71 3.3 42.8 1.0
CG B:GLN71 3.4 41.5 1.0
N B:GLN71 3.5 38.8 1.0
C B:GLY68 3.5 43.9 1.0
CA B:GLY68 3.5 43.4 1.0
N B:ALA70 3.6 42.6 1.0
N B:GLY69 3.7 43.7 1.0
CD B:GLN71 3.9 42.2 1.0
CB B:GLN71 4.0 39.3 1.0
O B:GLY68 4.0 44.0 1.0
CB B:ALA70 4.1 43.4 1.0
CA B:ALA70 4.2 41.9 1.0
C B:ALA70 4.3 40.5 1.0
C B:GLY69 4.3 43.6 1.0
N B:GLY68 4.3 42.3 1.0
CA B:GLN71 4.4 38.9 1.0
CA B:GLY69 4.5 43.5 1.0

Chlorine binding site 5 out of 15 in 3dji

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Chlorine binding site 5 out of 15 in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi


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 Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:45.7
occ:1.00
 O B:HOH326 3.1 35.2 1.0
N B:GLY17 3.2 32.1 1.0
N B:LEU19 3.3 25.9 1.0
N B:PHE18 3.3 30.1 1.0
CA B:GLY17 3.8 32.5 1.0
CB B:LEU19 3.8 31.9 1.0
C B:GLY17 3.8 31.5 1.0
O B:PRO15 3.8 36.4 1.0
CG B:LEU19 3.8 36.5 1.0
CA B:PHE18 4.1 29.1 1.0
CA B:LEU19 4.1 29.9 1.0
C B:ASP16 4.2 34.3 1.0
C B:PHE18 4.2 28.6 1.0
CD1 B:LEU19 4.3 36.6 1.0
CB B:PHE18 4.3 29.0 1.0
CA B:ASP16 4.3 36.2 1.0
O B:GLY17 4.7 30.3 1.0
C B:PRO15 4.8 36.9 1.0
N B:SER20 4.9 28.1 1.0
CD1 A:LEU46 5.0 34.2 1.0

Chlorine binding site 6 out of 15 in 3dji

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Chlorine binding site 6 out of 15 in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi


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 Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:35.7
occ:1.00
 O A:HOH705 3.1 25.3 1.0
ND2 B:ASN105 3.1 32.5 1.0
N B:ASN102 3.2 30.0 1.0
CA B:MET101 3.8 30.0 1.0
CG B:ASN102 3.8 36.0 1.0
O A:HOH736 3.9 38.8 1.0
CB B:ASN102 3.9 33.8 1.0
CB B:ASN105 4.0 28.4 1.0
C B:MET101 4.0 29.5 1.0
CG B:ASN105 4.0 31.8 1.0
OD1 B:ASN102 4.1 38.8 1.0
O B:ASP100 4.2 31.1 1.0
CA B:ASN102 4.2 32.5 1.0
ND2 B:ASN102 4.2 36.1 1.0
CE B:MET101 4.2 30.0 1.0
SD B:MET101 4.5 34.2 1.0
CB B:MET101 4.5 30.7 1.0
O A:HOH718 4.8 32.3 1.0
O B:ASN102 4.8 33.6 1.0
N B:MET101 4.9 30.3 1.0
C B:ASP100 4.9 31.3 1.0
O B:HOH338 5.0 40.1 1.0
O A:TYR98 5.0 24.9 1.0

Chlorine binding site 7 out of 15 in 3dji

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Chlorine binding site 7 out of 15 in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi


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 Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:48.9
occ:1.00
 NE2 C:GLN71 3.3 28.6 1.0
CG C:GLN71 3.6 30.1 1.0
N C:ALA70 3.6 30.9 1.0
C C:GLY68 3.6 33.1 1.0
CA C:GLY68 3.6 32.7 1.0
N C:GLN71 3.7 30.6 1.0
N C:GLY69 3.7 33.2 1.0
CD C:GLN71 3.9 28.0 1.0
CB C:ALA70 4.0 32.4 1.0
O C:GLY68 4.1 30.6 1.0
CB C:GLN71 4.2 28.6 1.0
CA C:ALA70 4.2 30.5 1.0
C C:GLY69 4.4 32.4 1.0
N C:GLY68 4.4 31.1 1.0
C C:ALA70 4.4 30.2 1.0
CA C:GLY69 4.5 31.7 1.0
CA C:GLN71 4.6 29.2 1.0
C C:ILE67 5.0 30.6 1.0
O C:ILE67 5.0 29.6 1.0

Chlorine binding site 8 out of 15 in 3dji

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Chlorine binding site 8 out of 15 in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi


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 Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:34.8
occ:1.00
 O B:HOH316 3.1 30.1 1.0
N C:ASN102 3.2 25.0 1.0
ND2 C:ASN105 3.3 29.6 1.0
O C:HOH352 3.4 39.6 1.0
CA C:MET101 3.8 24.5 1.0
O C:HOH355 3.9 40.2 1.0
CG C:ASN102 3.9 34.5 1.0
CE C:MET101 3.9 27.4 1.0
CB C:ASN105 3.9 27.8 1.0
CB C:ASN102 4.0 30.0 1.0
C C:MET101 4.0 24.3 1.0
OD1 C:ASN102 4.1 38.0 1.0
CG C:ASN105 4.1 28.7 1.0
CA C:ASN102 4.1 28.2 1.0
O C:ASP100 4.2 25.7 1.0
ND2 C:ASN102 4.2 36.3 1.0
SD C:MET101 4.4 32.7 1.0
CB C:MET101 4.4 23.8 1.0
O C:ASN102 4.5 25.1 1.0
O B:HOH327 4.6 35.3 1.0
N C:MET101 4.9 24.3 1.0
C C:ASN102 4.9 27.4 1.0
C C:ASP100 5.0 26.4 1.0
O B:TYR98 5.0 27.7 1.0

Chlorine binding site 9 out of 15 in 3dji

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Chlorine binding site 9 out of 15 in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi


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 Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl203

b:26.1
occ:1.00
 O C:HOH314 2.9 27.8 1.0
O B:HOH305 3.1 26.8 1.0
CG C:GLN35 3.6 23.8 1.0
NE2 C:GLN35 4.3 27.8 1.0
CD C:GLN35 4.4 22.8 1.0
CB C:GLN35 4.7 22.4 1.0
O B:GLY50 4.9 23.6 1.0

Chlorine binding site 10 out of 15 in 3dji

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Chlorine binding site 10 out of 15 in the Crystal Structure of Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi


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 Macrophage Migration Inhibitory Factor Bound to An Acetaminophen Dimer Derived From Napqi within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl201

b:42.3
occ:1.00
 NE2 D:GLN71 3.2 37.7 1.0
CG D:GLN71 3.3 34.4 1.0
CA D:GLY68 3.4 33.9 1.0
C D:GLY68 3.4 34.5 1.0
N D:ALA70 3.5 32.0 1.0
N D:GLN71 3.5 29.5 1.0
N D:GLY69 3.7 33.5 1.0
CD D:GLN71 3.8 35.5 1.0
CB D:GLN71 3.8 30.7 1.0
O D:GLY68 3.9 34.8 1.0
N D:GLY68 4.1 33.9 1.0
CB D:ALA70 4.1 32.7 1.0
CA D:ALA70 4.2 31.4 1.0
CA D:GLN71 4.3 30.2 1.0
C D:GLY69 4.3 32.3 1.0
C D:ALA70 4.4 29.8 1.0
CA D:GLY69 4.4 32.3 1.0
O D:ILE67 4.6 32.9 1.0
C D:ILE67 4.6 33.6 1.0
OE1 D:GLN71 5.0 36.4 1.0

Reference:

G.V.Crichlow, J.B.Lubetsky, L.Leng, R.Bucala, E.J.Lolis. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions. Biochemistry V. 48 132 2009.
ISSN: ISSN 0006-2960
PubMed: 19090677
DOI: 10.1021/BI8014423
Page generated: Sat Jul 20 18:18:18 2024

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