Atomistry » Zinc » PDB 7lyt-7mj2 » 7mfh
Atomistry »
  Zinc »
    PDB 7lyt-7mj2 »
      7mfh »

Zinc in PDB 7mfh: Crystal Structure of Bio-32546 Bound Mouse Autotaxin

Enzymatic activity of Crystal Structure of Bio-32546 Bound Mouse Autotaxin

All present enzymatic activity of Crystal Structure of Bio-32546 Bound Mouse Autotaxin:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Bio-32546 Bound Mouse Autotaxin, PDB code: 7mfh was solved by J.V.Chodaparambil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.13 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.02, 61.62, 67.32, 89.07, 74.2, 79.88
R / Rfree (%) 21.5 / 26.8

Other elements in 7mfh:

The structure of Crystal Structure of Bio-32546 Bound Mouse Autotaxin also contains other interesting chemical elements:

Iodine (I) 1 atom
Fluorine (F) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin (pdb code 7mfh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin, PDB code: 7mfh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7mfh

Go back to Zinc Binding Sites List in 7mfh
Zinc binding site 1 out of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:66.5
occ:1.00
 OD1 A:ASP739 2.4 46.5 1.0
OD1 A:ASN741 2.4 46.0 1.0
OD1 A:ASP747 2.5 45.0 1.0
OD1 A:ASN743 2.5 44.5 1.0
O A:HOH1012 2.6 40.4 1.0
O A:LEU745 2.6 47.5 1.0
CG A:ASN743 3.3 46.6 1.0
CG A:ASP739 3.3 48.9 1.0
CG A:ASN741 3.4 53.2 1.0
C A:LEU745 3.5 36.0 1.0
ND2 A:ASN743 3.6 46.1 1.0
CG A:ASP747 3.6 51.0 1.0
ND2 A:ASN741 3.7 58.1 1.0
CA A:ASP739 3.8 41.2 1.0
CB A:ASP739 3.9 48.9 1.0
N A:ASP747 4.1 50.1 1.0
N A:LEU745 4.1 45.0 1.0
C A:ARG746 4.1 45.9 1.0
OE1 A:GLU751 4.1 49.0 1.0
OD2 A:ASP739 4.2 45.1 1.0
CA A:ASP747 4.2 37.6 1.0
O A:ARG746 4.2 52.0 1.0
CA A:LEU745 4.2 44.2 1.0
N A:ASN743 4.4 47.4 1.0
N A:ARG746 4.4 37.5 1.0
C A:ASP739 4.4 51.1 1.0
CB A:LEU745 4.4 37.9 1.0
OD2 A:ASP747 4.5 53.0 1.0
O A:PHE738 4.5 47.1 1.0
N A:TYR740 4.5 49.6 1.0
N A:ASN741 4.5 42.0 1.0
CB A:ASP747 4.5 51.3 1.0
CB A:ASN743 4.6 37.2 1.0
CB A:ASN741 4.7 43.5 1.0
CA A:ARG746 4.7 41.8 1.0
N A:TYR742 4.8 45.0 1.0
CA A:ASN743 4.9 49.2 1.0
CA A:ASN741 4.9 45.4 1.0
C A:ASN741 5.0 43.7 1.0
N A:ASP739 5.0 47.1 1.0

Zinc binding site 2 out of 7 in 7mfh

Go back to Zinc Binding Sites List in 7mfh
Zinc binding site 2 out of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn912

b:50.8
occ:1.00
 OD1 A:ASP311 2.2 52.9 1.0
OD2 A:ASP311 2.3 56.0 1.0
NE2 A:HIS315 2.3 57.5 1.0
O A:HOH1156 2.3 55.5 1.0
NE2 A:HIS474 2.3 63.2 1.0
CG A:ASP311 2.6 45.2 1.0
CD2 A:HIS315 3.1 44.8 1.0
CD2 A:HIS474 3.2 45.5 1.0
CE1 A:HIS474 3.3 55.4 1.0
CE1 A:HIS315 3.4 47.6 1.0
O A:HOH1026 3.5 47.8 1.0
OG1 A:THR209 3.9 63.4 1.0
CB A:ASP311 4.0 55.1 1.0
CE1 A:HIS359 4.1 49.4 1.0
CG A:HIS315 4.3 50.2 1.0
OD2 A:ASP171 4.3 77.4 1.0
ND1 A:HIS474 4.4 45.9 1.0
CG A:HIS474 4.4 58.4 1.0
ND1 A:HIS315 4.4 61.0 1.0
NE2 A:HIS359 4.4 64.5 1.0
O A:ASP311 4.8 62.6 1.0
OD1 A:ASP171 4.9 58.7 1.0
CG A:ASP171 4.9 61.9 1.0
CA A:ASP311 5.0 50.3 1.0

Zinc binding site 3 out of 7 in 7mfh

Go back to Zinc Binding Sites List in 7mfh
Zinc binding site 3 out of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn913

b:68.5
occ:1.00
 OE2 A:GLU847 1.9 108.8 1.0
CD A:GLU847 3.1 109.9 1.0
N A:LEU788 3.3 46.3 1.0
CA A:PRO787 3.8 58.3 1.0
CG A:GLU847 3.8 109.4 1.0
CB A:PRO787 4.1 52.9 1.0
OE1 A:GLU847 4.1 111.6 1.0
C A:PRO787 4.1 64.9 1.0
O A:LEU788 4.1 53.1 1.0
CD1 A:LEU851 4.2 43.1 1.0
CA A:LEU788 4.3 52.7 1.0
CG A:ARG843 4.3 70.5 1.0
O A:GLU847 4.3 59.3 1.0
CB A:LEU788 4.4 42.7 1.0
CB A:LEU851 4.4 45.3 1.0
CG A:LEU788 4.4 60.2 1.0
CD2 A:LEU851 4.5 56.1 1.0
CD1 A:ILE848 4.5 53.3 1.0
CG A:LEU851 4.6 59.6 1.0
C A:LEU788 4.6 55.6 1.0
CB A:GLU847 4.7 108.8 1.0
C A:GLU847 4.7 54.1 1.0
NE A:ARG843 4.9 59.3 1.0
CD1 A:LEU788 4.9 42.0 1.0
CB A:ARG843 4.9 72.9 1.0
CD A:ARG843 4.9 58.0 1.0

Zinc binding site 4 out of 7 in 7mfh

Go back to Zinc Binding Sites List in 7mfh
Zinc binding site 4 out of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn919

b:90.3
occ:1.00
 ND1 A:HIS281 2.3 71.0 1.0
CE1 A:HIS281 2.8 77.0 1.0
OG A:SER307 3.0 62.9 1.0
CG A:HIS281 3.5 60.4 1.0
OG1 A:THR334 3.6 50.7 1.0
CB A:SER307 3.7 59.0 1.0
CZ A:PHE305 3.9 54.2 1.0
NE2 A:HIS281 4.1 63.8 1.0
CB A:HIS281 4.2 55.6 1.0
CE1 A:PHE305 4.2 57.4 1.0
CB A:THR334 4.3 48.4 1.0
CG2 A:THR334 4.4 44.3 1.0
CD2 A:HIS281 4.4 62.3 1.0
CA A:ILE331 4.8 53.2 1.0
CA A:SER307 4.8 61.4 1.0
CG1 A:ILE331 4.8 72.9 1.0
O A:GLU330 4.9 58.9 1.0

Zinc binding site 5 out of 7 in 7mfh

Go back to Zinc Binding Sites List in 7mfh
Zinc binding site 5 out of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn920

b:44.5
occ:1.00
 O A:HOH1063 2.1 63.2 1.0
N A:TRP275 3.6 49.8 1.0
NH1 A:ARG284 3.9 47.9 1.0
CA A:PHE274 4.0 52.4 1.0
O A:TRP275 4.0 53.2 1.0
C4 A:ZF7901 4.1 40.3 1.0
C2 A:ZF7901 4.1 37.2 1.0
C A:PHE274 4.3 47.7 1.0
CD2 A:TYR306 4.5 68.1 1.0
CA A:TRP275 4.5 52.4 1.0
CB A:PHE274 4.5 53.0 1.0
C3 A:ZF7901 4.6 51.4 1.0
CD1 A:PHE274 4.6 49.0 1.0
CB A:TRP275 4.6 59.4 1.0
CB A:TYR306 4.6 41.5 1.0
O A:PHE273 4.6 56.9 1.0
C A:TRP275 4.7 52.2 1.0

Zinc binding site 6 out of 7 in 7mfh

Go back to Zinc Binding Sites List in 7mfh
Zinc binding site 6 out of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn921

b:63.9
occ:1.00
 O A:HOH1148 2.0 58.9 1.0
NH2 A:ARG393 3.1 49.1 1.0
C A:MET232 3.6 54.0 1.0
O A:MET232 3.8 53.0 1.0
N A:TYR233 3.9 50.4 1.0
CB A:TYR233 3.9 45.1 1.0
N A:MET232 4.0 46.6 1.0
CA A:MET232 4.0 55.4 1.0
CG2 A:VAL385 4.2 44.2 1.0
CZ A:ARG393 4.3 41.6 1.0
CA A:TYR233 4.4 41.7 1.0
C A:SER231 4.5 51.0 1.0
CG2 A:THR240 4.6 108.7 1.0
CE1 A:HIS242 4.7 65.6 1.0
NH1 A:ARG393 4.7 43.5 1.0
CB A:THR240 4.7 107.7 1.0
CB A:SER231 4.8 37.1 1.0
O A:HOH1049 4.9 36.4 1.0
NE2 A:HIS242 5.0 74.0 1.0
O A:SER231 5.0 50.6 1.0

Zinc binding site 7 out of 7 in 7mfh

Go back to Zinc Binding Sites List in 7mfh
Zinc binding site 7 out of 7 in the Crystal Structure of Bio-32546 Bound Mouse Autotaxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Bio-32546 Bound Mouse Autotaxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn922

b:27.9
occ:1.00
 NZ A:LYS208 3.4 70.7 1.0
N A:ASN230 3.5 44.5 1.0
NH1 A:ARG391 3.7 45.7 1.0
CD2 A:LEU389 3.8 61.3 1.0
N A:SER231 3.8 43.0 1.0
CA A:GLY229 3.9 49.2 1.0
O A:SER231 4.1 50.6 1.0
CG A:LYS208 4.1 55.0 1.0
CG1 A:VAL385 4.1 36.3 1.0
C A:GLY229 4.2 60.0 1.0
CD1 A:LEU389 4.2 52.2 1.0
CE A:LYS208 4.3 78.8 1.0
CA A:ASN230 4.4 47.1 1.0
CG A:LEU389 4.5 45.5 1.0
CB A:ASN230 4.5 46.9 1.0
C A:ASN230 4.6 44.5 1.0
CA A:SER231 4.7 46.5 1.0
CB A:SER231 4.7 37.1 1.0
CD A:LYS208 4.8 56.3 1.0
C A:SER231 4.9 51.0 1.0
CZ A:ARG391 4.9 44.4 1.0

Reference:

B.Ma, L.Zhang, L.Sun, Z.Xin, G.Kumaravel, D.Marcotte, J.V.Chodaparambil, Q.Wang, A.Wehr, J.Jing, V.S.Hong, T.Wang, C.Huang, Z.Shao, S.Mi. Discovery of Potent Selective Nonzinc Binding Autotaxin Inhibitor Bio-32546. Acs Med.Chem.Lett. V. 12 1124 2021.
ISSN: ISSN 1948-5875
PubMed: 34267882
DOI: 10.1021/ACSMEDCHEMLETT.1C00211
Page generated: Tue Oct 29 23:18:05 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy