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

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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

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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

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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

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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

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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

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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

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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: Sat Apr 8 00:34:44 2023

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