Zinc in PDB 9eu5: Ssx Structure of Autotaxin at Room Temperature

Enzymatic activity of Ssx Structure of Autotaxin at Room Temperature

All present enzymatic activity of Ssx Structure of Autotaxin at Room Temperature:
3.1.4.39;

Protein crystallography data

The structure of Ssx Structure of Autotaxin at Room Temperature, PDB code: 9eu5 was solved by M.C.Eymery, A.A.Mccarthy, N.Foos, S.Basu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.45 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.51, 61.19, 65.01, 102.57, 99.13, 93.67
R / Rfree (%) 22.5 / 28.1

Other elements in 9eu5:

The structure of Ssx Structure of Autotaxin at Room Temperature also contains other interesting chemical elements:

Iodine (I) 15 atoms
Sodium (Na) 2 atoms
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Ssx Structure of Autotaxin at Room Temperature (pdb code 9eu5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Ssx Structure of Autotaxin at Room Temperature, PDB code: 9eu5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 9eu5

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Zinc binding site 1 out of 9 in the Ssx Structure of Autotaxin at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ssx Structure of Autotaxin at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn905

b:88.6
occ:1.00
 ND1 A:HIS822 2.3 46.2 1.0
O A:ILE794 2.8 28.2 1.0
CB A:HIS822 2.9 32.0 1.0
CG A:HIS822 3.0 38.2 1.0
N A:LYS430 3.3 30.6 1.0
CA A:HIS822 3.4 37.1 1.0
CA A:PRO429 3.5 31.9 1.0
CE1 A:HIS822 3.5 42.0 1.0
O A:HIS822 3.6 34.9 1.0
C A:PRO429 3.8 33.3 1.0
C A:HIS822 3.9 43.2 1.0
C A:ILE794 3.9 36.0 1.0
CB A:PRO429 3.9 33.5 1.0
CG A:LYS430 4.2 32.6 1.0
CD2 A:HIS822 4.2 32.6 1.0
CB A:ILE794 4.3 16.8 1.0
CB A:LYS430 4.3 38.8 1.0
CA A:LYS430 4.4 36.0 1.0
NE2 A:HIS822 4.4 42.1 1.0
CA A:ILE794 4.5 32.3 1.0
N A:ILE794 4.6 36.6 1.0
CD A:PRO796 4.6 33.6 1.0
N A:HIS822 4.7 34.0 1.0
N A:PRO429 4.7 36.0 1.0
O A:THR823 4.7 41.6 1.0
CG A:PRO429 4.8 42.6 1.0
CG2 A:ILE794 4.9 23.9 1.0
N A:ARG431 4.9 34.5 1.0
O A:LEU428 4.9 42.8 1.0
N A:LEU795 5.0 31.1 1.0

Zinc binding site 2 out of 9 in 9eu5

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Zinc binding site 2 out of 9 in the Ssx Structure of Autotaxin at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ssx Structure of Autotaxin at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn906

b:161.3
occ:1.00
 CD2 A:PHE738 2.9 46.1 1.0
N A:PHE738 3.0 36.0 1.0
CB A:PHE738 3.3 47.1 1.0
O A:LEU832 3.4 36.0 1.0
CG A:PHE738 3.5 43.0 1.0
CA A:PHE738 3.6 38.7 1.0
CG A:ARG746 3.6 44.0 1.0
O A:PHE738 3.6 37.7 1.0
CE2 A:PHE738 3.9 41.7 1.0
C A:ILE737 4.0 37.0 1.0
C A:PHE738 4.1 35.3 1.0
CA A:ILE737 4.1 36.4 1.0
O A:HOH1014 4.2 47.1 1.0
N A:ASP747 4.3 49.9 1.0
CB A:ARG746 4.4 37.6 1.0
CA A:ARG746 4.5 40.1 1.0
C A:LEU832 4.5 36.3 1.0
CA A:THR833 4.6 36.3 1.0
O A:ASP747 4.6 49.8 1.0
CD A:ARG746 4.7 40.8 1.0
CD1 A:PHE738 4.8 48.4 1.0
O A:PRO736 4.9 49.2 1.0
C A:ARG746 4.9 45.4 1.0
N A:ILE737 4.9 41.0 1.0

Zinc binding site 3 out of 9 in 9eu5

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Zinc binding site 3 out of 9 in the Ssx Structure of Autotaxin at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ssx Structure of Autotaxin at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn907

b:84.4
occ:1.00
 ND1 A:HIS444 2.3 36.0 1.0
O A:ILE443 3.0 44.7 0.8
CG A:HIS444 3.1 37.6 1.0
CG A:ARG391 3.1 38.8 1.0
CB A:HIS444 3.1 37.1 1.0
CD A:ARG391 3.2 30.6 1.0
O A:ILE443 3.2 44.9 0.2
CE1 A:HIS444 3.4 28.4 1.0
O A:GLU441 3.5 45.9 1.0
CA A:HIS444 3.5 38.9 1.0
CB A:ARG391 3.6 42.0 1.0
C A:ILE443 3.8 43.0 0.8
CA A:ARG391 3.8 45.7 1.0
C A:ILE443 3.9 46.0 0.2
O A:GLY390 3.9 43.2 1.0
N A:HIS444 4.0 39.4 1.0
CG2 A:ILE440 4.2 42.5 1.0
N A:GLU441 4.2 44.5 1.0
C A:GLU441 4.2 45.5 1.0
CD2 A:HIS444 4.3 34.3 1.0
OE1 A:GLU441 4.3 44.2 1.0
CB A:GLU441 4.4 49.5 1.0
NE2 A:HIS444 4.4 31.5 1.0
NE A:ARG391 4.4 33.6 1.0
CE2 A:TYR434 4.5 38.0 1.0
CA A:GLU441 4.5 48.5 1.0
N A:ARG391 4.7 39.8 1.0
C A:GLY390 4.7 40.6 1.0
C A:HIS444 4.9 34.2 1.0
C A:ARG391 5.0 48.0 1.0
C A:ILE440 5.0 42.6 1.0

Zinc binding site 4 out of 9 in 9eu5

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Zinc binding site 4 out of 9 in the Ssx Structure of Autotaxin at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ssx Structure of Autotaxin at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn908

b:158.1
occ:1.00
 CG2 A:VAL184 3.8 99.8 1.0
CG2 A:THR325 4.6 73.4 1.0
CB A:LYS183 5.0 81.9 1.0

Zinc binding site 5 out of 9 in 9eu5

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Zinc binding site 5 out of 9 in the Ssx Structure of Autotaxin at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ssx Structure of Autotaxin at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn909

b:226.1
occ:1.00
 O A:HOH1045 4.7 46.5 1.0
OE2 A:GLU561 4.9 81.3 1.0

Zinc binding site 6 out of 9 in 9eu5

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Zinc binding site 6 out of 9 in the Ssx Structure of Autotaxin at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ssx Structure of Autotaxin at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn910

b:47.3
occ:1.00
 NE2 A:HIS474 2.3 55.9 1.0
NE2 A:HIS315 2.3 51.5 1.0
OD1 A:ASP311 2.5 56.2 1.0
CD2 A:HIS474 2.6 45.5 1.0
OD2 A:ASP311 2.6 60.2 1.0
O4 A:PO4932 2.7 80.7 1.0
CG A:ASP311 2.9 56.4 1.0
CE1 A:HIS315 3.2 53.0 1.0
CD2 A:HIS315 3.3 51.8 1.0
P A:PO4932 3.4 98.5 1.0
O1 A:PO4932 3.5 82.8 1.0
O3 A:PO4932 3.5 86.1 1.0
CE1 A:HIS474 3.6 49.7 1.0
CG A:HIS474 3.8 41.8 1.0
CE1 A:HIS359 3.9 47.3 1.0
NE2 A:HIS359 4.1 46.6 1.0
OD1 A:ASP171 4.2 67.2 1.0
ND1 A:HIS474 4.3 42.4 1.0
ZN A:ZN913 4.3 137.6 1.0
ND1 A:HIS315 4.4 51.0 1.0
CB A:ASP311 4.4 54.6 1.0
OG1 A:THR209 4.4 69.9 1.0
CG A:HIS315 4.5 47.8 1.0
O2 A:PO4932 4.8 94.0 1.0
OD1 A:ASP473 5.0 38.8 1.0

Zinc binding site 7 out of 9 in 9eu5

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Zinc binding site 7 out of 9 in the Ssx Structure of Autotaxin at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ssx Structure of Autotaxin at Room Temperature within 5.0Å range:

Zinc binding site 8 out of 9 in 9eu5

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Zinc binding site 8 out of 9 in the Ssx Structure of Autotaxin at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Ssx Structure of Autotaxin at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn912

b:108.8
occ:1.00
 O A:LEU94 3.7 96.8 1.0
O A:ASP90 3.8 88.0 1.0
CB A:LEU94 4.4 84.9 1.0
CB A:ASP90 4.6 80.1 1.0
OG1 A:THR96 4.6 70.6 1.0
OD2 A:ASP90 4.7 76.7 1.0
C A:LEU94 4.8 90.3 1.0
C A:ASP90 4.8 84.3 1.0

Zinc binding site 9 out of 9 in 9eu5

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Zinc binding site 9 out of 9 in the Ssx Structure of Autotaxin at Room Temperature


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Ssx Structure of Autotaxin at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn913

b:137.6
occ:1.00
 OD1 A:ASP171 1.9 67.2 1.0
OG1 A:THR209 1.9 69.9 1.0
OD2 A:ASP358 2.1 54.0 1.0
NE2 A:HIS359 2.3 46.6 1.0
CG A:ASP171 2.5 60.5 1.0
OD2 A:ASP171 2.6 55.5 1.0
CB A:THR209 3.0 51.1 1.0
CG A:ASP358 3.1 49.8 1.0
CE1 A:HIS359 3.1 47.3 1.0
CD2 A:HIS359 3.2 43.1 1.0
CA A:THR209 3.4 41.9 1.0
O1 A:PO4932 3.4 82.8 1.0
CG2 A:THR209 3.5 54.0 1.0
OD1 A:ASP358 3.5 49.6 1.0
CB A:ASP171 3.9 47.8 1.0
N A:THR209 3.9 44.6 1.0
O4 A:PO4932 4.0 80.7 1.0
ND1 A:HIS359 4.2 41.9 1.0
N A:GLY172 4.2 40.5 1.0
CA A:ASP171 4.2 49.0 1.0
CG A:HIS359 4.2 42.8 1.0
ZN A:ZN910 4.3 47.3 1.0
CB A:ASP358 4.3 40.3 1.0
P A:PO4932 4.4 98.5 1.0
NE2 A:HIS474 4.4 55.9 1.0
OD1 A:ASP311 4.4 56.2 1.0
CG A:ASP311 4.5 56.4 1.0
CE1 A:HIS474 4.5 49.7 1.0
C A:ASP171 4.5 48.1 1.0
OD2 A:ASP311 4.6 60.2 1.0
C A:LYS208 4.7 41.6 1.0
C A:THR209 4.8 42.4 1.0
OH A:TYR306 4.8 49.5 1.0

Reference:

N.Foos, J.B.Florial, M.Eymery, J.Sinoir, F.Felisaz, M.Oscarsson, A.Beteva, M.W.Bowler, D.Nurizzo, G.Papp, M.Soler-Lopez, M.Nanao, S.Basu, A.A.Mccarthy. In Situ Serial Crystallography Facilitates 96-Well Plate Structural Analysis at Low Symmetry. Iucrj 2024.
ISSN: ESSN 2052-2525
PubMed: 39008358
DOI: 10.1107/S2052252524005785
Page generated: Thu Oct 31 15:28:56 2024

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