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Zinc in PDB 3nkn: Crystal Structure of Mouse Autotaxin in Complex with 14:0-Lpa

Enzymatic activity of Crystal Structure of Mouse Autotaxin in Complex with 14:0-Lpa

All present enzymatic activity of Crystal Structure of Mouse Autotaxin in Complex with 14:0-Lpa:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Mouse Autotaxin in Complex with 14:0-Lpa, PDB code: 3nkn was solved by H.Nishimasu, R.Ishitani, E.Mihara, J.Takagi, J.Aoki, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.85 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.580, 94.617, 75.372, 90.00, 94.86, 90.00
R / Rfree (%) 18.5 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mouse Autotaxin in Complex with 14:0-Lpa (pdb code 3nkn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Mouse Autotaxin in Complex with 14:0-Lpa, PDB code: 3nkn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3nkn

Go back to Zinc Binding Sites List in 3nkn
Zinc binding site 1 out of 2 in the Crystal Structure of Mouse Autotaxin in Complex with 14:0-Lpa


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 Mouse Autotaxin in Complex with 14:0-Lpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:19.4
occ:1.00
OD1 A:ASP171 1.9 15.9 1.0
OG1 A:THR209 2.0 23.6 1.0
NE2 A:HIS359 2.1 15.3 1.0
OD2 A:ASP358 2.2 19.0 1.0
CG A:ASP171 2.5 18.4 1.0
OD2 A:ASP171 2.7 20.2 1.0
CD2 A:HIS359 3.0 15.1 1.0
CG A:ASP358 3.1 17.8 1.0
CE1 A:HIS359 3.1 17.4 1.0
CB A:THR209 3.1 19.2 1.0
OD1 A:ASP358 3.3 16.2 1.0
CA A:THR209 3.5 15.6 1.0
CG2 A:THR209 3.5 21.0 1.0
OAB A:NKN1006 3.7 27.0 1.0
N A:THR209 3.8 17.2 1.0
OAD A:NKN1006 3.9 19.0 1.0
CB A:ASP171 4.0 16.0 1.0
OD1 A:ASP311 4.0 16.8 1.0
N A:GLY172 4.1 13.9 1.0
ND1 A:HIS359 4.1 12.9 1.0
CG A:HIS359 4.1 14.4 1.0
CG A:ASP311 4.2 19.3 1.0
CA A:ASP171 4.3 15.8 1.0
CE1 A:HIS474 4.4 16.9 1.0
PAC A:NKN1006 4.4 27.4 1.0
CB A:ASP358 4.5 17.4 1.0
ZN A:ZN1002 4.5 17.6 1.0
CAG A:NKN1006 4.5 33.5 1.0
C A:ASP171 4.6 15.5 1.0
OD2 A:ASP311 4.6 22.9 1.0
NE2 A:HIS474 4.6 19.6 1.0
C A:LYS208 4.6 17.1 1.0
CB A:ASP311 4.8 21.3 1.0
CA A:GLY172 4.8 16.0 1.0
C A:THR209 4.9 17.4 1.0

Zinc binding site 2 out of 2 in 3nkn

Go back to Zinc Binding Sites List in 3nkn
Zinc binding site 2 out of 2 in the Crystal Structure of Mouse Autotaxin in Complex with 14:0-Lpa


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 Mouse Autotaxin in Complex with 14:0-Lpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:17.6
occ:1.00
OAB A:NKN1006 1.8 27.0 1.0
NE2 A:HIS315 2.0 19.0 1.0
NE2 A:HIS474 2.1 19.6 1.0
OD1 A:ASP311 2.2 16.8 1.0
OD2 A:ASP311 2.4 22.9 1.0
CG A:ASP311 2.6 19.3 1.0
CE1 A:HIS315 2.8 17.7 1.0
CE1 A:HIS474 3.0 16.9 1.0
CD2 A:HIS315 3.0 20.2 1.0
CD2 A:HIS474 3.1 15.6 1.0
PAC A:NKN1006 3.1 27.4 1.0
OAA A:NKN1006 3.3 33.7 1.0
OAD A:NKN1006 3.9 19.0 1.0
ND1 A:HIS315 4.0 17.6 1.0
CE1 A:HIS359 4.1 17.4 1.0
OAF A:NKN1006 4.1 33.8 1.0
CG A:HIS315 4.1 19.9 1.0
ND1 A:HIS474 4.1 15.8 1.0
CB A:ASP311 4.2 21.3 1.0
CG A:HIS474 4.2 14.2 1.0
NE2 A:HIS359 4.4 15.3 1.0
CE A:MET361 4.4 17.5 1.0
ZN A:ZN1001 4.5 19.4 1.0
OD1 A:ASP171 4.5 15.9 1.0
CAG A:NKN1006 4.5 33.5 1.0
O A:HOH1082 4.5 29.9 1.0
OG1 A:THR209 4.8 23.6 1.0
O A:ASP311 4.9 20.2 1.0
CA A:ASP311 5.0 19.8 1.0

Reference:

H.Nishimasu, S.Okudaira, K.Hama, E.Mihara, N.Dohmae, A.Inoue, R.Ishitani, J.Takagi, J.Aoki, O.Nureki. Crystal Structure of Autotaxin and Insight Into Gpcr Activation By Lipid Mediators Nat.Struct.Mol.Biol. V. 18 205 2011.
ISSN: ISSN 1545-9993
PubMed: 21240269
DOI: 10.1038/NSMB.1998
Page generated: Sat Sep 26 12:03:05 2020
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