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Zinc in PDB 3nkp: Crystal Structure of Mouse Autotaxin in Complex with 18:1-Lpa

Enzymatic activity of Crystal Structure of Mouse Autotaxin in Complex with 18:1-Lpa

All present enzymatic activity of Crystal Structure of Mouse Autotaxin in Complex with 18:1-Lpa:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Mouse Autotaxin in Complex with 18:1-Lpa, PDB code: 3nkp 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) 26.53 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.523, 94.518, 75.503, 90.00, 94.55, 90.00
R / Rfree (%) 18.9 / 22.2

Other elements in 3nkp:

The structure of Crystal Structure of Mouse Autotaxin in Complex with 18:1-Lpa also contains other interesting chemical elements:

Potassium (K) 1 atom
Calcium (Ca) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mouse Autotaxin in Complex with 18:1-Lpa (pdb code 3nkp). 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 18:1-Lpa, PDB code: 3nkp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3nkp

Go back to Zinc Binding Sites List in 3nkp
Zinc binding site 1 out of 2 in the Crystal Structure of Mouse Autotaxin in Complex with 18:1-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 18:1-Lpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:21.9
occ:1.00
OD1 A:ASP171 1.9 18.0 1.0
OG1 A:THR209 2.1 23.7 1.0
NE2 A:HIS359 2.2 14.2 1.0
OD2 A:ASP358 2.2 19.1 1.0
CG A:ASP171 2.6 20.1 1.0
OD2 A:ASP171 2.8 21.6 1.0
CD2 A:HIS359 2.9 15.6 1.0
OAB A:NKP1006 3.0 31.5 1.0
CG A:ASP358 3.1 16.3 1.0
CB A:THR209 3.1 19.8 1.0
CE1 A:HIS359 3.2 16.8 1.0
OD1 A:ASP358 3.3 16.8 1.0
CA A:THR209 3.5 16.8 1.0
CG2 A:THR209 3.6 21.0 1.0
N A:THR209 3.8 16.6 1.0
OD1 A:ASP311 4.0 19.3 1.0
CB A:ASP171 4.0 17.6 1.0
OAD A:NKP1006 4.0 21.2 1.0
OBC A:NKP1006 4.0 37.3 1.0
CG A:HIS359 4.1 13.9 1.0
N A:GLY172 4.1 15.3 1.0
PAC A:NKP1006 4.1 28.0 1.0
ND1 A:HIS359 4.2 12.6 1.0
CG A:ASP311 4.2 19.5 1.0
CA A:ASP171 4.3 16.9 1.0
CE1 A:HIS474 4.4 15.6 1.0
CB A:ASP358 4.5 17.2 1.0
ZN A:ZN1002 4.5 18.3 1.0
C A:ASP171 4.5 17.1 1.0
C A:LYS208 4.6 18.5 1.0
OD2 A:ASP311 4.6 24.2 1.0
NE2 A:HIS474 4.7 17.5 1.0
CB A:ASP311 4.7 20.9 1.0
CA A:GLY172 4.8 15.4 1.0
C A:THR209 4.9 16.0 1.0

Zinc binding site 2 out of 2 in 3nkp

Go back to Zinc Binding Sites List in 3nkp
Zinc binding site 2 out of 2 in the Crystal Structure of Mouse Autotaxin in Complex with 18:1-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 18:1-Lpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:18.3
occ:1.00
NE2 A:HIS315 2.0 17.8 1.0
NE2 A:HIS474 2.0 17.5 1.0
OD1 A:ASP311 2.3 19.3 1.0
OAA A:NKP1006 2.4 34.2 1.0
OD2 A:ASP311 2.4 24.2 1.0
OAB A:NKP1006 2.5 31.5 1.0
CG A:ASP311 2.7 19.5 1.0
PAC A:NKP1006 3.0 28.0 1.0
CE1 A:HIS474 3.0 15.6 1.0
CE1 A:HIS315 3.0 19.3 1.0
CD2 A:HIS315 3.1 18.9 1.0
CD2 A:HIS474 3.1 15.1 1.0
OAD A:NKP1006 3.9 21.2 1.0
CE1 A:HIS359 4.1 16.8 1.0
ND1 A:HIS474 4.1 16.1 1.0
ND1 A:HIS315 4.1 18.8 1.0
OAF A:NKP1006 4.1 33.7 1.0
CG A:HIS315 4.2 21.5 1.0
CB A:ASP311 4.2 20.9 1.0
CG A:HIS474 4.2 13.3 1.0
NE2 A:HIS359 4.3 14.2 1.0
OBC A:NKP1006 4.3 37.3 1.0
CE A:MET361 4.4 15.3 1.0
ZN A:ZN1001 4.5 21.9 1.0
OD1 A:ASP171 4.5 18.0 1.0
O A:HOH1427 4.7 33.9 1.0
OG1 A:THR209 4.7 23.7 1.0
O A:ASP311 4.9 21.9 1.0
CAH A:NKP1006 4.9 40.9 1.0
CA A:ASP311 5.0 22.0 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 Oct 26 10:24:08 2024

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