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Zinc in PDB 4tnl: 1.8 A Resolution Room Temperature Structure of Thermolysin Recorded Using An Xfel

Enzymatic activity of 1.8 A Resolution Room Temperature Structure of Thermolysin Recorded Using An Xfel

All present enzymatic activity of 1.8 A Resolution Room Temperature Structure of Thermolysin Recorded Using An Xfel:
3.4.24.27;

Protein crystallography data

The structure of 1.8 A Resolution Room Temperature Structure of Thermolysin Recorded Using An Xfel, PDB code: 4tnl was solved by J.Kern, R.Tran, R.Alonso-Mori, S.Koroidov, N.Echols, J.Hattne, M.Ibrahim, S.Gul, H.Laksmono, R.G.Sierra, R.J.Gildea, G.Han, J.Hellmich, B.Lassalle-Kaiser, R.Chatterjee, A.Brewster, C.A.Stan, C.Gloeckner, A.Lampe, D.Difiore, D.Milathianaki, A.R.Fry, M.M.Seibert, J.E.Koglin, E.Gallo, J.Uhlig, D.Sokaras, T.-C.Weng, P.H.Zwart, D.E.Skinner, M.J.Bogan, M.Messerschmidt, P.Glatzel, G.J.Williams, S.Boutet, P.D.Adams, A.Zouni, J.Messinger, N.K.Sauter, U.Bergmann, J.Yano, V.K.Yachandra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.27 / 1.80
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.041, 93.041, 130.410, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 23.3

Other elements in 4tnl:

The structure of 1.8 A Resolution Room Temperature Structure of Thermolysin Recorded Using An Xfel also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the 1.8 A Resolution Room Temperature Structure of Thermolysin Recorded Using An Xfel (pdb code 4tnl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the 1.8 A Resolution Room Temperature Structure of Thermolysin Recorded Using An Xfel, PDB code: 4tnl:

Zinc binding site 1 out of 1 in 4tnl

Go back to Zinc Binding Sites List in 4tnl
Zinc binding site 1 out of 1 in the 1.8 A Resolution Room Temperature Structure of Thermolysin Recorded Using An Xfel


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.8 A Resolution Room Temperature Structure of Thermolysin Recorded Using An Xfel within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:18.9
occ:1.00
 NE2 A:HIS142 2.0 12.5 1.0
NE2 A:HIS146 2.0 12.7 1.0
O A:HOH637 2.0 18.5 1.0
OE2 A:GLU166 2.2 16.0 1.0
CD A:GLU166 2.8 14.6 1.0
OE1 A:GLU166 2.8 15.2 1.0
CE1 A:HIS142 3.0 12.6 1.0
CE1 A:HIS146 3.0 12.9 1.0
CD2 A:HIS142 3.0 12.2 1.0
CD2 A:HIS146 3.0 12.3 1.0
O A:HOH694 3.1 21.4 1.0
HE1 A:HIS146 3.2 15.5 1.0
HD2 A:HIS142 3.2 14.7 1.0
HE1 A:HIS142 3.2 15.2 1.0
HD2 A:HIS146 3.2 14.8 1.0
HA A:GLU166 3.9 17.6 1.0
HB2 A:SER169 4.0 15.5 1.0
HG A:SER169 4.1 15.2 1.0
ND1 A:HIS142 4.1 12.6 1.0
ND1 A:HIS146 4.1 12.8 1.0
CG A:HIS142 4.1 12.3 1.0
CG A:HIS146 4.2 12.4 1.0
O A:HOH695 4.2 19.9 1.0
CG A:GLU166 4.2 16.7 1.0
HB3 A:SER169 4.3 15.5 1.0
NE2 A:HIS231 4.4 16.6 1.0
OE1 A:GLU143 4.4 14.9 1.0
HG2 A:GLU166 4.5 20.0 1.0
CB A:SER169 4.5 12.9 1.0
OE2 A:GLU143 4.5 15.9 1.0
O A:HOH783 4.6 29.4 1.0
O A:HOH685 4.6 29.3 1.0
HD2 A:HIS231 4.6 19.3 1.0
O A:HOH638 4.6 25.4 1.0
OG A:SER169 4.7 12.6 1.0
HE1 A:TYR157 4.7 26.4 1.0
CA A:GLU166 4.8 14.7 1.0
CD A:GLU143 4.8 15.6 1.0
HH22 A:ARG203 4.8 16.3 1.0
HG3 A:GLU166 4.8 20.0 1.0
CD2 A:HIS231 4.8 16.1 1.0
HD1 A:HIS142 4.9 15.1 1.0
HD1 A:HIS146 4.9 15.3 1.0
CB A:GLU166 5.0 15.8 1.0
HA A:GLU143 5.0 17.6 1.0

Reference:

J.Kern, R.Tran, R.Alonso-Mori, S.Koroidov, N.Echols, J.Hattne, M.Ibrahim, S.Gul, H.Laksmono, R.G.Sierra, R.J.Gildea, G.Han, J.Hellmich, B.Lassalle-Kaiser, R.Chatterjee, A.S.Brewster, C.A.Stan, C.Glockner, A.Lampe, D.Difiore, D.Milathianaki, A.R.Fry, M.M.Seibert, J.E.Koglin, E.Gallo, J.Uhlig, D.Sokaras, T.C.Weng, P.H.Zwart, D.E.Skinner, M.J.Bogan, M.Messerschmidt, P.Glatzel, G.J.Williams, S.Boutet, P.D.Adams, A.Zouni, J.Messinger, N.K.Sauter, U.Bergmann, J.Yano, V.K.Yachandra. Taking Snapshots of Photosynthetic Water Oxidation Using Femtosecond X-Ray Diffraction and Spectroscopy. Nat Commun V. 5 4371 2014.
ISSN: ESSN 2041-1723
PubMed: 25006873
DOI: 10.1038/NCOMMS5371
Page generated: Sun Oct 27 08:23:06 2024

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