Atomistry » Calcium » PDB 4ry0-4twe » 4tnl
Atomistry »
  Calcium »
    PDB 4ry0-4twe »
      4tnl »

Calcium 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:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the 1.8 A Resolution Room Temperature Structure of Thermolysin Recorded Using An Xfel, PDB code: 4tnl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4tnl

Go back to Calcium Binding Sites List in 4tnl
Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca402

b:13.0
occ:1.00
 O A:GLU187 2.4 15.0 1.0
O A:HOH629 2.4 12.6 1.0
OD1 A:ASP185 2.5 15.7 1.0
OE1 A:GLU177 2.5 14.9 1.0
OE1 A:GLU190 2.5 15.2 1.0
OE2 A:GLU190 2.5 15.3 1.0
OD2 A:ASP138 2.6 14.1 1.0
OE2 A:GLU177 2.7 15.4 1.0
CD A:GLU190 2.8 15.5 1.0
CD A:GLU177 2.9 15.2 1.0
C A:GLU187 3.4 15.1 1.0
CG A:ASP138 3.5 14.1 1.0
CG A:ASP185 3.5 16.2 1.0
HB3 A:ASP138 3.5 16.8 1.0
H A:GLU187 3.6 18.6 1.0
HA A:ILE188 3.7 17.5 1.0
CA A:CA403 3.7 17.9 1.0
HB2 A:GLU187 3.8 19.9 1.0
OD2 A:ASP185 3.9 16.9 1.0
H A:GLY189 3.9 17.5 1.0
CB A:ASP138 4.0 14.0 1.0
O A:ASP185 4.1 16.4 1.0
N A:GLU187 4.1 15.5 1.0
H A:GLU190 4.2 18.3 1.0
HD13 A:ILE188 4.2 17.8 1.0
CA A:GLU187 4.2 15.4 1.0
H A:ASP185 4.2 19.8 1.0
N A:ILE188 4.2 15.3 1.0
HB2 A:ASP138 4.3 16.8 1.0
CG A:GLU190 4.3 16.1 1.0
O A:HOH647 4.3 15.6 1.0
CA A:ILE188 4.4 14.6 1.0
CG A:GLU177 4.4 16.0 1.0
OD1 A:ASP138 4.4 14.1 1.0
CB A:GLU187 4.5 16.6 1.0
O A:HOH811 4.5 41.2 1.0
HG3 A:GLU190 4.5 19.3 1.0
N A:GLY189 4.5 14.6 1.0
C A:ASP185 4.6 16.3 1.0
HB2 A:GLU177 4.7 18.5 1.0
HB3 A:GLU177 4.7 18.5 1.0
HG2 A:GLU190 4.8 19.3 1.0
CB A:ASP185 4.8 17.1 1.0
HG2 A:GLU177 4.8 19.2 1.0
HA A:THR174 4.8 19.0 1.0
N A:ASP185 4.8 16.5 1.0
O A:HOH641 4.8 15.0 1.0
C A:ILE188 4.9 14.9 1.0
HG3 A:GLU177 4.9 19.2 1.0
CB A:GLU177 4.9 15.4 1.0
HB3 A:GLU187 4.9 19.9 1.0
HB3 A:GLU190 4.9 19.5 1.0
CA A:ASP185 5.0 16.5 1.0

Calcium binding site 2 out of 4 in 4tnl

Go back to Calcium Binding Sites List in 4tnl
Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca binding site number 2 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:Ca403

b:17.9
occ:1.00
 O A:ASN183 2.3 17.6 1.0
OE2 A:GLU190 2.4 15.3 1.0
O A:HOH641 2.4 15.0 1.0
O A:HOH623 2.4 14.2 1.0
OE2 A:GLU177 2.4 15.4 1.0
OD2 A:ASP185 2.4 16.9 1.0
CD A:GLU177 3.2 15.2 1.0
CG A:ASP185 3.2 16.2 1.0
CD A:GLU190 3.3 15.5 1.0
C A:ASN183 3.5 18.2 1.0
OD1 A:ASP185 3.5 15.7 1.0
HG3 A:GLU190 3.6 19.3 1.0
HA A:PRO184 3.6 20.0 1.0
OE1 A:GLU177 3.7 14.9 1.0
CA A:CA402 3.7 13.0 1.0
HG2 A:GLU190 3.8 19.3 1.0
CG A:GLU190 3.8 16.1 1.0
HB2 A:ASN183 3.9 23.6 1.0
H A:ASP185 4.0 19.8 1.0
HB3 A:ASN183 4.0 23.6 1.0
OD2 A:ASP191 4.1 16.3 1.0
CG A:GLU177 4.1 16.0 1.0
N A:ASP185 4.2 16.5 1.0
CA A:PRO184 4.2 16.7 1.0
HG2 A:GLU177 4.2 19.2 1.0
HG3 A:GLU177 4.2 19.2 1.0
OD1 A:ASP191 4.2 16.4 1.0
OE1 A:GLU190 4.2 15.2 1.0
C A:PRO184 4.3 16.8 1.0
N A:PRO184 4.3 17.1 1.0
O A:HOH531 4.3 25.2 1.0
CB A:ASN183 4.3 19.6 1.0
HB3 A:ASP185 4.3 20.5 1.0
CB A:ASP185 4.3 17.1 1.0
O A:HOH798 4.4 26.6 1.0
CG A:ASP191 4.5 15.9 1.0
CA A:ASN183 4.5 18.0 1.0
CA A:ASP185 4.9 16.5 1.0
O A:HOH811 4.9 41.2 1.0
O A:PRO184 4.9 17.4 1.0
O A:HOH647 5.0 15.6 1.0

Calcium binding site 3 out of 4 in 4tnl

Go back to Calcium Binding Sites List in 4tnl
Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca binding site number 3 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:Ca404

b:19.1
occ:1.00
 O A:HOH786 2.3 39.1 1.0
O A:TYR193 2.3 17.9 1.0
OD1 A:ASP200 2.3 19.3 1.0
O A:THR194 2.4 21.4 1.0
O A:ILE197 2.4 20.9 1.0
O A:HOH615 2.4 10.5 1.0
OG1 A:THR194 2.5 20.8 1.0
C A:THR194 3.2 21.3 1.0
C A:TYR193 3.3 17.6 1.0
CG A:ASP200 3.4 19.7 1.0
CB A:THR194 3.4 20.8 1.0
HB A:THR194 3.6 24.9 1.0
C A:ILE197 3.6 22.4 1.0
CA A:THR194 3.7 20.9 1.0
OD2 A:ASP200 3.7 19.7 1.0
HB A:ILE197 3.8 29.0 1.0
H A:ASP200 3.8 24.1 1.0
N A:THR194 3.9 19.0 1.0
HD2 A:TYR193 4.0 20.8 1.0
HB3 A:TYR193 4.1 19.7 1.0
HA A:SER198 4.1 28.6 1.0
H A:ILE197 4.1 27.9 1.0
N A:PRO195 4.3 19.7 1.0
HA A:PRO195 4.3 27.0 1.0
O A:ASP200 4.3 17.8 1.0
O A:HOH681 4.4 40.4 1.0
HG22 A:ILE197 4.4 28.1 1.0
O A:GLU190 4.5 16.8 1.0
CA A:ILE197 4.5 23.4 1.0
CB A:ILE197 4.5 24.1 1.0
O A:HOH725 4.5 29.3 1.0
CA A:TYR193 4.5 16.8 1.0
N A:ASP200 4.6 20.1 1.0
N A:SER198 4.6 24.3 1.0
HA A:THR194 4.6 25.1 1.0
CD2 A:TYR193 4.6 17.4 1.0
N A:ILE197 4.7 23.3 1.0
CB A:TYR193 4.7 16.4 1.0
CB A:ASP200 4.7 20.8 1.0
CA A:SER198 4.7 23.8 1.0
C A:ASP200 4.7 18.1 1.0
H A:THR194 4.7 22.8 1.0
H A:GLY199 4.8 26.2 1.0
O A:HOH569 4.8 30.7 1.0
H A:TYR193 4.8 21.0 1.0
CA A:PRO195 4.8 22.5 1.0
CG2 A:THR194 4.8 20.8 1.0
CA A:ASP200 4.9 19.1 1.0
C A:SER198 5.0 23.6 1.0
N A:TYR193 5.0 17.5 1.0
CG2 A:ILE197 5.0 23.4 1.0
HG23 A:THR194 5.0 25.0 1.0

Calcium binding site 4 out of 4 in 4tnl

Go back to Calcium Binding Sites List in 4tnl
Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca binding site number 4 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:Ca405

b:15.5
occ:1.00
 O A:GLN61 2.3 15.4 1.0
O A:HOH573 2.3 14.6 1.0
OD1 A:ASP59 2.4 15.9 1.0
OD1 A:ASP57 2.4 15.2 1.0
O A:HOH646 2.4 17.1 1.0
O A:HOH611 2.4 10.1 1.0
OD2 A:ASP57 2.7 16.0 1.0
CG A:ASP57 2.9 15.4 1.0
H A:GLN61 3.3 18.9 1.0
CG A:ASP59 3.3 16.9 1.0
C A:GLN61 3.4 15.7 1.0
H A:ASP59 3.5 20.2 1.0
HB2 A:GLN61 3.6 19.3 1.0
OD2 A:ASP59 3.7 17.2 1.0
HA A:PHE62 4.0 16.6 1.0
N A:GLN61 4.0 15.7 1.0
O A:HOH669 4.1 41.8 1.0
CA A:GLN61 4.1 15.4 1.0
H A:ALA58 4.2 20.9 1.0
CB A:GLN61 4.3 16.1 1.0
O A:HOH561 4.3 13.6 1.0
N A:ASP59 4.3 16.8 1.0
CB A:ASP57 4.3 15.7 1.0
O A:HOH599 4.4 37.0 1.0
H A:ASN60 4.4 20.1 1.0
N A:PHE62 4.5 14.1 1.0
O A:HOH628 4.5 14.1 1.0
OD2 A:ASP67 4.6 14.9 1.0
CB A:ASP59 4.6 17.4 1.0
N A:ALA58 4.7 17.4 1.0
CA A:PHE62 4.7 13.9 1.0
HB2 A:ASP57 4.7 18.9 1.0
N A:ASN60 4.7 16.8 1.0
O A:HOH593 4.7 21.4 1.0
HB3 A:GLN61 4.8 19.3 1.0
H A:PHE63 4.8 19.6 1.0
HB3 A:ASP57 4.8 18.9 1.0
HB3 A:ALA58 4.8 21.7 1.0
CA A:ASP59 4.9 17.1 1.0
HA A:ASP57 4.9 20.3 1.0
C A:ASP59 5.0 16.6 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: Sat Dec 12 05:08:02 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy