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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: Sun Jul 14 13:25:39 2024

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