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Calcium in PDB 6ig7: Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser

Enzymatic activity of Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser

All present enzymatic activity of Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser:
3.4.24.27;

Protein crystallography data

The structure of Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser, PDB code: 6ig7 was solved by K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.12 / 1.80
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.663, 92.663, 128.591, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 20.2

Other elements in 6ig7:

The structure of Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser (pdb code 6ig7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser, PDB code: 6ig7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6ig7

Go back to Calcium Binding Sites List in 6ig7
Calcium binding site 1 out of 4 in the Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:31.3
occ:1.00
 O A:ILE197 2.3 42.3 1.0
O A:TYR193 2.3 28.2 1.0
OG1 A:THR194 2.3 37.6 1.0
OD1 A:ASP200 2.3 34.5 1.0
O A:HOH589 2.3 34.4 1.0
O A:THR194 2.4 37.0 1.0
O A:HOH514 2.4 35.0 1.0
C A:THR194 3.2 38.9 1.0
C A:TYR193 3.3 31.9 1.0
CG A:ASP200 3.4 34.2 1.0
CB A:THR194 3.4 34.1 1.0
C A:ILE197 3.5 43.9 1.0
HB A:ILE197 3.6 58.8 1.0
H A:ILE197 3.6 53.6 1.0
CA A:THR194 3.6 34.1 1.0
HB A:THR194 3.7 41.0 1.0
OD2 A:ASP200 3.7 36.0 1.0
H A:ASP200 3.8 42.5 1.0
N A:THR194 3.8 34.4 1.0
HD2 A:TYR193 3.9 41.2 1.0
HA A:SER198 4.0 45.5 1.0
HB3 A:TYR193 4.0 37.1 1.0
HA A:PRO195 4.2 47.4 1.0
N A:PRO195 4.2 35.5 1.0
CA A:ILE197 4.2 38.5 1.0
N A:ILE197 4.3 44.7 1.0
CB A:ILE197 4.3 49.0 1.0
O A:ASP200 4.4 31.1 1.0
HG22 A:ILE197 4.4 49.8 1.0
O A:GLU190 4.4 28.7 1.0
CA A:TYR193 4.5 30.2 1.0
N A:SER198 4.5 40.9 1.0
CD2 A:TYR193 4.5 34.3 1.0
HA A:THR194 4.6 41.0 1.0
N A:ASP200 4.6 35.4 1.0
CA A:PRO195 4.6 39.5 1.0
CA A:SER198 4.6 37.9 1.0
CB A:TYR193 4.6 30.9 1.0
CG2 A:THR194 4.7 36.1 1.0
H A:THR194 4.7 41.3 1.0
CB A:ASP200 4.7 34.9 1.0
H A:TYR193 4.7 38.0 1.0
C A:ASP200 4.7 33.4 1.0
H A:GLY199 4.7 49.4 1.0
HG23 A:THR194 4.8 43.3 1.0
C A:PRO195 4.9 44.4 1.0
CG2 A:ILE197 4.9 41.5 1.0
CA A:ASP200 4.9 31.6 1.0
HG21 A:THR194 4.9 43.3 1.0
C A:SER198 4.9 41.5 1.0
N A:TYR193 4.9 31.6 1.0
CG A:TYR193 5.0 31.7 1.0
N A:GLY199 5.0 41.1 1.0

Calcium binding site 2 out of 4 in 6ig7

Go back to Calcium Binding Sites List in 6ig7
Calcium binding site 2 out of 4 in the Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:26.9
occ:1.00
 O A:GLU187 2.3 27.2 1.0
OE1 A:GLU190 2.4 27.2 1.0
OD1 A:ASP185 2.4 29.7 1.0
OE1 A:GLU177 2.4 27.6 1.0
OE2 A:GLU190 2.4 30.3 1.0
OD2 A:ASP138 2.5 29.4 1.0
O A:HOH546 2.5 29.8 1.0
OE2 A:GLU177 2.7 29.2 1.0
CD A:GLU190 2.7 27.3 1.0
CD A:GLU177 2.8 32.2 1.0
C A:GLU187 3.4 30.7 1.0
CG A:ASP138 3.4 29.9 1.0
CG A:ASP185 3.4 33.9 1.0
HB3 A:ASP138 3.5 29.8 1.0
HA A:ILE188 3.6 34.1 1.0
H A:GLU187 3.7 37.4 1.0
CA A:CA405 3.7 30.2 1.0
H A:GLY189 3.8 35.2 1.0
OD2 A:ASP185 3.8 29.7 1.0
HB2 A:GLU187 3.9 43.9 1.0
CB A:ASP138 3.9 24.8 1.0
H A:ASP185 4.0 33.9 1.0
H A:GLU190 4.1 31.6 1.0
HD13 A:ILE188 4.1 43.9 1.0
HB2 A:ASP138 4.2 29.8 1.0
O A:ASP185 4.2 31.6 1.0
N A:GLU187 4.2 31.2 1.0
N A:ILE188 4.2 28.3 1.0
CG A:GLU190 4.2 28.6 1.0
CA A:GLU187 4.3 29.4 1.0
OD1 A:ASP138 4.3 28.1 1.0
CA A:ILE188 4.3 28.4 1.0
CG A:GLU177 4.3 30.1 1.0
N A:GLY189 4.4 29.3 1.0
O A:HOH519 4.4 32.6 1.0
HG3 A:GLU190 4.5 34.3 1.0
C A:ASP185 4.6 27.9 1.0
CB A:GLU187 4.6 36.5 1.0
HB2 A:GLU177 4.6 35.2 1.0
N A:ASP185 4.7 28.3 1.0
CB A:ASP185 4.7 32.5 1.0
HB3 A:GLU177 4.7 35.2 1.0
HG2 A:GLU190 4.7 34.3 1.0
C A:ILE188 4.7 25.5 1.0
HG2 A:GLU177 4.8 36.2 1.0
HA A:THR174 4.8 35.1 1.0
O A:HOH522 4.8 32.9 1.0
CB A:GLU177 4.8 29.3 1.0
HG3 A:GLU177 4.8 36.2 1.0
HB3 A:GLU190 4.9 36.4 1.0
N A:GLU190 4.9 26.3 1.0
CA A:ASP185 4.9 24.8 1.0
OG1 A:THR174 5.0 30.0 1.0
HB2 A:ASP185 5.0 39.0 1.0

Calcium binding site 3 out of 4 in 6ig7

Go back to Calcium Binding Sites List in 6ig7
Calcium binding site 3 out of 4 in the Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:27.3
occ:1.00
 O A:GLN61 2.2 27.9 1.0
O A:HOH626 2.3 30.9 1.0
OD1 A:ASP59 2.3 32.1 1.0
OD1 A:ASP57 2.3 26.7 1.0
O A:HOH509 2.4 33.5 1.0
OD2 A:ASP57 2.4 31.8 1.0
O A:HOH554 2.4 30.8 1.0
CG A:ASP57 2.7 32.8 1.0
H A:GLN61 3.3 35.5 1.0
CG A:ASP59 3.3 36.1 1.0
C A:GLN61 3.4 30.4 1.0
H A:ASP59 3.5 36.5 1.0
OD2 A:ASP59 3.6 32.3 1.0
HB2 A:GLN61 3.7 41.3 1.0
HA A:PHE62 3.9 32.9 1.0
N A:GLN61 4.0 29.6 1.0
O A:HOH607 4.0 40.0 1.0
H A:ALA58 4.1 35.1 1.0
CA A:GLN61 4.1 31.1 1.0
CB A:ASP57 4.2 24.9 1.0
N A:ASP59 4.3 30.4 1.0
CB A:GLN61 4.4 34.4 1.0
N A:PHE62 4.4 26.0 1.0
H A:ASN60 4.4 38.4 1.0
O A:HOH511 4.5 26.1 1.0
OD2 A:ASP67 4.6 30.1 1.0
CB A:ASP59 4.6 30.9 1.0
HB2 A:ASP57 4.6 29.9 1.0
N A:ALA58 4.6 29.2 1.0
CA A:PHE62 4.6 27.4 1.0
HB3 A:ASP57 4.6 29.9 1.0
HA A:ASP57 4.7 35.7 1.0
N A:ASN60 4.7 32.0 1.0
HB3 A:GLN61 4.7 41.3 1.0
H A:PHE63 4.8 36.5 1.0
CA A:ASP59 4.8 30.1 1.0
CA A:ASP57 4.9 29.8 1.0
C A:ASP59 4.9 35.0 1.0
HB3 A:ALA58 4.9 42.1 1.0

Calcium binding site 4 out of 4 in 6ig7

Go back to Calcium Binding Sites List in 6ig7
Calcium binding site 4 out of 4 in the Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Thermolysin Delivered in Polyacrylamide Using X- Ray Free Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:30.2
occ:1.00
 OE2 A:GLU190 2.2 30.3 1.0
OD2 A:ASP185 2.2 29.7 1.0
OE2 A:GLU177 2.3 29.2 1.0
O A:ASN183 2.3 33.8 1.0
O A:HOH561 2.3 34.8 1.0
O A:HOH522 2.4 32.9 1.0
CG A:ASP185 3.1 33.9 1.0
CD A:GLU177 3.1 32.2 1.0
CD A:GLU190 3.2 27.3 1.0
C A:ASN183 3.4 37.6 1.0
HG3 A:GLU190 3.5 34.3 1.0
OD1 A:ASP185 3.5 29.7 1.0
HA A:PRO184 3.5 36.6 1.0
HB3 A:ASN183 3.6 53.8 1.0
OE1 A:GLU177 3.7 27.6 1.0
CA A:CA403 3.7 26.9 1.0
CG A:GLU190 3.7 28.6 1.0
HG2 A:GLU190 3.7 34.3 1.0
HB2 A:ASN183 3.8 53.8 1.0
H A:ASP185 3.8 33.9 1.0
O A:LYS182 3.8 45.6 1.0
N A:ASP185 4.0 28.3 1.0
CB A:ASN183 4.1 44.8 1.0
HG2 A:GLU177 4.1 36.2 1.0
CA A:PRO184 4.1 30.5 1.0
CG A:GLU177 4.1 30.1 1.0
O A:HOH544 4.1 46.3 1.0
C A:PRO184 4.2 35.3 1.0
OE1 A:GLU190 4.2 27.2 1.0
N A:PRO184 4.2 39.9 1.0
CB A:ASP185 4.3 32.5 1.0
OD1 A:ASP191 4.3 31.6 1.0
HG3 A:GLU177 4.3 36.2 1.0
HB3 A:ASP185 4.3 39.0 1.0
OD2 A:ASP191 4.3 32.1 1.0
CA A:ASN183 4.4 38.3 1.0
CG A:ASP191 4.6 37.3 1.0
O A:HOH637 4.7 52.0 1.0
CA A:ASP185 4.8 24.8 1.0
O A:PRO184 4.8 32.3 1.0
C A:LYS182 4.9 42.4 1.0

Reference:

J.Park, S.Park, J.Kim, G.Park, Y.Cho, K.H.Nam. Polyacrylamide Injection Matrix For Serial Femtosecond Crystallography. Sci Rep V. 9 2525 2019.
ISSN: ESSN 2045-2322
PubMed: 30792457
DOI: 10.1038/S41598-019-39020-9
Page generated: Tue Jul 16 09:23:47 2024

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