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Calcium in PDB 1z9g: Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan

Enzymatic activity of Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan

All present enzymatic activity of Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan:
3.4.24.27;

Protein crystallography data

The structure of Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan, PDB code: 1z9g was solved by S.L.Roderick, M.C.Fournie-Zaluski, B.P.Roques, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.000, 94.000, 132.000, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Other elements in 1z9g:

The structure of Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan (pdb code 1z9g). 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 Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan, PDB code: 1z9g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1z9g

Go back to Calcium Binding Sites List in 1z9g
Calcium binding site 1 out of 4 in the Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1001

b:12.9
occ:1.00
 O E:GLU187 2.3 10.8 1.0
OD1 E:ASP138 2.4 13.1 1.0
OE1 E:GLU190 2.4 11.9 1.0
OE2 E:GLU190 2.4 11.3 1.0
OD2 E:ASP185 2.5 10.0 1.0
OE1 E:GLU177 2.6 13.8 1.0
O E:HOH346 2.6 11.4 1.0
CD E:GLU190 2.7 7.9 1.0
OE2 E:GLU177 2.9 11.0 1.0
CD E:GLU177 3.1 13.3 1.0
CG E:ASP138 3.4 16.2 1.0
C E:GLU187 3.4 16.2 1.0
CG E:ASP185 3.5 15.8 1.0
OD1 E:ASP185 3.7 12.0 1.0
CA E:CA1002 3.8 14.4 1.0
CB E:ASP138 4.0 11.3 1.0
CG E:GLU190 4.2 8.9 1.0
N E:ILE188 4.2 10.1 1.0
N E:GLU187 4.3 14.0 1.0
O E:ASP185 4.3 13.5 1.0
CA E:GLU187 4.3 13.6 1.0
CA E:ILE188 4.3 10.9 1.0
OD2 E:ASP138 4.3 12.4 1.0
O E:HOH469 4.4 29.3 1.0
O E:HOH350 4.5 15.5 1.0
CG E:GLU177 4.5 11.5 1.0
N E:GLY189 4.5 16.5 1.0
CB E:GLU187 4.6 10.8 1.0
C E:ASP185 4.7 12.6 1.0
CB E:ASP185 4.8 8.8 1.0
N E:ASP185 4.8 11.8 1.0
C E:ILE188 4.8 13.5 1.0
CD1 E:ILE188 4.9 21.6 1.0
N E:GLU190 5.0 11.5 1.0
OG1 E:THR174 5.0 11.4 1.0
CB E:GLU177 5.0 8.1 1.0

Calcium binding site 2 out of 4 in 1z9g

Go back to Calcium Binding Sites List in 1z9g
Calcium binding site 2 out of 4 in the Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1002

b:14.4
occ:1.00
 O E:HOH475 1.8 23.3 1.0
OE2 E:GLU177 2.2 11.0 1.0
OE2 E:GLU190 2.3 11.3 1.0
O E:HOH353 2.4 12.8 1.0
O E:ASN183 2.5 19.3 1.0
OD1 E:ASP185 2.5 12.0 1.0
CD E:GLU177 3.2 13.3 1.0
CG E:ASP185 3.4 15.8 1.0
CD E:GLU190 3.4 7.9 1.0
C E:ASN183 3.6 14.1 1.0
OD2 E:ASP185 3.7 10.0 1.0
OE1 E:GLU177 3.8 13.8 1.0
CA E:CA1001 3.8 12.9 1.0
CG E:GLU190 3.8 8.9 1.0
O E:LYS182 3.9 23.0 1.0
CB E:ASN183 4.1 21.9 1.0
CA E:PRO184 4.1 16.4 1.0
CG E:GLU177 4.2 11.5 1.0
OD2 E:ASP191 4.2 15.8 1.0
C E:PRO184 4.2 18.1 1.0
N E:ASP185 4.3 11.8 1.0
N E:PRO184 4.3 17.3 1.0
OE1 E:GLU190 4.4 11.9 1.0
OD1 E:ASP191 4.5 13.8 1.0
CA E:ASN183 4.6 19.9 1.0
CB E:ASP185 4.6 8.8 1.0
CG E:ASP191 4.6 15.2 1.0
O E:HOH469 4.7 29.3 1.0
O E:PRO184 4.8 18.7 1.0
C E:LYS182 4.9 21.0 1.0

Calcium binding site 3 out of 4 in 1z9g

Go back to Calcium Binding Sites List in 1z9g
Calcium binding site 3 out of 4 in the Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1003

b:11.9
occ:1.00
 OD1 E:ASP57 2.1 13.4 1.0
O E:HOH482 2.2 17.0 1.0
O E:GLN61 2.3 11.8 1.0
O E:HOH503 2.4 16.7 1.0
OD1 E:ASP59 2.4 15.3 1.0
OD2 E:ASP57 2.5 12.0 1.0
O E:HOH419 2.5 17.4 1.0
CG E:ASP57 2.7 13.8 1.0
C E:GLN61 3.5 13.9 1.0
CG E:ASP59 3.5 18.8 1.0
OD2 E:ASP59 3.9 17.4 1.0
N E:GLN61 4.0 13.4 1.0
O E:HOH484 4.1 26.4 1.0
CB E:ASP57 4.2 4.9 1.0
CA E:GLN61 4.2 20.1 1.0
CB E:GLN61 4.3 17.1 1.0
N E:ASP59 4.4 13.0 1.0
N E:PHE62 4.5 15.8 1.0
OD2 E:ASP67 4.6 13.9 1.0
O E:HOH508 4.6 15.2 1.0
O E:HOH356 4.7 12.2 1.0
N E:ASN60 4.7 10.3 1.0
CA E:PHE62 4.7 8.5 1.0
CB E:ASP59 4.7 12.7 1.0
N E:ALA58 4.8 10.9 1.0
CA E:ASP59 4.8 13.4 1.0
C E:ASP59 4.9 14.4 1.0
CA E:ASP57 5.0 7.8 1.0

Calcium binding site 4 out of 4 in 1z9g

Go back to Calcium Binding Sites List in 1z9g
Calcium binding site 4 out of 4 in the Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (R)-Retro-Thiorphan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1004

b:16.6
occ:1.00
 O E:HOH480 1.9 29.7 1.0
O E:ILE197 2.3 26.8 1.0
OD1 E:ASP200 2.3 17.6 1.0
OG1 E:THR194 2.4 16.2 1.0
O E:THR194 2.5 19.4 1.0
O E:HOH354 2.5 14.9 1.0
O E:TYR193 2.5 13.2 1.0
C E:THR194 3.3 18.4 1.0
CG E:ASP200 3.3 13.4 1.0
C E:TYR193 3.4 11.7 1.0
C E:ILE197 3.4 28.1 1.0
CB E:THR194 3.6 12.9 1.0
OD2 E:ASP200 3.8 16.8 1.0
CA E:THR194 3.8 11.3 1.0
N E:THR194 3.9 12.3 1.0
N E:ILE197 4.1 30.9 1.0
CA E:ILE197 4.2 22.0 1.0
N E:PRO195 4.2 21.2 1.0
CB E:ILE197 4.3 25.5 1.0
O E:ASP200 4.3 16.3 1.0
N E:SER198 4.4 25.4 1.0
N E:ASP200 4.5 21.8 1.0
CA E:SER198 4.6 26.8 1.0
O E:GLU190 4.6 13.6 1.0
CA E:TYR193 4.6 9.5 1.0
CG2 E:ILE197 4.7 30.5 1.0
CD2 E:TYR193 4.7 12.3 1.0
CB E:ASP200 4.7 16.6 1.0
CA E:PRO195 4.7 15.8 1.0
O E:HOH505 4.8 48.0 1.0
C E:ASP200 4.8 9.4 1.0
CB E:TYR193 4.8 15.4 1.0
CG2 E:THR194 4.8 11.6 1.0
C E:SER198 4.8 25.6 1.0
CA E:ASP200 4.9 10.8 1.0
C E:PRO195 5.0 25.6 1.0

Reference:

S.L.Roderick, M.C.Fournie-Zaluski, B.P.Roques, B.W.Matthews. Thiorphan and Retro-Thiorphan Display Equivalent Interactions When Bound to Crystalline Thermolysin Biochemistry V. 28 1493 1989.
ISSN: ISSN 0006-2960
PubMed: 2719912
DOI: 10.1021/BI00430A011
Page generated: Fri Jul 12 08:21:46 2024

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