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Calcium in PDB 1zdp: Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-Thiorphan

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

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

Protein crystallography data

The structure of Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-Thiorphan, PDB code: 1zdp 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, 132.100, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / n/a

Other elements in 1zdp:

The structure of Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-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 (S)-Thiorphan (pdb code 1zdp). 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 (S)-Thiorphan, PDB code: 1zdp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1zdp

Go back to Calcium Binding Sites List in 1zdp
Calcium binding site 1 out of 4 in the Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-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 (S)-Thiorphan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1001

b:13.7
occ:1.00
 O E:GLU187 2.3 9.6 1.0
OD1 E:ASP138 2.4 14.2 1.0
OE2 E:GLU190 2.5 10.4 1.0
OD2 E:ASP185 2.5 11.9 1.0
OE1 E:GLU177 2.6 14.4 1.0
OE1 E:GLU190 2.6 11.6 1.0
O E:HOH346 2.7 9.6 1.0
CD E:GLU190 2.8 6.2 1.0
OE2 E:GLU177 2.9 10.4 1.0
CD E:GLU177 3.1 12.1 1.0
C E:GLU187 3.4 11.3 1.0
CG E:ASP138 3.4 13.9 1.0
CG E:ASP185 3.5 10.5 1.0
CA E:CA1002 3.8 15.1 1.0
OD1 E:ASP185 3.8 13.5 1.0
CB E:ASP138 4.1 6.8 1.0
N E:ILE188 4.2 10.7 1.0
O E:ASP185 4.2 14.4 1.0
OD2 E:ASP138 4.2 10.7 1.0
CA E:ILE188 4.3 7.1 1.0
CG E:GLU190 4.3 7.3 1.0
N E:GLU187 4.3 13.8 1.0
O E:HOH469 4.3 32.2 1.0
CA E:GLU187 4.3 10.4 1.0
CG E:GLU177 4.5 9.1 1.0
N E:GLY189 4.5 14.8 1.0
CB E:GLU187 4.6 15.3 1.0
O E:HOH350 4.6 15.6 1.0
C E:ASP185 4.7 12.5 1.0
CB E:ASP185 4.8 15.2 1.0
C E:ILE188 4.8 11.1 1.0
N E:ASP185 4.9 14.1 1.0
N E:GLU190 4.9 10.2 1.0
OG1 E:THR174 5.0 8.4 1.0
CB E:GLU177 5.0 7.4 1.0

Calcium binding site 2 out of 4 in 1zdp

Go back to Calcium Binding Sites List in 1zdp
Calcium binding site 2 out of 4 in the Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-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 (S)-Thiorphan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1002

b:15.1
occ:1.00
 O E:HOH475 1.9 22.6 1.0
OE2 E:GLU177 2.3 10.4 1.0
OE2 E:GLU190 2.4 10.4 1.0
OD1 E:ASP185 2.4 13.5 1.0
O E:HOH353 2.4 13.2 1.0
O E:ASN183 2.6 22.1 1.0
CG E:ASP185 3.2 10.5 1.0
CD E:GLU177 3.3 12.1 1.0
CD E:GLU190 3.4 6.2 1.0
OD2 E:ASP185 3.6 11.9 1.0
C E:ASN183 3.7 17.2 1.0
CA E:CA1001 3.8 13.7 1.0
CG E:GLU190 3.8 7.3 1.0
O E:LYS182 3.9 22.3 1.0
OE1 E:GLU177 3.9 14.4 1.0
CB E:ASN183 4.1 24.7 1.0
CA E:PRO184 4.2 13.3 1.0
C E:PRO184 4.2 21.4 1.0
CG E:GLU177 4.2 9.1 1.0
N E:ASP185 4.2 14.1 1.0
OD2 E:ASP191 4.3 15.2 1.0
OE1 E:GLU190 4.4 11.6 1.0
N E:PRO184 4.4 18.3 1.0
CB E:ASP185 4.4 15.2 1.0
OD1 E:ASP191 4.5 15.0 1.0
O E:HOH469 4.6 32.2 1.0
CG E:ASP191 4.7 15.4 1.0
CA E:ASN183 4.7 19.1 1.0
O E:PRO184 4.8 18.7 1.0
ND2 E:ASN183 5.0 37.8 1.0
CA E:ASP185 5.0 8.7 1.0
C E:LYS182 5.0 18.7 1.0

Calcium binding site 3 out of 4 in 1zdp

Go back to Calcium Binding Sites List in 1zdp
Calcium binding site 3 out of 4 in the Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-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 (S)-Thiorphan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1003

b:10.6
occ:1.00
 OD1 E:ASP57 2.1 12.5 1.0
O E:GLN61 2.2 11.8 1.0
O E:HOH482 2.2 17.1 1.0
O E:HOH503 2.4 14.3 1.0
OD1 E:ASP59 2.4 19.6 1.0
O E:HOH419 2.4 16.9 1.0
OD2 E:ASP57 2.7 9.3 1.0
CG E:ASP57 2.8 13.7 1.0
CG E:ASP59 3.4 18.2 1.0
C E:GLN61 3.4 9.8 1.0
OD2 E:ASP59 3.8 18.1 1.0
N E:GLN61 4.0 12.7 1.0
CA E:GLN61 4.1 15.2 1.0
O E:HOH484 4.2 28.3 1.0
N E:ASP59 4.3 13.9 1.0
CB E:ASP57 4.3 5.8 1.0
CB E:GLN61 4.4 15.4 1.0
N E:PHE62 4.5 11.7 1.0
O E:HOH508 4.5 15.3 1.0
OD2 E:ASP67 4.6 10.3 1.0
CB E:ASP59 4.7 10.6 1.0
O E:HOH356 4.7 12.0 1.0
N E:ALA58 4.7 10.1 1.0
N E:ASN60 4.7 12.1 1.0
CA E:PHE62 4.8 10.9 1.0
CA E:ASP59 4.8 12.2 1.0
C E:ASP59 4.9 9.6 1.0

Calcium binding site 4 out of 4 in 1zdp

Go back to Calcium Binding Sites List in 1zdp
Calcium binding site 4 out of 4 in the Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-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 (S)-Thiorphan within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1004

b:17.4
occ:1.00
 O E:ILE197 2.3 28.6 1.0
OD1 E:ASP200 2.3 18.1 1.0
O E:HOH480 2.3 28.6 1.0
OG1 E:THR194 2.5 14.5 1.0
O E:HOH354 2.6 16.3 1.0
O E:TYR193 2.6 14.6 1.0
O E:THR194 2.6 18.6 1.0
C E:THR194 3.3 22.9 1.0
CG E:ASP200 3.3 13.2 1.0
C E:ILE197 3.4 26.8 1.0
C E:TYR193 3.5 13.7 1.0
CB E:THR194 3.6 13.4 1.0
OD2 E:ASP200 3.8 16.9 1.0
CA E:THR194 3.8 17.5 1.0
N E:THR194 4.0 11.6 1.0
N E:ILE197 4.1 28.6 1.0
CA E:ILE197 4.1 24.9 1.0
CB E:ILE197 4.3 26.5 1.0
N E:PRO195 4.3 20.3 1.0
O E:ASP200 4.3 16.8 1.0
N E:SER198 4.4 24.1 1.0
O E:GLU190 4.6 11.8 1.0
N E:ASP200 4.6 18.3 1.0
CA E:TYR193 4.6 12.7 1.0
CA E:SER198 4.6 30.6 1.0
CB E:ASP200 4.7 11.0 1.0
C E:ASP200 4.7 9.2 1.0
CD2 E:TYR193 4.8 14.5 1.0
CA E:PRO195 4.8 15.2 1.0
CB E:TYR193 4.8 13.9 1.0
CG2 E:THR194 4.8 11.1 1.0
CG2 E:ILE197 4.9 28.3 1.0
C E:SER198 4.9 23.6 1.0
CA E:ASP200 4.9 12.7 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 08:22:45 2024

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