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Calcium in PDB 2tmn: Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin

Enzymatic activity of Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin

All present enzymatic activity of Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin:
3.4.24.27;

Protein crystallography data

The structure of Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin, PDB code: 2tmn was solved by D.E.Tronrud, A.F.Monzingo, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.60
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.100, 94.100, 131.400, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Other elements in 2tmn:

The structure of Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin (pdb code 2tmn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin, PDB code: 2tmn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2tmn

Go back to Calcium Binding Sites List in 2tmn
Calcium binding site 1 out of 4 in the Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca317

b:11.6
occ:1.00
 O E:GLU187 2.3 8.6 1.0
OD1 E:ASP138 2.3 13.4 1.0
OE2 E:GLU190 2.4 12.6 1.0
OE1 E:GLU190 2.5 12.3 1.0
OD2 E:ASP185 2.5 11.1 1.0
OE1 E:GLU177 2.6 13.1 1.0
O E:HOH338 2.6 10.0 1.0
CD E:GLU190 2.8 11.5 1.0
OE2 E:GLU177 2.9 11.0 1.0
CD E:GLU177 3.1 13.3 1.0
C E:GLU187 3.4 13.2 1.0
CG E:ASP138 3.4 10.8 1.0
CG E:ASP185 3.5 14.3 1.0
OD1 E:ASP185 3.7 13.9 1.0
CA E:CA318 3.8 13.1 1.0
CB E:ASP138 4.1 5.6 1.0
N E:ILE188 4.2 11.3 1.0
CG E:GLU190 4.2 8.8 1.0
OD2 E:ASP138 4.2 12.1 1.0
N E:GLU187 4.2 15.7 1.0
O E:HOH426 4.3 38.6 1.0
CA E:ILE188 4.3 13.0 1.0
O E:ASP185 4.3 16.0 1.0
CA E:GLU187 4.3 11.2 1.0
O E:HOH342 4.5 14.6 1.0
CB E:GLU187 4.5 12.0 1.0
CG E:GLU177 4.5 9.0 1.0
N E:GLY189 4.6 17.1 1.0
C E:ASP185 4.7 11.3 1.0
N E:ASP185 4.8 12.4 1.0
CB E:ASP185 4.8 10.9 1.0
C E:ILE188 4.9 19.9 1.0
N E:GLU190 4.9 11.8 1.0

Calcium binding site 2 out of 4 in 2tmn

Go back to Calcium Binding Sites List in 2tmn
Calcium binding site 2 out of 4 in the Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca318

b:13.1
occ:1.00
 O E:HOH431 2.0 23.8 1.0
OE2 E:GLU177 2.3 11.0 1.0
OE2 E:GLU190 2.3 12.6 1.0
O E:HOH345 2.4 13.5 1.0
OD1 E:ASP185 2.5 13.9 1.0
O E:ASN183 2.5 21.4 1.0
CD E:GLU177 3.3 13.3 1.0
CG E:ASP185 3.4 14.3 1.0
CD E:GLU190 3.4 11.5 1.0
C E:ASN183 3.7 14.9 1.0
OD2 E:ASP185 3.7 11.1 1.0
CA E:CA317 3.8 11.6 1.0
CG E:GLU190 3.8 8.8 1.0
OE1 E:GLU177 3.8 13.1 1.0
O E:LYS182 3.9 25.4 1.0
CB E:ASN183 4.1 21.8 1.0
CA E:PRO184 4.2 15.6 1.0
OD2 E:ASP191 4.2 17.5 1.0
C E:PRO184 4.3 20.5 1.0
N E:ASP185 4.3 12.4 1.0
CG E:GLU177 4.3 9.0 1.0
N E:PRO184 4.4 13.7 1.0
OE1 E:GLU190 4.4 12.3 1.0
OD1 E:ASP191 4.4 15.7 1.0
O E:HOH426 4.5 38.6 1.0
CB E:ASP185 4.6 10.9 1.0
CG E:ASP191 4.6 18.7 1.0
CA E:ASN183 4.6 18.9 1.0
ND2 E:ASN183 4.8 44.7 1.0
O E:PRO184 4.8 20.0 1.0
C E:LYS182 5.0 23.8 1.0

Calcium binding site 3 out of 4 in 2tmn

Go back to Calcium Binding Sites List in 2tmn
Calcium binding site 3 out of 4 in the Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca319

b:12.1
occ:1.00
 OD1 E:ASP57 2.2 12.2 1.0
O E:GLN61 2.3 12.7 1.0
O E:HOH438 2.3 15.1 1.0
O E:HOH454 2.4 17.0 1.0
OD1 E:ASP59 2.5 17.8 1.0
O E:HOH394 2.5 17.8 1.0
OD2 E:ASP57 2.6 12.3 1.0
CG E:ASP57 2.8 13.7 1.0
CG E:ASP59 3.5 17.7 1.0
C E:GLN61 3.5 17.7 1.0
OD2 E:ASP59 3.9 18.7 1.0
O E:HOH440 4.0 23.4 1.0
N E:GLN61 4.0 16.8 1.0
CA E:GLN61 4.2 16.9 1.0
CB E:ASP57 4.3 6.4 1.0
N E:ASP59 4.4 13.6 1.0
CB E:GLN61 4.4 15.0 1.0
O E:HOH459 4.5 16.2 1.0
OD2 E:ASP67 4.5 11.8 1.0
N E:PHE62 4.6 15.2 1.0
O E:HOH348 4.6 11.2 1.0
CA E:PHE62 4.7 7.4 1.0
N E:ALA58 4.7 9.7 1.0
CB E:ASP59 4.7 6.0 1.0
N E:ASN60 4.8 10.9 1.0
CA E:ASP59 4.9 10.9 1.0
C E:ASP59 5.0 14.0 1.0

Calcium binding site 4 out of 4 in 2tmn

Go back to Calcium Binding Sites List in 2tmn
Calcium binding site 4 out of 4 in the Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca320

b:16.3
occ:1.00
 O E:HOH436 2.1 29.5 1.0
OD1 E:ASP200 2.2 17.6 1.0
O E:ILE197 2.3 25.8 1.0
OG1 E:THR194 2.4 13.5 1.0
O E:THR194 2.5 19.9 1.0
O E:TYR193 2.5 12.8 1.0
O E:HOH346 2.5 15.0 1.0
CG E:ASP200 3.3 10.3 1.0
C E:THR194 3.3 21.2 1.0
C E:TYR193 3.4 13.0 1.0
C E:ILE197 3.4 28.2 1.0
CB E:THR194 3.6 13.9 1.0
OD2 E:ASP200 3.7 17.2 1.0
CA E:THR194 3.8 13.2 1.0
N E:THR194 3.9 13.3 1.0
N E:ILE197 4.2 29.5 1.0
CA E:ILE197 4.2 19.5 1.0
N E:PRO195 4.3 20.3 1.0
CB E:ILE197 4.3 27.4 1.0
O E:ASP200 4.4 14.9 1.0
N E:SER198 4.4 26.5 1.0
O E:GLU190 4.5 16.1 1.0
CA E:SER198 4.5 29.8 1.0
N E:ASP200 4.6 19.4 1.0
CA E:TYR193 4.6 11.8 1.0
CB E:ASP200 4.6 15.0 1.0
CA E:PRO195 4.7 21.2 1.0
CD2 E:TYR193 4.7 15.6 1.0
C E:ASP200 4.8 11.3 1.0
CG2 E:THR194 4.8 10.6 1.0
CB E:TYR193 4.8 15.1 1.0
C E:SER198 4.8 24.6 1.0
O E:HOH456 4.9 54.0 1.0
CG2 E:ILE197 4.9 28.8 1.0
CA E:ASP200 4.9 13.6 1.0
N E:GLY199 4.9 25.8 1.0
C E:PRO195 5.0 26.4 1.0

Reference:

D.E.Tronrud, A.F.Monzingo, B.W.Matthews. Crystallographic Structural Analysis of Phosphoramidates As Inhibitors and Transition-State Analogs of Thermolysin. Eur.J.Biochem. V. 157 261 1986.
ISSN: ISSN 0014-2956
PubMed: 3709536
DOI: 10.1111/J.1432-1033.1986.TB09664.X
Page generated: Fri Jul 12 17:43:30 2024

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