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Calcium in PDB 8ekg: Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP

Enzymatic activity of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP

All present enzymatic activity of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP:
3.1.1.102;

Protein crystallography data

The structure of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP, PDB code: 8ekg was solved by J.W.Saunders, R.L.Frkic, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.87 / 2.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.967, 120.514, 126.29, 90.44, 95.15, 90.2
R / Rfree (%) 18.4 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP (pdb code 8ekg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP, PDB code: 8ekg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8ekg

Go back to Calcium Binding Sites List in 8ekg
Calcium binding site 1 out of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:55.5
occ:1.00
O A:ILE313 2.3 55.6 1.0
OD1 A:ASP311 2.4 62.5 1.0
OD1 A:ASP304 2.6 47.3 1.0
OD1 A:ASP307 2.6 51.1 1.0
O A:LEU309 2.7 50.4 1.0
O A:ASP304 2.7 44.0 1.0
OD2 A:ASP307 2.8 61.1 1.0
CG A:ASP307 2.9 56.0 1.0
CG A:ASP311 3.3 61.6 1.0
OD2 A:ASP311 3.5 58.3 1.0
C A:ILE313 3.5 45.4 1.0
C A:ASP304 3.8 42.3 1.0
CG A:ASP304 3.8 53.0 1.0
C A:LEU309 3.9 44.4 1.0
O A:HOH820 4.0 35.8 1.0
OD2 A:ASP315 4.2 65.3 1.0
CA A:ASP304 4.3 47.3 1.0
CB A:ASP307 4.3 41.8 1.0
N A:ASP311 4.3 41.4 1.0
N A:ILE313 4.3 50.0 1.0
N A:ASP315 4.3 45.8 1.0
CA A:ILE313 4.3 49.2 1.0
N A:VAL314 4.5 39.2 1.0
CB A:ILE313 4.5 42.4 1.0
CA A:VAL314 4.6 44.3 1.0
OD2 A:ASP304 4.6 42.9 1.0
CB A:ASP311 4.7 42.7 1.0
CB A:ASP304 4.7 51.9 1.0
CA A:LEU309 4.7 46.6 1.0
N A:LEU309 4.7 51.4 1.0
CB A:ASP315 4.8 48.1 1.0
CG2 A:ILE313 4.8 39.0 1.0
CB A:LEU309 4.8 41.2 1.0
N A:ALA310 4.8 47.5 1.0
CA A:ALA310 4.9 43.0 1.0
CG A:ASP315 4.9 64.1 1.0
N A:ALA305 4.9 45.3 1.0
CA A:ASP311 5.0 36.7 1.0

Calcium binding site 2 out of 6 in 8ekg

Go back to Calcium Binding Sites List in 8ekg
Calcium binding site 2 out of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:53.9
occ:1.00
OD1 B:ASP311 2.3 51.8 1.0
O B:ILE313 2.3 53.0 1.0
O B:LEU309 2.4 49.5 1.0
OD2 B:ASP307 2.5 60.1 1.0
OD1 B:ASP304 2.5 48.4 1.0
O B:ASP304 2.6 52.8 1.0
OD1 B:ASP307 2.9 73.8 1.0
CG B:ASP307 3.0 64.6 1.0
CG B:ASP311 3.4 55.5 1.0
C B:ILE313 3.5 47.9 1.0
C B:ASP304 3.6 50.6 1.0
C B:LEU309 3.6 50.0 1.0
CG B:ASP304 3.7 49.5 1.0
OD2 B:ASP315 3.7 73.5 1.0
OD2 B:ASP311 3.9 56.6 1.0
CA B:ASP304 4.0 50.6 1.0
N B:ASP311 4.0 40.1 1.0
N B:ILE313 4.2 39.1 1.0
CA B:ILE313 4.3 35.8 1.0
CB B:ASP304 4.5 53.5 1.0
N B:ALA310 4.5 45.1 1.0
CA B:LEU309 4.5 50.3 1.0
N B:VAL314 4.5 46.4 1.0
CB B:ASP307 4.5 59.4 1.0
O B:HOH810 4.5 50.5 1.0
CA B:ALA310 4.5 44.4 1.0
N B:ASP315 4.5 64.5 1.0
CB B:ILE313 4.6 44.0 1.0
N B:LEU309 4.6 51.9 1.0
OD2 B:ASP304 4.6 44.2 1.0
CB B:ASP311 4.6 52.3 1.0
N B:ALA305 4.6 50.3 1.0
CB B:LEU309 4.7 42.7 1.0
CA B:VAL314 4.7 51.3 1.0
O B:HOH838 4.8 42.1 1.0
C B:ALA310 4.8 47.1 1.0
CA B:ASP311 4.8 41.7 1.0
CG B:ASP315 4.8 75.3 1.0
N B:GLY312 4.9 49.3 1.0
CA B:ALA305 5.0 53.7 1.0

Calcium binding site 3 out of 6 in 8ekg

Go back to Calcium Binding Sites List in 8ekg
Calcium binding site 3 out of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:58.0
occ:1.00
O C:LEU309 2.2 63.3 1.0
OD1 C:ASP307 2.4 66.7 1.0
O C:ASP304 2.5 51.1 1.0
OD1 C:ASP311 2.5 52.1 1.0
OD1 C:ASP304 2.6 68.1 1.0
O C:ILE313 2.7 54.1 1.0
OD2 C:ASP307 3.0 68.5 1.0
CG C:ASP307 3.1 71.9 1.0
C C:LEU309 3.4 50.0 1.0
CG C:ASP311 3.6 55.1 1.0
C C:ASP304 3.6 58.3 1.0
CG C:ASP304 3.7 68.2 1.0
OD1 C:ASP315 3.7 87.2 1.0
C C:ILE313 3.9 50.5 1.0
N C:ASP311 4.0 55.6 1.0
OD2 C:ASP311 4.0 54.6 1.0
CA C:ASP304 4.2 56.4 1.0
CA C:LEU309 4.3 49.3 1.0
N C:LEU309 4.4 58.7 1.0
N C:ALA310 4.4 56.5 1.0
OD2 C:ASP304 4.4 59.7 1.0
N C:ILE313 4.4 54.9 1.0
CA C:ALA310 4.5 58.1 1.0
CB C:ASP304 4.5 58.4 1.0
CB C:LEU309 4.5 46.2 1.0
CB C:ASP307 4.5 66.5 1.0
N C:ALA305 4.6 61.9 1.0
CA C:ILE313 4.6 56.3 1.0
CB C:ASP311 4.7 52.0 1.0
C C:ALA310 4.7 55.7 1.0
CA C:ASP311 4.8 50.6 1.0
N C:VAL314 4.9 52.7 1.0
CG C:ASP315 4.9 72.6 1.0
N C:ASP315 4.9 47.7 1.0
CA C:ALA305 4.9 59.5 1.0
CB C:ILE313 4.9 52.3 1.0

Calcium binding site 4 out of 6 in 8ekg

Go back to Calcium Binding Sites List in 8ekg
Calcium binding site 4 out of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:60.4
occ:1.00
OD1 D:ASP311 2.3 61.5 1.0
OD1 D:ASP307 2.3 60.3 1.0
O D:ILE313 2.4 61.5 1.0
O D:LEU309 2.4 69.5 1.0
OD2 D:ASP307 2.6 66.3 1.0
CG D:ASP307 2.8 62.0 1.0
OD1 D:ASP304 2.8 58.0 1.0
O D:ASP304 3.0 51.1 1.0
CG D:ASP311 3.1 66.8 1.0
OD2 D:ASP311 3.4 62.3 1.0
C D:LEU309 3.6 60.9 1.0
C D:ILE313 3.6 51.1 1.0
OD2 D:ASP315 3.9 71.7 1.0
C D:ASP304 4.0 52.2 1.0
CG D:ASP304 4.0 61.3 1.0
N D:ASP311 4.1 58.1 1.0
CB D:ASP307 4.3 56.8 1.0
N D:ILE313 4.3 54.6 1.0
CA D:LEU309 4.4 63.9 1.0
CA D:ILE313 4.4 52.5 1.0
N D:LEU309 4.4 61.9 1.0
CA D:ASP304 4.4 54.0 1.0
N D:ASP315 4.5 60.4 1.0
CB D:ASP311 4.5 65.8 1.0
CB D:LEU309 4.5 56.6 1.0
N D:ALA310 4.5 57.9 1.0
N D:VAL314 4.6 59.7 1.0
CB D:ILE313 4.6 53.9 1.0
CA D:ALA310 4.7 57.3 1.0
CA D:VAL314 4.7 61.4 1.0
CG D:ASP315 4.7 74.1 1.0
CA D:ASP311 4.8 62.7 1.0
C D:ALA310 4.9 63.9 1.0
CB D:ASP304 4.9 64.5 1.0
OD2 D:ASP304 4.9 54.8 1.0
CG2 D:ILE313 4.9 51.6 1.0

Calcium binding site 5 out of 6 in 8ekg

Go back to Calcium Binding Sites List in 8ekg
Calcium binding site 5 out of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca701

b:64.1
occ:1.00
OD1 E:ASP311 2.3 77.9 1.0
O E:LEU309 2.3 74.5 1.0
OD1 E:ASP307 2.4 63.9 1.0
OD1 E:ASP304 2.6 68.6 1.0
O E:ILE313 2.6 66.6 1.0
OD2 E:ASP307 2.8 77.1 1.0
O E:ASP304 2.8 81.9 1.0
CG E:ASP307 2.9 72.2 1.0
CG E:ASP311 3.2 71.0 1.0
OD2 E:ASP311 3.4 60.9 1.0
C E:LEU309 3.5 73.9 1.0
OD2 E:ASP315 3.7 93.1 1.0
C E:ASP304 3.8 84.7 1.0
CG E:ASP304 3.8 72.6 1.0
C E:ILE313 3.8 70.2 1.0
N E:ASP311 4.0 68.3 1.0
CA E:ASP304 4.2 80.8 1.0
CA E:ALA310 4.4 71.6 1.0
N E:ALA310 4.4 77.2 1.0
CB E:ASP307 4.4 76.8 1.0
CA E:LEU309 4.5 68.8 1.0
N E:ILE313 4.5 57.1 1.0
CB E:ASP311 4.5 64.3 1.0
N E:LEU309 4.6 62.8 1.0
C E:ALA310 4.6 69.8 1.0
CB E:ASP304 4.6 75.2 1.0
CA E:ILE313 4.6 69.5 1.0
N E:ASP315 4.7 73.3 1.0
OD2 E:ASP304 4.7 75.1 1.0
CB E:LEU309 4.8 72.9 1.0
N E:VAL314 4.8 72.1 1.0
CG E:ASP315 4.8 102.7 1.0
CA E:ASP311 4.8 68.4 1.0
N E:ALA305 4.8 84.9 1.0
CA E:VAL314 4.9 72.5 1.0
CB E:ILE313 4.9 71.0 1.0
CD1 E:LEU309 5.0 71.5 1.0

Calcium binding site 6 out of 6 in 8ekg

Go back to Calcium Binding Sites List in 8ekg
Calcium binding site 6 out of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca701

b:60.6
occ:1.00
OD1 F:ASP311 2.3 66.7 1.0
O F:LEU309 2.3 65.0 1.0
O F:ILE313 2.5 61.8 1.0
OD2 F:ASP307 2.5 75.4 1.0
OD1 F:ASP307 2.5 69.5 1.0
O F:ASP304 2.8 65.9 1.0
OD1 F:ASP304 2.8 60.1 1.0
CG F:ASP307 2.9 72.7 1.0
CG F:ASP311 3.4 66.3 1.0
C F:LEU309 3.6 65.1 1.0
C F:ILE313 3.7 63.8 1.0
C F:ASP304 3.7 68.9 1.0
OD2 F:ASP311 3.8 68.7 1.0
N F:ASP311 3.9 61.3 1.0
CG F:ASP304 4.0 65.3 1.0
CA F:ASP304 4.1 70.1 1.0
OD2 F:ASP315 4.2 88.5 1.0
N F:ILE313 4.3 50.7 1.0
CA F:ALA310 4.3 64.8 1.0
CB F:ASP307 4.4 73.4 1.0
N F:ALA310 4.4 63.8 1.0
CA F:ILE313 4.4 61.3 1.0
N F:ASP315 4.5 63.5 1.0
CA F:LEU309 4.6 65.2 1.0
CB F:ASP311 4.6 65.6 1.0
C F:ALA310 4.6 63.2 1.0
N F:LEU309 4.6 69.9 1.0
CB F:ASP304 4.6 68.6 1.0
CB F:ILE313 4.7 56.1 1.0
N F:VAL314 4.7 68.0 1.0
CA F:ASP311 4.7 65.1 1.0
N F:ALA305 4.7 75.0 1.0
CA F:VAL314 4.8 60.2 1.0
CG F:ASP315 4.9 88.8 1.0
OD2 F:ASP304 4.9 74.3 1.0
CB F:LEU309 4.9 58.6 1.0
CB F:ASP315 5.0 72.9 1.0

Reference:

J.W.Saunders, A.D.Damry, V.Vongsouthi, R.L.Frkic, M.A.Spence, P.M.Yates, M.D.Mcleod, N.Tokuriki, C.J.Jackson. Mhetase Protein Engineering Using A Novel Colorimetric Assay To Be Published.
Page generated: Fri Jul 19 08:12:28 2024

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