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Calcium in PDB 1yja: Subtilisin Bpn' 8397+1 (E.C. 3.4.21.14) (Mutant with Met 50 Replaced By Phe, Asn 76 Replaced By Asp, Gly 169 Replaced By Ala, Gln 206 Replaced By Cys, Asn 218 Replaced By Ser and Lys 256 Replaced By Tyr) (M50F, N76D, G169A, Q206C, N218S, and K256Y) in 20% Dimethylformamide

Enzymatic activity of Subtilisin Bpn' 8397+1 (E.C. 3.4.21.14) (Mutant with Met 50 Replaced By Phe, Asn 76 Replaced By Asp, Gly 169 Replaced By Ala, Gln 206 Replaced By Cys, Asn 218 Replaced By Ser and Lys 256 Replaced By Tyr) (M50F, N76D, G169A, Q206C, N218S, and K256Y) in 20% Dimethylformamide

All present enzymatic activity of Subtilisin Bpn' 8397+1 (E.C. 3.4.21.14) (Mutant with Met 50 Replaced By Phe, Asn 76 Replaced By Asp, Gly 169 Replaced By Ala, Gln 206 Replaced By Cys, Asn 218 Replaced By Ser and Lys 256 Replaced By Tyr) (M50F, N76D, G169A, Q206C, N218S, and K256Y) in 20% Dimethylformamide:
3.4.21.14;

Protein crystallography data

The structure of Subtilisin Bpn' 8397+1 (E.C. 3.4.21.14) (Mutant with Met 50 Replaced By Phe, Asn 76 Replaced By Asp, Gly 169 Replaced By Ala, Gln 206 Replaced By Cys, Asn 218 Replaced By Ser and Lys 256 Replaced By Tyr) (M50F, N76D, G169A, Q206C, N218S, and K256Y) in 20% Dimethylformamide, PDB code: 1yja was solved by R.D.Kidd, G.K.Farber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.570, 79.670, 37.220, 90.00, 114.13, 90.00
R / Rfree (%) 21.5 / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Subtilisin Bpn' 8397+1 (E.C. 3.4.21.14) (Mutant with Met 50 Replaced By Phe, Asn 76 Replaced By Asp, Gly 169 Replaced By Ala, Gln 206 Replaced By Cys, Asn 218 Replaced By Ser and Lys 256 Replaced By Tyr) (M50F, N76D, G169A, Q206C, N218S, and K256Y) in 20% Dimethylformamide (pdb code 1yja). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Subtilisin Bpn' 8397+1 (E.C. 3.4.21.14) (Mutant with Met 50 Replaced By Phe, Asn 76 Replaced By Asp, Gly 169 Replaced By Ala, Gln 206 Replaced By Cys, Asn 218 Replaced By Ser and Lys 256 Replaced By Tyr) (M50F, N76D, G169A, Q206C, N218S, and K256Y) in 20% Dimethylformamide, PDB code: 1yja:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1yja

Go back to Calcium Binding Sites List in 1yja
Calcium binding site 1 out of 2 in the Subtilisin Bpn' 8397+1 (E.C. 3.4.21.14) (Mutant with Met 50 Replaced By Phe, Asn 76 Replaced By Asp, Gly 169 Replaced By Ala, Gln 206 Replaced By Cys, Asn 218 Replaced By Ser and Lys 256 Replaced By Tyr) (M50F, N76D, G169A, Q206C, N218S, and K256Y) in 20% Dimethylformamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Subtilisin Bpn' 8397+1 (E.C. 3.4.21.14) (Mutant with Met 50 Replaced By Phe, Asn 76 Replaced By Asp, Gly 169 Replaced By Ala, Gln 206 Replaced By Cys, Asn 218 Replaced By Ser and Lys 256 Replaced By Tyr) (M50F, N76D, G169A, Q206C, N218S, and K256Y) in 20% Dimethylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca290

b:20.4
occ:1.00
 OD1 A:ASN77 2.3 16.0 1.0
O A:LEU75 2.3 12.2 1.0
OD1 A:ASP41 2.4 8.8 1.0
OE1 A:GLN2 2.4 20.1 1.0
O A:VAL81 2.4 11.9 1.0
O A:ILE79 2.4 21.5 1.0
OD2 A:ASP41 3.0 15.1 1.0
CG A:ASP41 3.1 15.8 1.0
CG A:ASN77 3.4 18.0 1.0
C A:LEU75 3.5 12.1 1.0
CD A:GLN2 3.5 9.2 1.0
C A:VAL81 3.6 12.9 1.0
C A:ILE79 3.7 22.4 1.0
N A:ASN77 3.8 18.2 1.0
CG A:GLN2 3.9 13.2 1.0
N A:VAL81 4.0 15.7 1.0
ND2 A:ASN77 4.0 16.3 1.0
C A:GLY80 4.2 15.9 1.0
CA A:LEU75 4.3 10.3 1.0
N A:ASP76 4.4 11.2 1.0
N A:LEU75 4.4 11.1 1.0
CA A:VAL81 4.4 13.7 1.0
CA A:ASP76 4.5 14.5 1.0
CA A:GLY80 4.5 16.9 1.0
N A:ILE79 4.5 18.5 1.0
N A:LEU82 4.5 10.7 1.0
N A:GLY80 4.5 20.9 1.0
CB A:ASP41 4.5 12.6 1.0
CB A:ASN77 4.6 15.7 1.0
CA A:ASN77 4.6 18.1 1.0
C A:ASP76 4.6 15.7 1.0
CB A:LEU75 4.6 10.6 1.0
NE2 A:GLN2 4.6 12.6 1.0
CA A:LEU82 4.7 11.7 1.0
CA A:ILE79 4.7 21.4 1.0
CG1 A:ILE79 4.7 21.4 1.0
C A:ASN77 4.7 19.4 1.0
O A:GLY80 4.7 12.7 1.0
O A:ASN77 4.8 20.4 1.0
C A:ALA74 4.8 14.6 1.0
CB A:GLN2 4.8 15.8 1.0

Calcium binding site 2 out of 2 in 1yja

Go back to Calcium Binding Sites List in 1yja
Calcium binding site 2 out of 2 in the Subtilisin Bpn' 8397+1 (E.C. 3.4.21.14) (Mutant with Met 50 Replaced By Phe, Asn 76 Replaced By Asp, Gly 169 Replaced By Ala, Gln 206 Replaced By Cys, Asn 218 Replaced By Ser and Lys 256 Replaced By Tyr) (M50F, N76D, G169A, Q206C, N218S, and K256Y) in 20% Dimethylformamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Subtilisin Bpn' 8397+1 (E.C. 3.4.21.14) (Mutant with Met 50 Replaced By Phe, Asn 76 Replaced By Asp, Gly 169 Replaced By Ala, Gln 206 Replaced By Cys, Asn 218 Replaced By Ser and Lys 256 Replaced By Tyr) (M50F, N76D, G169A, Q206C, N218S, and K256Y) in 20% Dimethylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca291

b:23.6
occ:1.00
 O A:ALA169 2.2 10.7 1.0
O A:VAL174 2.2 10.3 1.0
O A:HOH350 2.3 21.9 1.0
O A:TYR171 2.4 17.2 1.0
C A:VAL174 3.3 11.1 1.0
C A:ALA169 3.4 12.1 1.0
C A:TYR171 3.4 13.1 1.0
C A:LYS170 3.9 14.7 1.0
CB A:VAL174 3.9 10.5 1.0
N A:TYR171 3.9 14.5 1.0
CA A:VAL174 4.0 10.2 1.0
OD2 A:ASP197 4.0 12.7 1.0
N A:ALA176 4.1 8.8 1.0
CB A:ALA176 4.1 6.9 1.0
O A:GLU195 4.1 17.0 1.0
N A:VAL174 4.1 13.7 1.0
O A:LYS170 4.2 18.8 1.0
CA A:PRO172 4.2 9.8 1.0
N A:PRO172 4.2 10.9 1.0
O A:PRO172 4.2 16.0 1.0
N A:LYS170 4.2 11.6 1.0
C A:PRO172 4.3 9.6 1.0
CA A:LYS170 4.3 11.8 1.0
CA A:TYR171 4.3 11.2 1.0
CA A:ALA169 4.3 7.3 1.0
N A:ILE175 4.4 10.8 1.0
C A:ILE175 4.5 9.6 1.0
NH2 A:ARG247 4.6 11.5 1.0
CA A:ALA176 4.6 6.5 1.0
CA A:ILE175 4.6 7.4 1.0
CG1 A:VAL174 4.7 6.4 1.0
O A:PRO168 4.7 11.7 1.0
N A:SER173 4.9 11.8 1.0
CB A:GLU195 4.9 14.6 1.0
CG2 A:VAL174 5.0 11.6 1.0

Reference:

R.D.Kidd, P.Sears, D.H.Huang, K.Witte, C.H.Wong, G.K.Farber. Breaking the Low Barrier Hydrogen Bond in A Serine Protease. Protein Sci. V. 8 410 1999.
ISSN: ISSN 0961-8368
PubMed: 10048334
Page generated: Fri Jul 12 08:06:03 2024

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