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Calcium in PDB 2dij: Complex of A Y195F Mutant Cgtase From B. Circulans Strain 251 Complexed with A Maltononaose Inhibitor at pH 9.8 Obtained After Soaking the Crystal with Acarbose and Maltohexaose

Enzymatic activity of Complex of A Y195F Mutant Cgtase From B. Circulans Strain 251 Complexed with A Maltononaose Inhibitor at pH 9.8 Obtained After Soaking the Crystal with Acarbose and Maltohexaose

All present enzymatic activity of Complex of A Y195F Mutant Cgtase From B. Circulans Strain 251 Complexed with A Maltononaose Inhibitor at pH 9.8 Obtained After Soaking the Crystal with Acarbose and Maltohexaose:
2.4.1.19;

Protein crystallography data

The structure of Complex of A Y195F Mutant Cgtase From B. Circulans Strain 251 Complexed with A Maltononaose Inhibitor at pH 9.8 Obtained After Soaking the Crystal with Acarbose and Maltohexaose, PDB code: 2dij was solved by B.V.Strokopytov, R.M.A.Knegtel, J.C.M.Uitdehaag, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119.964, 111.282, 67.977, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 21.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of A Y195F Mutant Cgtase From B. Circulans Strain 251 Complexed with A Maltononaose Inhibitor at pH 9.8 Obtained After Soaking the Crystal with Acarbose and Maltohexaose (pdb code 2dij). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Complex of A Y195F Mutant Cgtase From B. Circulans Strain 251 Complexed with A Maltononaose Inhibitor at pH 9.8 Obtained After Soaking the Crystal with Acarbose and Maltohexaose, PDB code: 2dij:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2dij

Go back to Calcium Binding Sites List in 2dij
Calcium binding site 1 out of 2 in the Complex of A Y195F Mutant Cgtase From B. Circulans Strain 251 Complexed with A Maltononaose Inhibitor at pH 9.8 Obtained After Soaking the Crystal with Acarbose and Maltohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of A Y195F Mutant Cgtase From B. Circulans Strain 251 Complexed with A Maltononaose Inhibitor at pH 9.8 Obtained After Soaking the Crystal with Acarbose and Maltohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca688

b:27.5
occ:1.00
 OD1 A:ASN33 2.0 32.8 1.0
OD2 A:ASP53 2.3 34.7 1.0
OD1 A:ASN32 2.3 24.3 1.0
OD1 A:ASP27 2.4 28.4 1.0
O A:HOH764 2.4 23.2 1.0
O A:ASN29 2.5 29.6 1.0
O A:GLY51 2.8 26.4 1.0
CG A:ASP27 3.2 24.6 1.0
C A:ASN29 3.2 30.2 1.0
CG A:ASN33 3.3 34.9 1.0
CG A:ASP53 3.4 33.6 1.0
CG A:ASN32 3.4 30.0 1.0
C A:GLY51 3.8 27.5 1.0
CB A:ASP53 3.8 20.7 1.0
OD2 A:ASP27 3.8 20.4 1.0
N A:PRO30 3.9 30.1 1.0
N A:ASN33 3.9 28.2 1.0
CA A:PRO30 4.0 30.9 1.0
ND2 A:ASN32 4.0 22.3 1.0
ND2 A:ASN33 4.0 23.9 1.0
N A:ASN29 4.1 26.6 1.0
CA A:ASN29 4.1 25.5 1.0
CA A:GLY51 4.2 22.6 1.0
CB A:ASP27 4.2 20.6 1.0
CA A:ASN33 4.3 27.6 1.0
C A:ASN32 4.3 32.3 1.0
CB A:ASN33 4.4 21.8 1.0
O A:ALA111 4.4 27.6 1.0
OD1 A:ASP53 4.4 32.4 1.0
C A:PRO30 4.5 33.7 1.0
CA A:ASP27 4.5 20.9 1.0
N A:ASN32 4.5 31.9 1.0
CB A:ASN29 4.6 24.8 1.0
CB A:ASN32 4.6 22.9 1.0
CA A:ASN32 4.7 29.9 1.0
N A:ASP53 4.8 16.9 1.0
C A:GLY52 4.8 21.8 1.0
C A:ASP27 4.8 28.6 1.0
O A:PRO30 4.8 34.8 1.0
N A:GLY52 4.9 24.0 1.0
CA A:ASP53 4.9 17.3 1.0
O A:ASN32 4.9 31.1 1.0
O A:GLY52 5.0 19.4 1.0
N A:GLY28 5.0 26.5 1.0

Calcium binding site 2 out of 2 in 2dij

Go back to Calcium Binding Sites List in 2dij
Calcium binding site 2 out of 2 in the Complex of A Y195F Mutant Cgtase From B. Circulans Strain 251 Complexed with A Maltononaose Inhibitor at pH 9.8 Obtained After Soaking the Crystal with Acarbose and Maltohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of A Y195F Mutant Cgtase From B. Circulans Strain 251 Complexed with A Maltononaose Inhibitor at pH 9.8 Obtained After Soaking the Crystal with Acarbose and Maltohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca689

b:21.8
occ:1.00
 O A:HOH750 2.3 22.6 1.0
O A:HOH779 2.4 17.5 1.0
OD1 A:ASN139 2.5 13.0 1.0
OD1 A:ASP199 2.5 22.5 1.0
OD2 A:ASP199 2.5 31.3 1.0
O A:ILE190 2.6 24.6 1.0
O A:HIS233 2.6 19.7 1.0
CG A:ASP199 2.8 25.0 1.0
CG A:ASN139 3.6 23.8 1.0
C A:ILE190 3.7 24.2 1.0
C A:HIS233 3.8 20.9 1.0
CB A:ASP199 4.3 16.4 1.0
ND2 A:ASN139 4.3 15.3 1.0
O A:HOH754 4.4 26.8 1.0
CA A:ILE190 4.4 17.6 1.0
O A:LYS192 4.4 30.2 1.0
O A:ASN139 4.4 18.1 1.0
CB A:HIS233 4.5 15.1 1.0
ND1 A:HIS176 4.6 27.8 1.0
O A:LEU200 4.6 22.2 1.0
CA A:MET234 4.6 17.1 1.0
CG A:MET234 4.6 22.8 1.0
N A:MET234 4.7 18.2 1.0
CA A:HIS233 4.7 15.2 1.0
O A:GLY189 4.7 26.3 1.0
CB A:ASN139 4.8 15.5 1.0
N A:TYR191 4.8 20.6 1.0
CG2 A:ILE190 4.8 16.3 1.0
CE1 A:HIS176 4.9 26.8 1.0
O A:HOH737 4.9 19.1 1.0

Reference:

B.Strokopytov, R.M.Knegtel, D.Penninga, H.J.Rozeboom, K.H.Kalk, L.Dijkhuizen, B.W.Dijkstra. Structure of Cyclodextrin Glycosyltransferase Complexed with A Maltononaose Inhibitor at 2.6 Angstrom Resolution. Implications For Product Specificity. Biochemistry V. 35 4241 1996.
ISSN: ISSN 0006-2960
PubMed: 8672460
DOI: 10.1021/BI952339H
Page generated: Sat Dec 12 03:35:11 2020

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