Atomistry » Calcium » PDB 3whi-3ws5 » 3wnp
Atomistry »
  Calcium »
    PDB 3whi-3ws5 »
      3wnp »

Calcium in PDB 3wnp: D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose

Enzymatic activity of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose

All present enzymatic activity of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose:
2.4.1.248;

Protein crystallography data

The structure of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose, PDB code: 3wnp was solved by R.Suzuki, N.Suzuki, Z.Fujimoto, M.Momma, K.Kimura, S.Kitamura, A.Kimura, K.Funane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.85 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.987, 172.813, 172.305, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.3

Other elements in 3wnp:

The structure of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose (pdb code 3wnp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose, PDB code: 3wnp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3wnp

Go back to Calcium Binding Sites List in 3wnp
Calcium binding site 1 out of 2 in the D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:67.7
occ:1.00
 O A:GLY446 2.3 67.2 1.0
OD1 A:ASP541 2.4 75.0 1.0
OE1 A:GLU424 2.5 66.3 1.0
O A:ASP541 2.6 56.4 1.0
OE1 A:GLU426 2.6 66.5 1.0
O A:THR443 2.6 59.9 1.0
OE2 A:GLU426 2.9 66.5 1.0
CD A:GLU426 3.1 66.9 1.0
CG A:ASP541 3.3 69.2 1.0
C A:ASP541 3.5 56.6 1.0
C A:GLY446 3.5 66.1 1.0
CD A:GLU424 3.7 69.5 1.0
C A:THR443 3.7 77.3 1.0
CA A:ASP541 3.8 59.9 1.0
OG1 A:THR443 3.9 77.5 1.0
OD2 A:ASP541 4.1 68.8 1.0
N A:THR443 4.1 75.9 1.0
CB A:ASP541 4.2 62.2 1.0
CA A:PHE447 4.3 65.8 1.0
N A:PHE447 4.4 61.9 1.0
N A:GLY446 4.4 73.9 1.0
CA A:THR443 4.4 78.3 1.0
OE2 A:GLU424 4.4 65.0 1.0
N A:ALA425 4.4 58.2 1.0
CA A:GLY446 4.5 67.7 1.0
CB A:GLU424 4.6 62.6 1.0
CG A:GLU426 4.6 66.7 1.0
CG A:GLU424 4.6 67.3 1.0
CB A:PHE447 4.6 67.3 1.0
N A:GLY444 4.7 71.5 1.0
N A:SER542 4.7 54.4 1.0
CA A:GLU424 4.8 57.8 1.0
CB A:THR443 4.8 81.2 1.0
CB A:SER542 4.9 58.7 1.0
CB A:TYR442 4.9 74.2 1.0
N A:GLU426 5.0 64.2 1.0
CD1 A:TYR442 5.0 72.8 1.0

Calcium binding site 2 out of 2 in 3wnp

Go back to Calcium Binding Sites List in 3wnp
Calcium binding site 2 out of 2 in the D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:67.3
occ:1.00
 OD1 B:ASP541 2.3 74.4 1.0
O B:GLY446 2.3 59.2 1.0
OE1 B:GLU424 2.5 66.7 1.0
O B:ASP541 2.5 56.1 1.0
OE1 B:GLU426 2.6 64.8 1.0
O B:THR443 2.7 73.1 1.0
OE2 B:GLU426 2.8 66.7 1.0
CD B:GLU426 3.1 69.2 1.0
CG B:ASP541 3.3 69.3 1.0
C B:GLY446 3.5 67.2 1.0
C B:ASP541 3.5 56.7 1.0
OG1 B:THR443 3.6 83.8 1.0
CD B:GLU424 3.7 72.3 1.0
C B:THR443 3.7 80.9 1.0
CA B:ASP541 3.9 63.1 1.0
OD2 B:ASP541 4.0 73.0 1.0
N B:THR443 4.2 78.8 1.0
CB B:ASP541 4.2 58.8 1.0
CA B:PHE447 4.3 68.4 1.0
N B:PHE447 4.3 62.3 1.0
CA B:THR443 4.3 84.7 1.0
N B:ALA425 4.4 56.3 1.0
N B:GLY446 4.4 72.8 1.0
OE2 B:GLU424 4.4 64.7 1.0
CB B:GLU424 4.4 64.5 1.0
CA B:GLY446 4.5 68.7 1.0
CG B:GLU424 4.6 68.1 1.0
CG B:GLU426 4.6 71.6 1.0
CB B:PHE447 4.6 74.2 1.0
CB B:THR443 4.6 86.9 1.0
CA B:GLU424 4.6 60.8 1.0
N B:SER542 4.7 50.8 1.0
N B:GLY444 4.7 77.3 1.0
CB B:SER542 4.8 60.0 1.0
CB B:TYR442 4.9 79.5 1.0
N B:GLU426 5.0 66.0 1.0
CA B:GLY444 5.0 69.1 1.0

Reference:

N.Suzuki, Z.Fujimoto, Y.M.Kim, M.Momma, N.Kishine, R.Suzuki, S.Suzuki, S.Kitamura, M.Kobayashi, A.Kimura, K.Funane. Structural Elucidation of Cyclization Mechanism of Alpha-1,6-Glucan By Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase To Be Published.
Page generated: Sat Jul 13 21:15:59 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy