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Calcium in PDB 5x7h: Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltoheptaose

Enzymatic activity of Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltoheptaose

All present enzymatic activity of Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltoheptaose:
2.4.1.248;

Protein crystallography data

The structure of Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltoheptaose, PDB code: 5x7h was solved by Z.Fujimoto, N.Kishine, N.Suzuki, R.Suzuki, M.Momma, K.Funane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.73 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.844, 112.844, 122.275, 90.00, 90.00, 120.00
R / Rfree (%) 15.5 / 21.5

Other elements in 5x7h:

The structure of Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltoheptaose also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltoheptaose (pdb code 5x7h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltoheptaose, PDB code: 5x7h:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5x7h

Go back to Calcium Binding Sites List in 5x7h
Calcium binding site 1 out of 2 in the Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltoheptaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltoheptaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:56.9
occ:1.00
 OD1 A:ASP542 2.3 44.4 1.0
OE1 A:GLU425 2.3 38.7 1.0
OE2 A:GLU427 2.4 48.5 1.0
O A:GLY447 2.4 61.7 1.0
O A:THR444 2.4 41.5 1.0
O A:ASP542 2.8 37.5 1.0
OE1 A:GLU427 3.0 56.8 1.0
CD A:GLU427 3.1 60.9 1.0
CG A:ASP542 3.3 45.4 1.0
CD A:GLU425 3.4 36.1 1.0
C A:GLY447 3.6 57.5 1.0
C A:ASP542 3.6 36.5 1.0
C A:THR444 3.6 42.7 1.0
CA A:ASP542 3.8 40.1 1.0
N A:THR444 3.9 39.0 1.0
CB A:GLU425 4.1 38.1 1.0
OE2 A:GLU425 4.1 34.2 1.0
OG1 A:THR444 4.1 28.6 1.0
OD2 A:ASP542 4.1 48.9 1.0
CB A:ASP542 4.2 40.0 1.0
CA A:PHE448 4.2 51.6 1.0
CG A:GLU425 4.2 35.8 1.0
CA A:THR444 4.3 39.5 1.0
N A:PHE448 4.3 53.3 1.0
CB A:TYR443 4.4 46.0 1.0
N A:ALA426 4.4 50.7 1.0
N A:GLY447 4.5 61.9 1.0
CB A:PHE448 4.5 52.6 1.0
CG A:GLU427 4.6 59.3 1.0
N A:GLY445 4.6 43.5 1.0
CA A:GLY447 4.6 61.8 1.0
CA A:GLU425 4.6 41.9 1.0
N A:SER543 4.7 38.1 1.0
CA A:GLY445 4.8 46.6 1.0
CB A:THR444 4.9 36.1 1.0
CB A:SER543 4.9 35.6 1.0
C A:TYR443 4.9 39.9 1.0
N A:GLU427 4.9 55.9 1.0
C A:GLU425 5.0 44.5 1.0

Calcium binding site 2 out of 2 in 5x7h

Go back to Calcium Binding Sites List in 5x7h
Calcium binding site 2 out of 2 in the Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltoheptaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltoheptaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:60.5
occ:1.00
 O A:HOH1042 2.3 27.7 1.0
OD1 A:ASP665 2.4 27.1 1.0
O A:HOH994 2.5 25.4 1.0
O A:GLN667 2.5 38.1 1.0
O A:HOH1000 2.5 28.7 1.0
C A:GLN667 3.6 32.9 1.0
CG A:ASP665 3.6 28.8 1.0
O A:HOH956 3.8 25.9 1.0
OH A:TYR389 4.0 29.4 1.0
N A:GLN667 4.0 31.2 1.0
O A:ASN670 4.0 30.0 1.0
O A:ASP665 4.1 29.5 1.0
CA A:GLN667 4.2 31.9 1.0
OD2 A:ASP665 4.2 29.1 1.0
CB A:GLN667 4.2 33.8 1.0
C A:ASP665 4.3 29.7 1.0
N A:ASP665 4.3 28.2 1.0
CB A:ALA672 4.5 26.8 1.0
O A:HOH928 4.5 25.0 1.0
CA A:ASP665 4.7 29.6 1.0
N A:TRP668 4.7 32.2 1.0
CB A:ASP665 4.7 28.7 1.0
CZ A:TYR389 4.7 30.4 1.0
O A:SER671 4.8 28.6 1.0
CB A:ASN664 4.8 28.5 1.0
CE2 A:TYR389 4.8 30.2 1.0
N A:ASN666 4.9 32.3 1.0
C A:ASN670 5.0 30.1 1.0
CA A:TRP668 5.0 31.5 1.0

Reference:

Z.Fujimoto, N.Kishine, N.Suzuki, R.Suzuki, D.Mizushima, M.Momma, K.Kimura, K.Funane. Isomaltooligosaccharide-Binding Structure Ofpaenibacillussp. 598K Cycloisomaltooligosaccharide Glucanotransferase Biosci. Rep. V. 37 2017.
ISSN: ISSN 1573-4935
PubMed: 28385816
DOI: 10.1042/BSR20170253
Page generated: Mon Jul 15 14:46:13 2024

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