Calcium in PDB 5x7g: Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase

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

The structure of Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase, PDB code: 5x7g 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)	98.45 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.680, 113.680, 121.635, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 22.2

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

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase (pdb code 5x7g). 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, PDB code: 5x7g:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:76.8 occ:1.00 OE1 A:GLU425 2.3 47.8 1.0 OD1 A:ASP542 2.4 51.1 1.0 O A:THR444 2.5 43.3 1.0 O A:GLY447 2.6 53.3 1.0 OE2 A:GLU427 2.7 55.7 1.0 O A:ASP542 2.9 46.2 1.0 OE1 A:GLU427 3.3 66.3 1.0 CD A:GLU427 3.3 64.0 1.0 CG A:ASP542 3.3 49.5 1.0 CD A:GLU425 3.4 50.2 1.0 C A:THR444 3.5 44.5 1.0 C A:ASP542 3.7 44.6 1.0 C A:GLY447 3.7 57.7 1.0 OG1 A:THR444 3.8 46.0 1.0 CA A:ASP542 3.9 44.0 1.0 N A:THR444 3.9 44.7 1.0 OD2 A:ASP542 4.0 46.5 1.0 OE2 A:GLU425 4.0 46.6 1.0 CB A:ASP542 4.2 46.0 1.0 CA A:THR444 4.3 44.1 1.0 CB A:GLU425 4.4 47.3 1.0 CA A:PHE448 4.4 53.0 1.0 CG A:GLU425 4.4 45.1 1.0 N A:GLY445 4.5 46.6 1.0 N A:PHE448 4.5 51.0 1.0 N A:ALA426 4.5 49.9 1.0 N A:GLY447 4.5 63.3 1.0 CB A:TYR443 4.5 48.1 1.0 CB A:PHE448 4.6 53.4 1.0 CA A:GLY445 4.7 48.8 1.0 CB A:THR444 4.7 42.9 1.0 CA A:GLY447 4.7 59.0 1.0 CA A:GLU425 4.7 45.6 1.0 CG A:GLU427 4.8 62.6 1.0 N A:SER543 4.8 44.5 1.0 CD1 A:TYR443 4.9 54.2 1.0 CB A:SER543 5.0 41.2 1.0 C A:TYR443 5.0 48.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Paenibacillus Sp. 598K Cycloisomaltooligosaccharide Glucanotransferase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:57.7 occ:1.00 O A:HOH947 2.3 27.4 1.0 O A:HOH968 2.4 29.0 1.0 O A:GLN667 2.4 31.7 1.0 OD1 A:ASP665 2.4 35.6 1.0 O A:HOH941 2.6 30.2 1.0 C A:GLN667 3.5 33.9 1.0 CG A:ASP665 3.6 34.8 1.0 O A:HOH1092 3.8 35.9 1.0 N A:GLN667 3.9 32.0 1.0 O A:ASN670 3.9 33.0 1.0 OH A:TYR389 4.0 31.2 1.0 CA A:GLN667 4.1 33.9 1.0 O A:ASP665 4.1 33.4 1.0 OD2 A:ASP665 4.2 36.9 1.0 CB A:GLN667 4.3 35.6 1.0 C A:ASP665 4.3 33.0 1.0 N A:ASP665 4.4 31.0 1.0 O A:HOH919 4.6 28.8 1.0 N A:TRP668 4.6 31.1 1.0 CB A:ALA672 4.7 32.5 1.0 CA A:ASP665 4.7 30.4 1.0 CB A:ASP665 4.7 32.8 1.0 CZ A:TYR389 4.8 30.6 1.0 O A:SER671 4.8 32.5 1.0 C A:ASN670 4.9 33.2 1.0 N A:ASN666 4.9 34.0 1.0 CE2 A:TYR389 4.9 32.7 1.0 CA A:TRP668 4.9 32.7 1.0 CB A:ASN664 4.9 31.2 1.0 C A:ASN666 4.9 33.1 1.0 N A:ASN670 4.9 31.8 1.0 C A:TRP668 5.0 32.9 1.0

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