Calcium in PDB 6int: Xylose Isomerase From Paenibacillus Sp. R4

The structure of Xylose Isomerase From Paenibacillus Sp. R4, PDB code: 6int was solved by J.H.Lee, C.W.Lee, S.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.83 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.282, 124.039, 315.001, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Calcium atom in the Xylose Isomerase From Paenibacillus Sp. R4 (pdb code 6int). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 24 binding sites of Calcium where determined in the Xylose Isomerase From Paenibacillus Sp. R4, PDB code: 6int:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 24 in the Xylose Isomerase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xylose Isomerase From Paenibacillus Sp. R4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:16.3 occ:1.00 O A:HOH744 2.3 14.8 1.0 O A:GLY191 2.3 15.0 1.0 O A:HOH813 2.4 14.6 1.0 O A:HOH692 2.5 11.1 1.0 O A:HOH665 2.5 15.8 1.0 OE1 A:GLU203 2.5 11.0 1.0 OE2 A:GLU203 2.6 14.8 1.0 CD A:GLU203 2.9 17.4 1.0 C A:GLY191 3.5 15.8 1.0 O A:THR154 3.9 13.4 1.0 O A:HIS150 3.9 15.6 1.0 CA A:TYR192 4.1 14.6 1.0 OH A:TYR241 4.1 13.6 1.0 N A:TYR192 4.3 14.2 1.0 O A:HOH767 4.4 26.7 1.0 CG A:GLU203 4.4 16.8 1.0 O A:HOH724 4.4 17.8 1.0 CB A:TYR192 4.4 13.6 1.0 N A:GLY191 4.5 14.7 1.0 OG1 A:THR154 4.6 15.8 1.0 OH B:TYR386 4.6 16.8 1.0 CA A:GLY191 4.6 13.8 1.0 CB A:THR154 4.8 13.7 1.0 OG1 A:THR198 4.8 15.3 1.0 CE2 A:TYR241 4.9 14.1 1.0 C A:THR154 4.9 14.6 1.0 CZ A:TYR241 4.9 15.5 1.0 O A:HOH672 4.9 11.9 1.0 CG2 A:THR198 5.0 15.6 1.0

Calcium binding site 2 out of 24 in the Xylose Isomerase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xylose Isomerase From Paenibacillus Sp. R4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:17.4 occ:1.00 OE2 A:GLU230 2.2 22.4 1.0 OD2 A:ASP294 2.3 17.6 1.0 OD2 A:ASP338 2.3 21.0 1.0 OE1 A:GLU266 2.3 19.6 1.0 O A:HOH752 2.3 20.9 1.0 O A:HOH800 2.5 27.3 1.0 CD A:GLU230 2.9 18.1 1.0 OE1 A:GLU230 2.9 20.1 1.0 CG A:ASP338 3.4 17.4 1.0 CG A:ASP294 3.4 16.7 1.0 CD A:GLU266 3.5 19.2 1.0 O A:HOH788 3.8 23.1 1.0 CB A:ASP338 4.0 15.1 1.0 CB A:ASP294 4.0 13.9 1.0 O A:HOH797 4.3 29.5 1.0 CG A:GLU230 4.4 17.0 1.0 CG A:GLU266 4.4 14.6 1.0 OE2 A:GLU266 4.4 16.0 1.0 OD1 A:ASP294 4.4 21.8 1.0 ND2 A:ASN264 4.4 15.0 1.0 CB A:GLU266 4.4 13.0 1.0 OD1 A:ASP338 4.4 19.7 1.0 CE1 A:HIS269 4.7 17.9 1.0

Calcium binding site 3 out of 24 in the Xylose Isomerase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xylose Isomerase From Paenibacillus Sp. R4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:18.0 occ:1.00 OE2 A:GLU266 2.2 16.0 1.0 O A:HOH788 2.3 23.1 1.0 OD2 A:ASP305 2.3 24.9 1.0 OD1 A:ASP307 2.5 20.6 1.0 NE2 A:HIS269 2.6 13.0 1.0 OD1 A:ASP305 2.8 26.6 1.0 OD2 A:ASP307 2.8 25.3 1.0 CG A:ASP305 2.9 24.1 1.0 CG A:ASP307 3.0 17.6 1.0 CD A:GLU266 3.2 19.2 1.0 CD2 A:HIS269 3.3 12.5 1.0 OE1 A:GLU266 3.5 19.6 1.0 CE1 A:HIS269 3.6 17.9 1.0 CB A:ASP305 4.4 21.0 1.0 ND2 A:ASN296 4.4 12.0 1.0 CB A:ASP307 4.5 20.5 1.0 CE A:LYS232 4.5 19.3 1.0 CG A:GLU266 4.5 14.6 1.0 CG A:HIS269 4.5 11.1 1.0 O A:HOH752 4.5 20.9 1.0 O A:HOH619 4.6 29.6 1.0 ND1 A:HIS269 4.6 11.7 1.0 NZ A:LYS232 4.6 21.3 1.0 NZ A:LYS340 4.9 37.3 1.0 CB A:ASN268 4.9 11.2 1.0

Calcium binding site 4 out of 24 in the Xylose Isomerase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Xylose Isomerase From Paenibacillus Sp. R4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:19.3 occ:1.00 OE2 B:GLU266 2.2 18.4 1.0 OD2 B:ASP305 2.3 24.0 1.0 OD1 B:ASP307 2.4 23.2 1.0 O B:HOH763 2.5 28.1 1.0 NE2 B:HIS269 2.5 17.4 1.0 O B:HOH765 2.6 28.8 1.0 OD1 B:ASP305 2.7 27.0 1.0 CG B:ASP305 2.9 21.8 1.0 OD2 B:ASP307 3.0 27.8 1.0 CG B:ASP307 3.1 18.0 1.0 CD B:GLU266 3.1 19.9 1.0 CD2 B:HIS269 3.3 15.4 1.0 OE1 B:GLU266 3.4 20.2 1.0 CE1 B:HIS269 3.6 18.3 1.0 O B:HOH692 4.3 30.4 1.0 CB B:ASP305 4.3 21.9 1.0 ND2 B:ASN296 4.4 13.7 1.0 CG B:GLU266 4.5 15.0 1.0 CG B:HIS269 4.5 13.6 1.0 CB B:ASP307 4.5 18.3 1.0 O B:HOH721 4.6 23.6 1.0 CE B:LYS232 4.6 20.7 1.0 ND1 B:HIS269 4.6 13.7 1.0 NZ B:LYS232 4.6 23.4 1.0 CB B:ASN268 4.8 13.5 1.0 NZ B:LYS340 5.0 36.5 1.0

Calcium binding site 5 out of 24 in the Xylose Isomerase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Xylose Isomerase From Paenibacillus Sp. R4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:20.9 occ:1.00 OD2 B:ASP294 2.2 22.2 1.0 OD2 B:ASP338 2.2 27.1 1.0 O B:HOH721 2.3 23.6 1.0 OE1 B:GLU266 2.3 20.2 1.0 OE1 B:GLU230 2.4 26.5 1.0 OE2 B:GLU230 2.8 25.3 1.0 CD B:GLU230 2.9 19.8 1.0 CG B:ASP294 3.4 16.3 1.0 CG B:ASP338 3.4 20.5 1.0 CD B:GLU266 3.5 19.9 1.0 O B:HOH765 3.9 28.8 1.0 CB B:ASP338 4.0 18.2 1.0 CB B:ASP294 4.0 15.5 1.0 O B:HOH712 4.1 34.1 1.0 CG B:GLU266 4.3 15.0 1.0 CG B:GLU230 4.4 18.8 1.0 CB B:GLU266 4.4 15.2 1.0 OE2 B:GLU266 4.4 18.4 1.0 OD1 B:ASP294 4.4 22.5 1.0 OD1 B:ASP338 4.4 21.0 1.0 O B:HOH763 4.5 28.1 1.0 ND2 B:ASN264 4.5 18.2 1.0 CE1 B:HIS269 4.7 18.3 1.0

Calcium binding site 6 out of 24 in the Xylose Isomerase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Xylose Isomerase From Paenibacillus Sp. R4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:16.8 occ:1.00 O B:HOH736 2.2 16.0 1.0 O B:HOH660 2.3 16.7 1.0 O B:GLY191 2.4 14.1 1.0 O B:HOH639 2.4 14.7 1.0 O B:HOH793 2.4 13.4 1.0 OE1 B:GLU203 2.5 13.1 1.0 OE2 B:GLU203 2.6 16.9 1.0 CD B:GLU203 2.9 16.4 1.0 C B:GLY191 3.6 14.8 1.0 O B:THR154 3.9 16.4 1.0 O B:HIS150 3.9 17.9 1.0 CA B:TYR192 4.1 16.2 1.0 OH B:TYR241 4.2 14.6 1.0 N B:TYR192 4.4 16.5 1.0 CG B:GLU203 4.4 18.0 1.0 O B:HOH770 4.4 29.5 1.0 OG1 B:THR154 4.4 16.7 1.0 CB B:TYR192 4.5 13.2 1.0 N B:GLY191 4.5 15.7 1.0 OH A:TYR386 4.6 18.3 1.0 CA B:GLY191 4.6 15.5 1.0 CE2 B:TYR241 4.8 15.5 1.0 CB B:THR154 4.8 18.6 1.0 C B:THR154 4.9 18.1 1.0 CZ B:TYR241 4.9 15.3 1.0 OG1 B:THR198 4.9 19.9 1.0 O B:HOH662 4.9 11.4 1.0 CG2 B:THR198 5.0 17.8 1.0 C B:HIS150 5.0 19.2 1.0

Calcium binding site 7 out of 24 in the Xylose Isomerase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Xylose Isomerase From Paenibacillus Sp. R4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:17.6 occ:1.00 OD2 C:ASP338 2.2 24.9 1.0 OE1 C:GLU266 2.2 13.9 1.0 OD2 C:ASP294 2.2 19.3 1.0 O C:HOH613 2.3 32.8 1.0 O C:HOH682 2.4 23.4 1.0 OE1 C:GLU230 2.4 20.6 1.0 OE2 C:GLU230 2.8 21.5 1.0 CD C:GLU230 2.9 14.6 1.0 CG C:ASP338 3.4 22.6 1.0 CG C:ASP294 3.4 18.2 1.0 CD C:GLU266 3.4 14.7 1.0 O C:HOH788 4.0 26.3 1.0 CB C:ASP338 4.0 19.9 1.0 CB C:ASP294 4.0 17.8 1.0 OE2 C:GLU266 4.2 14.3 1.0 CG C:GLU266 4.3 12.4 1.0 CG C:GLU230 4.4 13.8 1.0 CB C:GLU266 4.4 13.2 1.0 OD1 C:ASP338 4.4 21.2 1.0 OD1 C:ASP294 4.4 18.8 1.0 ND2 C:ASN264 4.5 14.6 1.0 O C:HOH811 4.5 23.4 1.0 CE1 C:HIS269 4.6 12.9 1.0 O C:HOH623 4.8 35.0 1.0

Calcium binding site 8 out of 24 in the Xylose Isomerase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Xylose Isomerase From Paenibacillus Sp. R4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:15.6 occ:1.00 OE2 C:GLU266 2.1 14.3 1.0 O C:HOH811 2.3 23.4 1.0 OD1 C:ASP307 2.3 20.7 1.0 O C:HOH788 2.5 26.3 1.0 OD2 C:ASP305 2.5 21.9 1.0 NE2 C:HIS269 2.6 11.3 1.0 OD1 C:ASP305 2.7 25.1 1.0 OD2 C:ASP307 2.9 27.2 1.0 CG C:ASP305 2.9 23.1 1.0 CG C:ASP307 3.0 18.3 1.0 CD C:GLU266 3.2 14.7 1.0 CD2 C:HIS269 3.3 11.9 1.0 OE1 C:GLU266 3.6 13.9 1.0 CE1 C:HIS269 3.6 12.9 1.0 ND2 C:ASN296 4.4 14.2 1.0 CB C:ASP307 4.4 19.6 1.0 CG C:GLU266 4.4 12.4 1.0 CB C:ASP305 4.4 19.6 1.0 CE C:LYS232 4.5 13.5 1.0 CG C:HIS269 4.5 11.2 1.0 O C:HOH682 4.6 23.4 1.0 ND1 C:HIS269 4.6 9.9 1.0 NZ C:LYS232 4.6 17.9 1.0 CB C:ASN268 4.8 10.7 1.0 NZ C:LYS340 5.0 30.5 1.0

Calcium binding site 9 out of 24 in the Xylose Isomerase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Xylose Isomerase From Paenibacillus Sp. R4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:11.1 occ:1.00 O C:GLY191 2.4 11.7 1.0 O C:HOH663 2.4 11.7 1.0 O C:HOH830 2.4 9.8 1.0 O C:HOH649 2.4 9.8 1.0 O C:HOH693 2.4 10.3 1.0 OE2 C:GLU203 2.5 12.8 1.0 OE1 C:GLU203 2.5 8.6 1.0 CD C:GLU203 2.9 12.3 1.0 C C:GLY191 3.6 11.1 1.0 O C:THR154 3.9 9.5 1.0 O C:HIS150 4.0 13.5 1.0 CA C:TYR192 4.0 13.3 1.0 OH C:TYR241 4.1 11.1 1.0 O C:HOH801 4.2 23.1 1.0 N C:TYR192 4.3 11.1 1.0 CB C:TYR192 4.3 10.1 1.0 CG C:GLU203 4.4 10.9 1.0 O D:HOH723 4.4 17.8 1.0 OG1 C:THR154 4.5 10.3 1.0 N C:GLY191 4.5 10.5 1.0 OH D:TYR386 4.5 13.3 1.0 CA C:GLY191 4.6 10.9 1.0 CB C:THR154 4.8 10.3 1.0 CE2 C:TYR241 4.9 10.5 1.0 OG1 C:THR198 4.9 10.8 1.0 CZ C:TYR241 4.9 13.5 1.0 O C:HOH723 4.9 10.5 1.0 C C:THR154 4.9 10.5 1.0 NH2 D:ARG385 4.9 23.9 1.0 CG2 C:THR198 5.0 12.7 1.0

Calcium binding site 10 out of 24 in the Xylose Isomerase From Paenibacillus Sp. R4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Xylose Isomerase From Paenibacillus Sp. R4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:15.3 occ:1.00 OD2 D:ASP305 2.1 21.7 1.0 OE2 D:GLU266 2.2 14.6 1.0 O D:HOH805 2.3 24.7 1.0 O D:HOH831 2.5 27.1 1.0 OD1 D:ASP307 2.5 21.2 1.0 NE2 D:HIS269 2.6 10.8 1.0 OD2 D:ASP307 2.7 25.8 1.0 CG D:ASP305 2.8 22.7 1.0 OD1 D:ASP305 2.9 27.5 1.0 CG D:ASP307 3.0 16.6 1.0 CD D:GLU266 3.2 15.7 1.0 CD2 D:HIS269 3.4 10.7 1.0 CE1 D:HIS269 3.6 11.5 1.0 OE1 D:GLU266 3.6 17.1 1.0 CB D:ASP305 4.3 21.0 1.0 ND2 D:ASN296 4.4 8.1 1.0 CB D:ASP307 4.5 16.2 1.0 CG D:GLU266 4.5 13.5 1.0 CE D:LYS232 4.5 17.0 1.0 CG D:HIS269 4.5 9.5 1.0 O D:HOH736 4.6 20.2 1.0 NZ D:LYS232 4.6 18.8 1.0 ND1 D:HIS269 4.6 8.3 1.0 O D:HOH607 4.7 27.2 1.0 CB D:ASN268 5.0 10.3 1.0

S.H.Park, S.Kwon, C.W.Lee, C.M.Kim, C.S.Jeong, K.J.Kim, J.W.Hong, H.J.Kim, H.H.Park, J.H.Lee. Crystal Structure and Functional Characterization of A Xylose Isomerase (Pbxi) From the Psychrophilic Soil Microorganism, Paenibacillus Sp. J. Microbiol. Biotechnol. V. 29 244 2019.
ISSN: ESSN 1738-8872
PubMed: 30602271
DOI: 10.4014/JMB.1810.10057