Calcium in PDB 4hpn: Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Ordered Loops

The structure of Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Ordered Loops, PDB code: 4hpn was solved by M.W.Vetting, J.T.Bouvier, L.L.Morisco, S.R.Wasserman, S.Sojitra, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.69 / 1.60
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	121.145, 121.145, 128.446, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 16.1

The structure of Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Ordered Loops also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Calcium atom in the Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Ordered Loops (pdb code 4hpn). 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 A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Ordered Loops, PDB code: 4hpn:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Ordered Loops


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 A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Ordered Loops within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:10.7 occ:1.00 OD2 A:ASP194 2.2 11.7 1.0 OE1 A:GLU246 2.2 15.6 1.0 O A:HOH517 2.3 11.9 1.0 O A:HOH606 2.3 17.8 1.0 OE2 A:GLU220 2.3 13.8 1.0 O A:HOH630 2.3 12.4 1.0 OE2 A:GLU246 2.8 16.2 1.0 CD A:GLU246 2.9 12.5 1.0 CG A:ASP194 3.3 11.1 1.0 CD A:GLU220 3.4 10.5 1.0 OD1 A:ASP194 3.6 10.0 1.0 CG A:GLU220 3.9 9.8 1.0 O A:HOH714 4.0 25.6 1.0 ND2 A:ASN196 4.1 12.9 1.0 CD2 A:HIS296 4.1 8.4 1.0 O A:HOH966 4.2 43.0 1.0 NE2 A:HIS296 4.3 9.7 1.0 NZ A:LYS164 4.3 10.4 1.0 CG A:GLU246 4.4 9.2 1.0 OE1 A:GLU220 4.4 8.2 1.0 OE1 A:GLU221 4.4 12.2 1.0 O A:HOH523 4.5 10.4 1.0 CB A:ASP194 4.6 7.8 1.0 O A:HOH524 4.6 9.7 1.0 OE2 A:GLU329 4.7 13.1 1.0 CE A:LYS164 4.8 10.9 1.0 CG A:ASN196 5.0 11.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Ordered Loops


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 A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Ordered Loops within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:17.8 occ:1.00 O A:HOH642 2.3 26.8 1.0 O A:GLY237 2.3 12.2 1.0 OD1 A:ASP209 2.4 16.5 1.0 OD2 A:ASP209 2.4 18.2 1.0 O A:HOH584 2.4 25.1 1.0 O A:HOH672 2.4 24.3 1.0 O A:HOH692 2.4 23.7 1.0 CG A:ASP209 2.8 14.8 1.0 C A:GLY237 3.5 10.1 1.0 O A:HOH859 4.1 37.8 1.0 CA A:GLN238 4.1 10.9 1.0 O A:HOH905 4.2 36.7 1.0 O A:HOH847 4.2 48.3 1.0 CB A:ASP209 4.3 10.8 1.0 N A:GLN238 4.3 11.9 1.0 CG2 A:ILE205 4.3 9.3 1.0 O A:HOH909 4.5 37.0 1.0 CA A:GLY237 4.6 9.7 1.0 O A:HOH854 4.6 31.9 1.0 CB A:GLN238 4.6 10.2 1.0 O A:HOH738 4.7 28.6 1.0

M.W.Vetting, J.T.Bouvier, J.A.Gerlt, S.C.Almo. Purification, Crystallization and Structural Elucidation of D-Galactaro-1,4-Lactone Cycloisomerase From Agrobacterium Tumefaciens Involved in Pectin Degradation. Acta Crystallogr F Struct V. 72 36 2016BIOL Commun.
PubMed: 26750482
DOI: 10.1107/S2053230X15023286