Nickel 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:

Calcium

(Ca)

2 atoms

The binding sites of Nickel 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 Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Ordered Loops, PDB code: 4hpn:

Nickel binding site 1 out of 1 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 Nickel with other atoms in the Ni 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:Ni404 b:15.6 occ:1.00 N1 A:IMD403 2.0 16.1 1.0 NE2 A:HIS13 2.0 16.4 1.0 NE2 A:HIS334 2.0 18.6 1.0 C2 A:IMD403 2.9 19.6 1.0 CE1 A:HIS13 2.9 21.6 1.0 CE1 A:HIS334 3.0 17.0 1.0 C5 A:IMD403 3.0 16.3 1.0 CD2 A:HIS334 3.1 15.7 1.0 CD2 A:HIS13 3.1 16.0 1.0 ND1 A:HIS13 4.1 16.0 1.0 N3 A:IMD403 4.1 19.8 1.0 CG A:PRO336 4.1 15.9 1.0 ND1 A:HIS334 4.1 18.9 1.0 C4 A:IMD403 4.1 16.5 1.0 CG A:HIS13 4.2 15.7 1.0 CG A:HIS334 4.2 16.6 1.0 CD A:PRO336 4.3 15.0 1.0 O A:HOH804 4.4 28.4 1.0 O A:ARG14 4.8 18.6 1.0 CB A:PRO336 4.8 16.0 1.0 O A:HOH657 4.9 23.7 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