Nickel in PDB 4h2h: Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)

The structure of Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine), PDB code: 4h2h was solved by M.W.Vetting, 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)	25.68 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.035, 152.824, 113.027, 90.00, 105.20, 90.00
R / Rfree (%)	15.9 / 19.2

The structure of Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Iodine	(I)	61 atoms

The binding sites of Nickel atom in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) (pdb code 4h2h). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine), PDB code: 4h2h:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:12.9 occ:0.83 O C:HOH507 2.1 12.5 1.0 O C:HOH505 2.1 14.3 1.0 NE2 C:HIS235 2.1 14.4 1.0 NE2 E:HIS235 2.1 17.8 1.0 NE2 A:HIS235 2.1 15.0 1.0 NE2 H:HIS235 2.1 15.1 1.0 CE1 E:HIS235 2.9 18.1 1.0 CE1 C:HIS235 3.0 12.6 1.0 CE1 H:HIS235 3.0 12.7 1.0 CE1 A:HIS235 3.0 14.9 1.0 CD2 C:HIS235 3.2 15.2 1.0 CD2 A:HIS235 3.2 13.8 1.0 CD2 H:HIS235 3.2 15.6 1.0 CD2 E:HIS235 3.2 15.8 1.0 ND1 E:HIS235 4.1 18.6 1.0 ND1 C:HIS235 4.2 15.7 1.0 ND1 A:HIS235 4.2 15.8 1.0 ND1 H:HIS235 4.2 14.8 1.0 O A:HOH710 4.2 29.2 1.0 CG C:HIS235 4.3 15.9 1.0 O C:HOH687 4.3 29.2 1.0 CG E:HIS235 4.3 15.2 1.0 CG A:HIS235 4.3 13.8 1.0 CG H:HIS235 4.3 15.8 1.0 O C:HOH719 4.4 32.8 1.0 O C:HOH771 4.5 48.7 1.0 O H:HOH633 4.5 40.8 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:12.6 occ:0.81 O F:HOH510 2.1 12.1 1.0 O D:HOH528 2.1 14.4 1.0 NE2 G:HIS235 2.1 16.4 1.0 NE2 F:HIS235 2.1 16.4 1.0 NE2 D:HIS235 2.1 16.9 1.0 NE2 B:HIS235 2.1 17.2 1.0 CE1 B:HIS235 3.0 15.5 1.0 CE1 G:HIS235 3.0 16.4 1.0 CE1 D:HIS235 3.0 16.6 1.0 CE1 F:HIS235 3.0 14.9 1.0 CD2 F:HIS235 3.2 15.3 1.0 CD2 D:HIS235 3.2 16.2 1.0 CD2 G:HIS235 3.2 17.2 1.0 CD2 B:HIS235 3.3 14.3 1.0 ND1 G:HIS235 4.2 18.8 1.0 ND1 B:HIS235 4.2 15.6 1.0 ND1 D:HIS235 4.2 14.1 1.0 ND1 F:HIS235 4.2 15.6 1.0 O B:HOH754 4.3 40.2 1.0 CG G:HIS235 4.3 16.9 1.0 CG D:HIS235 4.3 15.6 1.0 CG F:HIS235 4.3 12.9 1.0 O G:HOH628 4.3 28.5 1.0 CG B:HIS235 4.3 14.2 1.0 O F:HOH634 4.4 26.8 1.0 O B:HOH737 4.5 42.0 1.0 O F:HOH641 4.5 38.9 1.0 O F:HOH616 4.6 38.6 1.0

S.Zhao, R.Kumar, A.Sakai, M.W.Vetting, B.M.Wood, S.Brown, J.B.Bonanno, B.S.Hillerich, R.D.Seidel, P.C.Babbitt, S.C.Almo, J.V.Sweedler, J.A.Gerlt, J.E.Cronan, M.P.Jacobson. Discovery of New Enzymes and Metabolic Pathways By Using Structure and Genome Context. Nature V. 502 698 2013.
ISSN: ISSN 0028-0836
PubMed: 24056934
DOI: 10.1038/NATURE12576