Nickel in PDB 2glz: Crystal Structure of A Formylmethanofuran Dehydrogenase Subunit E-Like Protein (DHAF_2992) From Desulfitobacterium Hafniense Dcb-2 at 1.45 A Resolution

The structure of Crystal Structure of A Formylmethanofuran Dehydrogenase Subunit E-Like Protein (DHAF_2992) From Desulfitobacterium Hafniense Dcb-2 at 1.45 A Resolution, PDB code: 2glz was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.20 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.425, 84.791, 100.711, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.8

The structure of Crystal Structure of A Formylmethanofuran Dehydrogenase Subunit E-Like Protein (DHAF_2992) From Desulfitobacterium Hafniense Dcb-2 at 1.45 A Resolution also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of A Formylmethanofuran Dehydrogenase Subunit E-Like Protein (DHAF_2992) From Desulfitobacterium Hafniense Dcb-2 at 1.45 A Resolution (pdb code 2glz). 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 A Formylmethanofuran Dehydrogenase Subunit E-Like Protein (DHAF_2992) From Desulfitobacterium Hafniense Dcb-2 at 1.45 A Resolution, PDB code: 2glz:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of A Formylmethanofuran Dehydrogenase Subunit E-Like Protein (DHAF_2992) From Desulfitobacterium Hafniense Dcb-2 at 1.45 A Resolution


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 Formylmethanofuran Dehydrogenase Subunit E-Like Protein (DHAF_2992) From Desulfitobacterium Hafniense Dcb-2 at 1.45 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:29.2 occ:0.21 ZN A:ZN200 0.6 25.4 0.5 SG A:CYS55 2.0 31.5 1.0 NE2 A:HIS17 2.1 40.1 1.0 NE2 A:HIS15 2.3 27.4 1.0 SG A:CYS19 2.7 31.6 1.0 CB A:CYS55 3.0 28.1 1.0 CE1 A:HIS17 3.0 50.0 1.0 CD2 A:HIS17 3.0 43.8 1.0 CE1 A:HIS15 3.1 30.3 1.0 CD2 A:HIS15 3.5 24.8 1.0 O A:HOH285 3.7 31.5 1.0 CB A:CYS19 3.8 32.4 1.0 CD B:ARG70 4.1 46.0 1.0 ND1 A:HIS17 4.1 53.1 1.0 CG A:HIS17 4.2 40.8 1.0 ND1 A:HIS15 4.3 24.8 1.0 CA A:CYS55 4.3 25.5 1.0 C1 B:EDO202 4.4 37.2 1.0 CG A:HIS15 4.5 23.9 1.0 C2 B:EDO202 4.6 46.2 1.0 O2 B:EDO202 4.8 41.4 1.0 NE B:ARG70 4.9 52.1 1.0 CB A:ILE22 5.0 25.9 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of A Formylmethanofuran Dehydrogenase Subunit E-Like Protein (DHAF_2992) From Desulfitobacterium Hafniense Dcb-2 at 1.45 A Resolution


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 A Formylmethanofuran Dehydrogenase Subunit E-Like Protein (DHAF_2992) From Desulfitobacterium Hafniense Dcb-2 at 1.45 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:24.3 occ:0.21 ZN B:ZN200 0.5 25.6 0.5 NE2 B:HIS17 1.8 35.9 1.0 NE2 B:HIS15 2.2 28.4 1.0 SG B:CYS55 2.4 32.3 1.0 SG B:CYS19 2.6 30.7 1.0 CD2 B:HIS17 2.7 49.3 1.0 CE1 B:HIS17 2.9 50.6 1.0 CE1 B:HIS15 3.1 30.3 1.0 CD2 B:HIS15 3.3 27.7 1.0 CB B:CYS55 3.4 25.4 1.0 CB B:CYS19 3.7 30.8 1.0 CG B:HIS17 3.8 41.5 1.0 ND1 B:HIS17 3.9 53.4 1.0 C2 A:EDO205 3.9 48.2 1.0 CD A:ARG70 4.0 43.0 1.0 O B:HOH304 4.1 36.0 1.0 ND1 B:HIS15 4.3 26.6 1.0 CG B:HIS15 4.4 26.9 1.0 CA B:CYS55 4.6 26.3 1.0 O2 A:EDO205 4.7 45.7 1.0 NE A:ARG70 4.7 47.9 1.0 CA B:CYS19 5.0 29.3 1.0

H.L.Axelrod, D.Das, P.Abdubek, T.Astakhova, C.Bakolitsa, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, K.Ellrott, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, W.W.Lam, D.Marciano, D.Mcmullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, C.Puckett, R.Reyes, N.Sefcovic, H.J.Tien, C.B.Trame, H.Van Den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson. Structures of Three Members of Pfam PF02663 (Fmde) Implicated in Microbial Methanogenesis Reveal A Conserved Alpha+Beta Core Domain and An Auxiliary C-Terminal Treble-Clef Zinc Finger. Acta Crystallogr.,Sect.F V. 66 1335 2010.
ISSN: ESSN 1744-3091
PubMed: 20944230
DOI: 10.1107/S1744309110020166