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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

Protein crystallography data

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

Other elements in 2glz:

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

Nickel Binding Sites:

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 2glz

Go back to Nickel Binding Sites List in 2glz
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 2glz

Go back to Nickel Binding Sites List in 2glz
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

Reference:

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
Page generated: Wed Dec 16 01:18:11 2020

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