Zinc in PDB 2gvi: Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution

The structure of Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution, PDB code: 2gvi 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)	30.08 / 1.87
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.680, 97.650, 75.270, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 21.7

The binding sites of Zinc atom in the Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution (pdb code 2gvi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution, PDB code: 2gvi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn300 b:45.7 occ:1.00 NE2 A:HIS18 2.0 33.4 1.0 NE2 A:HIS16 2.0 40.2 1.0 SG A:CYS20 2.4 34.3 1.0 SG A:CYS61 2.8 42.2 1.0 CD2 A:HIS18 2.8 36.2 1.0 CD2 A:HIS16 2.9 34.8 1.0 CE1 A:HIS16 3.1 41.9 1.0 CE1 A:HIS18 3.1 37.5 1.0 CB A:CYS61 3.4 35.1 1.0 C6 A:UNL400 3.4 43.9 1.0 CB A:CYS20 3.5 32.2 1.0 C5 A:UNL400 3.5 43.9 1.0 CG A:HIS18 4.0 34.9 1.0 C4 A:UNL400 4.1 36.7 1.0 ND1 A:HIS18 4.1 37.8 1.0 CG A:HIS16 4.1 37.2 1.0 ND1 A:HIS16 4.1 34.2 1.0 C2 A:UNL400 4.4 40.5 1.0 O A:HOH420 4.7 23.3 1.0 CA A:CYS61 4.7 33.7 1.0 CA A:CYS20 4.8 30.4 1.0 C7 A:UNL400 4.8 44.7 1.0 CG A:PRO128 4.9 39.3 1.0 CB A:MSE23 4.9 27.4 1.0 N A:CYS20 4.9 31.5 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:29.8 occ:1.00 OD2 A:ASP198 2.0 29.0 1.0 SG A:CYS177 2.3 25.8 1.0 SG A:CYS195 2.3 28.6 1.0 SG A:CYS174 2.3 28.2 1.0 CG A:ASP198 3.1 36.0 1.0 CB A:CYS174 3.2 27.5 1.0 CB A:CYS177 3.3 27.7 1.0 CB A:CYS195 3.4 28.4 1.0 N A:CYS177 3.6 29.4 1.0 CB A:ASP198 3.6 33.8 1.0 N A:CYS195 3.9 30.5 1.0 CA A:CYS177 4.0 28.5 1.0 OD1 A:ASP198 4.1 34.9 1.0 CA A:CYS195 4.2 30.2 1.0 O A:ACY412 4.3 50.9 1.0 OXT A:ACY412 4.6 51.0 1.0 CB A:VAL176 4.6 28.0 1.0 CA A:CYS174 4.6 28.5 1.0 C A:VAL176 4.7 29.5 1.0 O A:CYS195 4.8 29.8 1.0 N A:ASP198 4.8 30.9 1.0 C A:CYS177 4.8 28.6 1.0 C A:ACY412 4.8 50.6 1.0 CA A:ASP198 4.8 32.9 1.0 C A:CYS195 4.8 29.1 1.0 N A:VAL176 4.9 28.8 1.0 N A:GLY178 4.9 29.6 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:21.3 occ:1.00 O A:HOH472 1.9 25.8 1.0 OE1 A:GLU153 2.0 28.5 1.0 O A:ACY410 2.0 27.4 1.0 ND1 A:HIS102 2.0 26.8 1.0 OXT A:ACY410 2.4 14.7 1.0 C A:ACY410 2.5 22.5 1.0 CD A:GLU153 2.8 33.1 1.0 CE1 A:HIS102 2.8 27.8 1.0 OE2 A:GLU153 3.0 27.5 1.0 CG A:HIS102 3.1 31.1 1.0 CB A:HIS102 3.7 26.9 1.0 CH3 A:ACY410 4.0 27.2 1.0 NE2 A:HIS102 4.0 29.0 1.0 CD2 A:HIS102 4.2 22.7 1.0 CG A:GLU153 4.2 26.1 1.0 O A:VAL103 4.3 27.3 1.0 CA A:ARG104 4.4 25.4 1.0 CB A:GLU153 4.6 26.4 1.0 C A:VAL103 4.7 27.6 1.0 O A:HIS102 4.8 27.2 1.0 N A:ARG104 4.8 25.1 1.0 C A:HIS102 4.8 25.9 1.0 CA A:HIS102 4.9 26.4 1.0 N A:ASN105 4.9 26.2 1.0 CH3 A:ACY407 5.0 28.2 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:45.4 occ:1.00 O A:ACY411 2.0 44.3 1.0 OE2 A:GLU130 2.0 35.5 1.0 O A:HOH521 2.9 46.5 1.0 CD A:GLU130 3.0 34.0 1.0 C A:ACY411 3.2 45.4 1.0 OE1 A:GLU130 3.3 30.0 1.0 O A:HOH492 3.3 40.6 1.0 O A:GLY125 3.9 31.4 1.0 CH3 A:ACY411 4.0 43.9 1.0 OXT A:ACY411 4.2 45.9 1.0 N A:GLU127 4.3 32.9 1.0 CG A:GLU130 4.3 36.3 1.0 CA A:TYR126 4.4 29.6 1.0 CG A:GLU127 4.5 39.3 1.0 C A:GLY125 4.8 30.6 1.0 CD1 A:TYR126 4.8 22.6 1.0 C A:TYR126 4.8 30.9 1.0 CB A:GLU127 5.0 34.4 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Putative Formylmethanofuran Dehydrogenase Subunit E (TA1109) From Thermoplasma Acidophilum at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:53.5 occ:1.00 O2 A:EDO406 1.9 41.6 1.0 O A:HOH513 2.2 52.0 1.0 OD2 A:ASP117 2.5 34.8 1.0 OD1 A:ASP117 2.5 32.7 1.0 O1 A:EDO406 2.6 54.5 1.0 CG A:ASP117 2.9 33.4 1.0 C2 A:EDO406 2.9 50.6 1.0 C1 A:EDO406 3.0 52.1 1.0 O A:HOH512 3.5 61.9 1.0 O1 A:EDO401 3.8 40.2 1.0 O A:HOH516 4.1 45.0 1.0 CB A:ASP117 4.4 28.9 1.0 O1 A:EDO405 4.5 60.3 1.0 C1 A:EDO405 4.6 61.8 1.0 C1 A:EDO401 4.7 36.5 1.0 O A:HOH501 4.7 38.0 1.0 NH1 A:ARG120 4.9 47.4 1.0 C2 A:EDO401 5.0 35.0 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