Magnesium in PDB 6ciq: Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Coenzyme A Bound

The structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Coenzyme A Bound, PDB code: 6ciq was solved by P.Y.-T.Chen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.25 / 3.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	337.710, 106.993, 120.465, 90.00, 109.85, 90.00
R / Rfree (%)	18.4 / 22.3

The structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Coenzyme A Bound also contains other interesting chemical elements:

Iron

(Fe)

36 atoms

The binding sites of Magnesium atom in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Coenzyme A Bound (pdb code 6ciq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Coenzyme A Bound, PDB code: 6ciq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Coenzyme A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Coenzyme A Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1205 b:35.3 occ:1.00 O3B A:TPP1204 2.0 80.9 1.0 OG1 A:THR995 2.1 93.4 1.0 O2A A:TPP1204 2.2 82.5 1.0 O A:HOH1303 2.2 34.4 1.0 OD1 A:ASP967 2.3 81.3 1.0 O A:VAL997 2.4 87.1 1.0 PB A:TPP1204 3.2 75.2 1.0 PA A:TPP1204 3.3 79.1 1.0 CG A:ASP967 3.4 80.7 1.0 CB A:THR995 3.4 97.7 1.0 O3A A:TPP1204 3.5 75.7 1.0 C A:VAL997 3.6 88.0 1.0 N A:ASP967 3.8 77.3 1.0 O1B A:TPP1204 3.9 72.6 1.0 OG A:SER999 3.9 93.0 1.0 CG2 A:THR995 3.9 0.4 1.0 N A:THR995 3.9 92.9 1.0 N A:SER999 4.1 89.1 1.0 CA A:THR995 4.1 95.7 1.0 O7 A:TPP1204 4.1 74.5 1.0 OD2 A:ASP967 4.1 81.2 1.0 N A:VAL997 4.2 92.7 1.0 N A:GLY968 4.3 71.0 1.0 O A:LEU993 4.3 91.3 1.0 C A:THR995 4.4 96.8 1.0 O2B A:TPP1204 4.4 73.2 1.0 CB A:ASP967 4.4 79.6 1.0 O1A A:TPP1204 4.5 77.5 1.0 CA A:TYR998 4.5 84.3 1.0 CB A:SER999 4.5 92.5 1.0 N A:TYR998 4.5 86.4 1.0 N A:GLU996 4.5 93.7 1.0 CA A:GLY966 4.5 73.1 1.0 CA A:VAL997 4.6 92.2 1.0 CA A:ASP967 4.6 76.6 1.0 C A:GLY966 4.6 76.3 1.0 OE2 A:GLU814 4.7 76.9 1.0 C A:TYR998 4.8 86.3 1.0 CA A:SER999 4.9 92.7 1.0 C A:ASP967 5.0 72.8 1.0

Magnesium binding site 2 out of 3 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Coenzyme A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Coenzyme A Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1205 b:30.6 occ:1.00 OD1 B:ASP967 1.9 82.8 1.0 O B:VAL997 2.0 77.6 1.0 O2A B:TPP1204 2.2 70.7 1.0 O3B B:TPP1204 2.2 67.0 1.0 O B:HOH1301 2.3 28.9 1.0 OG1 B:THR995 2.5 71.6 1.0 CG B:ASP967 3.1 85.5 1.0 C B:VAL997 3.2 78.0 1.0 PA B:TPP1204 3.3 63.5 1.0 PB B:TPP1204 3.4 64.9 1.0 O3A B:TPP1204 3.6 63.3 1.0 CB B:THR995 3.8 72.8 1.0 OG B:SER999 3.8 86.8 1.0 N B:SER999 3.8 81.6 1.0 OD2 B:ASP967 3.8 84.1 1.0 N B:ASP967 3.8 90.7 1.0 N B:VAL997 3.9 76.3 1.0 N B:THR995 4.0 74.3 1.0 O7 B:TPP1204 4.0 63.8 1.0 O2B B:TPP1204 4.1 65.7 1.0 N B:TYR998 4.1 78.4 1.0 CA B:TYR998 4.2 77.7 1.0 CA B:VAL997 4.2 76.6 1.0 CB B:ASP967 4.2 87.7 1.0 CA B:THR995 4.3 74.7 1.0 CG2 B:THR995 4.3 72.4 1.0 N B:GLY968 4.4 78.6 1.0 C B:THR995 4.4 75.8 1.0 CB B:SER999 4.4 84.9 1.0 N B:GLU996 4.5 75.0 1.0 O B:LEU993 4.5 75.0 1.0 CA B:ASP967 4.5 87.0 1.0 C B:TYR998 4.5 80.3 1.0 O1A B:TPP1204 4.5 63.5 1.0 O1B B:TPP1204 4.6 65.2 1.0 CA B:GLY966 4.7 96.2 1.0 C B:GLY966 4.7 96.4 1.0 CA B:SER999 4.8 83.8 1.0 CG2 B:VAL997 4.8 76.7 1.0 C B:ASP967 5.0 82.4 1.0 C B:GLU996 5.0 75.6 1.0

Magnesium binding site 3 out of 3 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Coenzyme A Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Coenzyme A Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1205 b:19.2 occ:1.00 OD1 C:ASP967 2.0 70.7 1.0 O C:VAL997 2.0 73.7 1.0 O3B C:TPP1204 2.2 71.4 1.0 O2A C:TPP1204 2.3 63.9 1.0 OG1 C:THR995 2.4 62.2 1.0 O C:HOH1301 2.5 15.0 1.0 CG C:ASP967 3.2 71.3 1.0 PB C:TPP1204 3.2 67.3 1.0 C C:VAL997 3.3 74.7 1.0 PA C:TPP1204 3.4 61.7 1.0 O3A C:TPP1204 3.5 63.1 1.0 CB C:THR995 3.7 63.0 1.0 O2B C:TPP1204 3.7 65.4 1.0 N C:SER999 3.8 74.9 1.0 OD2 C:ASP967 3.8 72.7 1.0 N C:ASP967 3.8 62.8 1.0 OG C:SER999 4.0 72.6 1.0 N C:THR995 4.0 70.4 1.0 N C:VAL997 4.0 73.1 1.0 O7 C:TPP1204 4.1 63.8 1.0 CA C:TYR998 4.1 73.4 1.0 N C:TYR998 4.1 75.2 1.0 CG2 C:THR995 4.2 61.9 1.0 CB C:ASP967 4.3 68.2 1.0 CA C:THR995 4.3 63.6 1.0 CA C:VAL997 4.3 74.1 1.0 N C:GLY968 4.3 65.9 1.0 CB C:SER999 4.4 74.3 1.0 O C:LEU993 4.5 58.2 1.0 C C:THR995 4.5 68.4 1.0 C C:TYR998 4.5 73.2 1.0 CA C:ASP967 4.5 65.9 1.0 O1B C:TPP1204 4.5 67.0 1.0 N C:GLU996 4.5 68.1 1.0 O1A C:TPP1204 4.6 63.3 1.0 CA C:GLY966 4.6 59.9 1.0 C C:GLY966 4.7 61.0 1.0 CA C:SER999 4.7 77.4 1.0 C C:ASP967 4.9 65.7 1.0 CG2 C:VAL997 4.9 75.4 1.0

P.Y.Chen, H.Aman, M.Can, S.W.Ragsdale, C.L.Drennan. Binding Site For Coenzyme A Revealed in the Structure of Pyruvate:Ferredoxin Oxidoreductase Frommoorella Thermoacetica. Proc. Natl. Acad. Sci. V. 115 3846 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29581263
DOI: 10.1073/PNAS.1722329115