Magnesium in PDB 6cin: Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica

The structure of Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica, PDB code: 6cin 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)	88.95 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	340.611, 106.634, 239.079, 90.00, 109.31, 90.00
R / Rfree (%)	19.5 / 22.7

The structure of Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica also contains other interesting chemical elements:

Iron

(Fe)

72 atoms

The binding sites of Magnesium atom in the Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica (pdb code 6cin). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica, PDB code: 6cin:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1205 b:44.7 occ:1.00 OD1 A:ASP967 2.0 95.4 1.0 O A:HOH1318 2.1 46.6 1.0 O3B A:TPP1204 2.1 95.8 1.0 O A:VAL997 2.1 0.0 1.0 OG1 A:THR995 2.3 79.5 1.0 O2A A:TPP1204 2.3 83.0 1.0 CG A:ASP967 3.1 91.4 1.0 PB A:TPP1204 3.3 86.9 1.0 C A:VAL997 3.4 0.5 1.0 PA A:TPP1204 3.5 79.1 1.0 CB A:THR995 3.6 79.5 1.0 O3A A:TPP1204 3.7 82.5 1.0 N A:ASP967 3.8 80.2 1.0 OD2 A:ASP967 3.8 93.6 1.0 OG A:SER999 3.8 0.9 1.0 N A:SER999 3.9 0.0 1.0 N A:THR995 4.0 74.0 1.0 O1B A:TPP1204 4.0 86.6 1.0 N A:VAL997 4.0 0.3 1.0 CG2 A:THR995 4.1 77.9 1.0 CA A:THR995 4.2 80.6 1.0 CB A:ASP967 4.2 86.8 1.0 N A:TYR998 4.2 0.7 1.0 O7 A:TPP1204 4.2 80.2 1.0 CA A:TYR998 4.3 0.7 1.0 N A:GLY968 4.3 66.5 1.0 CA A:VAL997 4.3 0.2 1.0 O A:LEU993 4.4 63.9 1.0 C A:THR995 4.5 86.7 1.0 N A:GLU996 4.5 92.3 1.0 CB A:SER999 4.5 0.5 1.0 CA A:ASP967 4.5 80.3 1.0 O2B A:TPP1204 4.5 86.0 1.0 CA A:GLY966 4.6 58.6 1.0 C A:TYR998 4.6 0.0 1.0 C A:GLY966 4.6 59.1 1.0 O1A A:TPP1204 4.7 75.6 1.0 CA A:SER999 4.8 0.5 1.0 CG2 A:VAL997 4.9 0.6 1.0 C A:ASP967 4.9 72.4 1.0 OE2 A:GLU814 5.0 77.3 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1205 b:32.7 occ:1.00 O1B B:TPP1204 2.1 87.4 1.0 OD1 B:ASP967 2.1 88.1 1.0 O1A B:TPP1204 2.2 83.4 1.0 OG1 B:THR995 2.2 78.5 1.0 O B:HOH1323 2.2 54.0 1.0 O B:VAL997 2.2 0.2 1.0 PB B:TPP1204 3.1 83.6 1.0 CG B:ASP967 3.3 83.9 1.0 PA B:TPP1204 3.3 76.5 1.0 O3A B:TPP1204 3.4 80.4 1.0 C B:VAL997 3.5 0.3 1.0 CB B:THR995 3.5 79.0 1.0 O3B B:TPP1204 3.7 84.3 1.0 N B:SER999 3.8 94.4 1.0 OD2 B:ASP967 3.9 86.7 1.0 N B:ASP967 3.9 67.8 1.0 OG B:SER999 3.9 86.9 1.0 CG2 B:THR995 4.0 78.0 1.0 N B:THR995 4.1 76.9 1.0 O7 B:TPP1204 4.1 75.7 1.0 CA B:TYR998 4.2 94.0 1.0 N B:VAL997 4.2 0.5 1.0 CA B:THR995 4.2 79.8 1.0 N B:TYR998 4.3 97.9 1.0 CB B:ASP967 4.4 77.8 1.0 O B:LEU993 4.4 64.4 1.0 CB B:SER999 4.4 87.6 1.0 N B:GLY968 4.4 65.4 1.0 O2B B:TPP1204 4.4 81.8 1.0 O2A B:TPP1204 4.5 75.8 1.0 CA B:VAL997 4.5 0.4 1.0 C B:TYR998 4.5 93.7 1.0 C B:THR995 4.6 83.4 1.0 CA B:GLY966 4.6 63.3 1.0 CA B:ASP967 4.6 71.2 1.0 N B:GLU996 4.6 88.0 1.0 C B:GLY966 4.7 63.8 1.0 CA B:SER999 4.7 94.0 1.0 CG2 B:VAL997 5.0 0.1 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1205 b:31.9 occ:1.00 O C:VAL997 2.0 92.4 1.0 OD1 C:ASP967 2.0 85.6 1.0 O C:HOH1352 2.1 40.9 1.0 O2A C:TPP1204 2.1 86.1 1.0 O3B C:TPP1204 2.2 88.0 1.0 OG1 C:THR995 2.3 62.6 1.0 CG C:ASP967 3.2 80.6 1.0 PB C:TPP1204 3.2 80.6 1.0 PA C:TPP1204 3.2 77.6 1.0 C C:VAL997 3.3 87.7 1.0 O3A C:TPP1204 3.5 80.6 1.0 CB C:THR995 3.6 68.1 1.0 OD2 C:ASP967 3.8 82.9 1.0 O2B C:TPP1204 3.8 80.6 1.0 N C:SER999 3.9 80.1 1.0 N C:ASP967 3.9 58.3 1.0 O7 C:TPP1204 4.0 75.2 1.0 N C:VAL997 4.0 88.7 1.0 N C:THR995 4.0 68.5 1.0 OG C:SER999 4.0 73.1 1.0 CA C:TYR998 4.1 79.0 1.0 N C:TYR998 4.1 82.6 1.0 CG2 C:THR995 4.2 60.8 1.0 CA C:THR995 4.2 71.0 1.0 CB C:ASP967 4.3 75.7 1.0 CA C:VAL997 4.3 89.5 1.0 N C:GLY968 4.3 57.2 1.0 O1A C:TPP1204 4.4 74.7 1.0 C C:THR995 4.5 76.1 1.0 N C:GLU996 4.5 79.9 1.0 C C:TYR998 4.5 78.2 1.0 O1B C:TPP1204 4.5 77.6 1.0 O C:LEU993 4.5 60.1 1.0 CA C:ASP967 4.6 71.3 1.0 CB C:SER999 4.6 74.2 1.0 CA C:GLY966 4.7 58.9 1.0 C C:GLY966 4.7 58.0 1.0 CA C:SER999 4.9 81.8 1.0 CG2 C:VAL997 4.9 76.3 1.0 C C:ASP967 4.9 57.8 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1205 b:32.8 occ:1.00 O3B D:TPP1204 2.0 82.6 1.0 O D:VAL997 2.0 88.5 1.0 OD1 D:ASP967 2.0 75.5 1.0 O D:HOH1329 2.2 33.9 1.0 O2A D:TPP1204 2.2 64.7 1.0 OG1 D:THR995 2.3 59.8 1.0 PB D:TPP1204 3.1 74.5 1.0 CG D:ASP967 3.2 69.9 1.0 C D:VAL997 3.2 84.2 1.0 PA D:TPP1204 3.4 64.0 1.0 O3A D:TPP1204 3.5 68.4 1.0 CB D:THR995 3.6 67.6 1.0 O2B D:TPP1204 3.7 72.2 1.0 OG D:SER999 3.8 76.8 1.0 N D:ASP967 3.8 63.3 1.0 N D:SER999 3.8 82.6 1.0 OD2 D:ASP967 3.8 71.2 1.0 N D:VAL997 4.0 79.4 1.0 N D:THR995 4.1 59.4 1.0 CG2 D:THR995 4.1 59.3 1.0 N D:TYR998 4.1 83.7 1.0 O7 D:TPP1204 4.2 64.2 1.0 CA D:TYR998 4.2 80.2 1.0 CA D:VAL997 4.2 81.9 1.0 CA D:THR995 4.2 60.9 1.0 CB D:ASP967 4.3 66.5 1.0 O1B D:TPP1204 4.4 71.9 1.0 N D:GLY968 4.4 63.0 1.0 O D:LEU993 4.4 61.1 1.0 CB D:SER999 4.5 77.7 1.0 C D:THR995 4.5 70.5 1.0 N D:GLU996 4.5 69.2 1.0 C D:TYR998 4.5 81.5 1.0 O1A D:TPP1204 4.5 63.7 1.0 CA D:GLY966 4.5 56.6 1.0 CA D:ASP967 4.6 63.4 1.0 C D:GLY966 4.7 53.6 1.0 CG2 D:VAL997 4.8 74.1 1.0 CA D:SER999 4.8 83.6 1.0 C D:ASP967 5.0 55.7 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1205 b:44.9 occ:1.00 OD1 E:ASP967 1.8 80.1 1.0 O1B E:TPP1204 2.0 82.8 1.0 O E:HOH1306 2.0 47.1 1.0 O E:VAL997 2.2 88.9 1.0 OG1 E:THR995 2.2 86.9 1.0 O1A E:TPP1204 2.4 70.3 1.0 CG E:ASP967 3.0 76.0 1.0 PB E:TPP1204 3.2 77.4 1.0 C E:VAL997 3.4 88.7 1.0 CB E:THR995 3.5 86.5 1.0 PA E:TPP1204 3.5 71.1 1.0 OD2 E:ASP967 3.6 77.6 1.0 O3A E:TPP1204 3.7 74.5 1.0 N E:ASP967 3.7 62.4 1.0 O3B E:TPP1204 3.8 75.6 1.0 OG E:SER999 3.8 91.4 1.0 N E:THR995 3.8 73.9 1.0 N E:SER999 4.0 94.0 1.0 CG2 E:THR995 4.0 84.9 1.0 N E:VAL997 4.0 85.6 1.0 CA E:THR995 4.1 82.1 1.0 CB E:ASP967 4.1 70.6 1.0 O E:LEU993 4.2 60.0 1.0 N E:TYR998 4.3 87.1 1.0 N E:GLY968 4.3 57.2 1.0 O7 E:TPP1204 4.3 73.2 1.0 CA E:TYR998 4.3 85.4 1.0 CA E:VAL997 4.4 87.2 1.0 C E:THR995 4.4 78.1 1.0 CA E:ASP967 4.4 64.1 1.0 O2B E:TPP1204 4.4 77.8 1.0 N E:GLU996 4.4 73.7 1.0 CB E:SER999 4.5 95.0 1.0 CA E:GLY966 4.6 55.9 1.0 C E:GLY966 4.6 58.8 1.0 C E:TYR998 4.7 88.3 1.0 O2A E:TPP1204 4.7 72.0 1.0 C E:ASP967 4.8 59.1 1.0 CA E:SER999 4.9 0.5 1.0 CG2 E:VAL997 4.9 91.8 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1205 b:35.5 occ:1.00 O F:HOH1331 2.0 33.6 1.0 O F:VAL997 2.0 83.2 1.0 OD1 F:ASP967 2.1 74.6 1.0 O3B F:TPP1204 2.1 77.1 1.0 OG1 F:THR995 2.2 66.4 1.0 O1A F:TPP1204 2.2 69.7 1.0 CG F:ASP967 3.2 70.7 1.0 PB F:TPP1204 3.2 71.9 1.0 C F:VAL997 3.2 80.5 1.0 PA F:TPP1204 3.4 70.4 1.0 O3A F:TPP1204 3.5 70.8 1.0 CB F:THR995 3.5 66.5 1.0 O1B F:TPP1204 3.7 68.6 1.0 OD2 F:ASP967 3.7 72.9 1.0 N F:ASP967 3.9 55.1 1.0 N F:SER999 3.9 80.1 1.0 N F:THR995 3.9 65.3 1.0 N F:VAL997 3.9 76.2 1.0 OG F:SER999 4.0 75.2 1.0 CG2 F:THR995 4.0 65.1 1.0 N F:TYR998 4.1 79.6 1.0 CA F:THR995 4.1 66.0 1.0 O7 F:TPP1204 4.2 70.3 1.0 CA F:TYR998 4.2 77.1 1.0 CA F:VAL997 4.2 79.1 1.0 N F:GLY968 4.3 48.1 1.0 CB F:ASP967 4.3 65.1 1.0 C F:THR995 4.4 65.3 1.0 N F:GLU996 4.4 67.2 1.0 O F:LEU993 4.5 51.1 1.0 O2B F:TPP1204 4.5 71.0 1.0 CB F:SER999 4.6 77.9 1.0 CA F:ASP967 4.6 58.2 1.0 C F:TYR998 4.6 78.9 1.0 O2A F:TPP1204 4.6 68.2 1.0 CA F:GLY966 4.7 53.1 1.0 C F:GLY966 4.8 54.2 1.0 CG2 F:VAL997 4.8 75.9 1.0 CA F:SER999 4.9 83.4 1.0 C F:ASP967 4.9 52.4 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