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Magnesium in PDB 6cio: Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp Bound

Protein crystallography data

The structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp Bound, PDB code: 6cio 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) 48.45 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 340.389, 107.095, 239.562, 90.00, 109.67, 90.00
R / Rfree (%) 20.7 / 24.1

Other elements in 6cio:

The structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp Bound also contains other interesting chemical elements:

Iron (Fe) 72 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 6cio

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Magnesium binding site 1 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp 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 Lactyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1205

b:32.9
occ:1.00
 O3B A:TDL1204 2.1 70.8 1.0
O2A A:TDL1204 2.1 75.9 1.0
OD1 A:ASP967 2.2 76.0 1.0
O A:HOH1301 2.2 45.0 1.0
OG1 A:THR995 2.3 54.1 1.0
O A:VAL997 2.4 87.7 1.0
PB A:TDL1204 3.3 62.1 1.0
CG A:ASP967 3.3 74.2 1.0
PA A:TDL1204 3.3 67.3 1.0
O3A A:TDL1204 3.6 67.6 1.0
C A:VAL997 3.6 84.8 1.0
CB A:THR995 3.6 56.9 1.0
OG A:SER999 3.8 68.8 1.0
N A:ASP967 3.8 67.0 1.0
O1B A:TDL1204 3.9 61.3 1.0
N A:THR995 3.9 62.1 1.0
OD2 A:ASP967 4.0 74.2 1.0
N A:SER999 4.0 77.2 1.0
O7 A:TDL1204 4.1 59.6 1.0
CG2 A:THR995 4.1 55.5 1.0
O A:LEU993 4.2 58.9 1.0
CA A:THR995 4.2 61.5 1.0
N A:GLY968 4.2 68.5 1.0
N A:VAL997 4.2 81.8 1.0
CB A:ASP967 4.3 73.6 1.0
CA A:TYR998 4.4 80.7 1.0
CB A:SER999 4.4 69.9 1.0
N A:TYR998 4.5 82.2 1.0
O1A A:TDL1204 4.5 63.8 1.0
O2B A:TDL1204 4.5 59.5 1.0
CA A:GLY966 4.5 64.2 1.0
CA A:ASP967 4.5 70.5 1.0
C A:THR995 4.6 66.2 1.0
CA A:VAL997 4.6 84.4 1.0
N A:GLU996 4.6 69.8 1.0
C A:GLY966 4.6 63.1 1.0
OE2 A:GLU814 4.7 69.9 1.0
C A:TYR998 4.7 80.0 1.0
CA A:SER999 4.8 72.6 1.0
C A:ASP967 4.9 70.7 1.0

Magnesium binding site 2 out of 6 in 6cio

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Magnesium binding site 2 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp 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 Lactyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1205

b:39.5
occ:1.00
 O1A B:TPP1204 2.0 88.2 1.0
OD1 B:ASP967 2.0 82.9 1.0
O B:VAL997 2.1 93.0 1.0
O1B B:TPP1204 2.1 87.8 1.0
O B:HOH1309 2.2 59.7 1.0
OG1 B:THR995 2.3 0.2 1.0
CG B:ASP967 3.2 76.8 1.0
PA B:TPP1204 3.2 78.4 1.0
PB B:TPP1204 3.2 78.2 1.0
C B:VAL997 3.3 84.5 1.0
O3A B:TPP1204 3.4 77.8 1.0
CB B:THR995 3.6 0.1 1.0
OD2 B:ASP967 3.8 78.9 1.0
N B:ASP967 3.8 72.6 1.0
O3B B:TPP1204 3.8 74.7 1.0
N B:SER999 3.9 78.2 1.0
N B:THR995 4.0 0.2 1.0
N B:VAL997 4.0 82.8 1.0
OG B:SER999 4.1 68.7 1.0
CA B:TYR998 4.1 76.3 1.0
O7 B:TPP1204 4.1 74.8 1.0
N B:TYR998 4.1 80.2 1.0
CG2 B:THR995 4.1 0.7 1.0
CA B:THR995 4.3 0.2 1.0
CB B:ASP967 4.3 71.8 1.0
O2A B:TPP1204 4.3 76.1 1.0
CA B:VAL997 4.3 83.1 1.0
N B:GLY968 4.3 63.5 1.0
O2B B:TPP1204 4.5 74.8 1.0
O B:LEU993 4.5 76.6 1.0
C B:THR995 4.5 0.4 1.0
C B:TYR998 4.5 74.7 1.0
CA B:ASP967 4.5 70.3 1.0
N B:GLU996 4.6 99.5 1.0
CB B:SER999 4.6 70.0 1.0
CA B:GLY966 4.6 78.5 1.0
C B:GLY966 4.7 75.0 1.0
CA B:SER999 4.9 78.4 1.0
C B:ASP967 4.9 66.1 1.0

Magnesium binding site 3 out of 6 in 6cio

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Magnesium binding site 3 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp 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 Lactyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1205

b:26.7
occ:1.00
 OD1 C:ASP967 2.0 66.5 1.0
O3B C:TDL1204 2.0 56.0 1.0
OG1 C:THR995 2.0 61.8 1.0
O C:VAL997 2.2 65.5 1.0
O C:HOH1302 2.2 28.6 1.0
O2A C:TDL1204 2.4 55.5 1.0
CG C:ASP967 3.1 64.5 1.0
PB C:TDL1204 3.2 51.3 1.0
CB C:THR995 3.3 61.9 1.0
C C:VAL997 3.4 68.8 1.0
PA C:TDL1204 3.5 52.6 1.0
O3A C:TDL1204 3.5 51.0 1.0
N C:ASP967 3.7 55.0 1.0
N C:THR995 3.8 59.0 1.0
O1B C:TDL1204 3.8 52.3 1.0
OD2 C:ASP967 3.8 65.1 1.0
CG2 C:THR995 3.9 60.4 1.0
OG C:SER999 3.9 88.1 1.0
CA C:THR995 4.0 63.9 1.0
N C:VAL997 4.0 67.7 1.0
N C:SER999 4.1 82.0 1.0
CB C:ASP967 4.2 61.8 1.0
C C:THR995 4.3 66.9 1.0
O C:LEU993 4.3 58.2 1.0
N C:GLY968 4.3 57.5 1.0
O7 C:TDL1204 4.3 54.1 1.0
N C:GLU996 4.3 65.5 1.0
N C:TYR998 4.3 70.5 1.0
CA C:TYR998 4.4 72.0 1.0
CA C:VAL997 4.4 69.1 1.0
O2B C:TDL1204 4.4 54.8 1.0
CA C:ASP967 4.4 58.2 1.0
CB C:SER999 4.5 87.5 1.0
CA C:GLY966 4.6 50.7 1.0
C C:GLY966 4.6 49.3 1.0
O1A C:TDL1204 4.7 52.0 1.0
C C:TYR998 4.8 73.3 1.0
C C:ASP967 4.8 57.6 1.0
OE2 C:GLU814 4.9 50.2 1.0
O C:THR995 5.0 72.4 1.0
C C:ASP994 5.0 58.0 1.0
CA C:SER999 5.0 85.0 1.0

Magnesium binding site 4 out of 6 in 6cio

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Magnesium binding site 4 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1205

b:22.2
occ:1.00
 O D:HOH1306 2.0 23.9 1.0
O D:VAL997 2.0 69.7 1.0
OG1 D:THR995 2.1 69.1 1.0
OD1 D:ASP967 2.1 66.9 1.0
O3B D:TDL1204 2.2 45.9 1.0
O2A D:TDL1204 2.2 52.3 1.0
PB D:TDL1204 3.2 51.7 1.0
CG D:ASP967 3.2 60.8 1.0
C D:VAL997 3.2 65.0 1.0
PA D:TDL1204 3.4 48.3 1.0
CB D:THR995 3.4 66.5 1.0
O3A D:TDL1204 3.5 51.1 1.0
O1B D:TDL1204 3.6 44.5 1.0
N D:SER999 3.9 71.0 1.0
OD2 D:ASP967 3.9 62.3 1.0
N D:THR995 3.9 58.6 1.0
N D:ASP967 3.9 52.0 1.0
CG2 D:THR995 3.9 66.4 1.0
OG D:SER999 4.0 75.6 1.0
N D:VAL997 4.0 61.4 1.0
CA D:TYR998 4.1 65.2 1.0
CA D:THR995 4.1 60.8 1.0
N D:TYR998 4.1 62.3 1.0
O7 D:TDL1204 4.2 52.5 1.0
CA D:VAL997 4.3 62.3 1.0
N D:GLY968 4.3 43.5 1.0
CB D:ASP967 4.3 54.1 1.0
C D:THR995 4.4 61.3 1.0
O D:LEU993 4.5 44.6 1.0
N D:GLU996 4.5 57.7 1.0
C D:TYR998 4.5 65.1 1.0
O1A D:TDL1204 4.5 45.6 1.0
CB D:SER999 4.5 75.3 1.0
O2B D:TDL1204 4.6 53.0 1.0
CA D:ASP967 4.6 52.4 1.0
CA D:GLY966 4.7 50.1 1.0
C D:GLY966 4.8 46.8 1.0
CA D:SER999 4.8 75.7 1.0
CG2 D:VAL997 4.9 52.7 1.0
C D:ASP967 5.0 48.8 1.0
OE2 D:GLU814 5.0 49.6 1.0

Magnesium binding site 5 out of 6 in 6cio

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Magnesium binding site 5 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1205

b:26.5
occ:1.00
 O E:VAL997 2.0 72.5 1.0
O2A E:TPP1204 2.0 63.0 1.0
O E:HOH1308 2.1 29.4 1.0
OG1 E:THR995 2.2 69.5 1.0
OD1 E:ASP967 2.2 64.0 1.0
O3B E:TPP1204 2.4 54.0 1.0
C E:VAL997 3.2 73.4 1.0
PA E:TPP1204 3.2 66.0 1.0
CG E:ASP967 3.4 63.5 1.0
PB E:TPP1204 3.4 57.5 1.0
O3A E:TPP1204 3.5 63.3 1.0
CB E:THR995 3.6 70.1 1.0
N E:SER999 3.7 76.3 1.0
OD2 E:ASP967 4.0 63.7 1.0
OG E:SER999 4.0 75.9 1.0
CA E:TYR998 4.0 73.0 1.0
O2B E:TPP1204 4.0 59.6 1.0
O7 E:TPP1204 4.0 66.6 1.0
N E:VAL997 4.0 77.0 1.0
N E:TYR998 4.0 71.0 1.0
N E:ASP967 4.1 68.4 1.0
CG2 E:THR995 4.2 67.1 1.0
N E:THR995 4.2 67.9 1.0
CA E:VAL997 4.3 75.5 1.0
CA E:THR995 4.3 71.8 1.0
N E:GLY968 4.4 59.6 1.0
O1A E:TPP1204 4.4 67.5 1.0
C E:TYR998 4.4 75.6 1.0
CB E:SER999 4.5 73.8 1.0
CB E:ASP967 4.5 63.9 1.0
C E:THR995 4.6 74.0 1.0
N E:GLU996 4.6 76.7 1.0
O1B E:TPP1204 4.7 51.2 1.0
O E:LEU993 4.7 49.2 1.0
CA E:SER999 4.7 75.5 1.0
CA E:ASP967 4.7 65.3 1.0
CA E:GLY966 4.9 74.5 1.0
CG2 E:VAL997 4.9 62.8 1.0
C E:GLY966 4.9 73.4 1.0

Magnesium binding site 6 out of 6 in 6cio

Go back to Magnesium Binding Sites List in 6cio
Magnesium binding site 6 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Lactyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1205

b:21.4
occ:1.00
 OD1 F:ASP967 2.1 72.5 1.0
O F:VAL997 2.1 68.5 1.0
O3B F:TDL1204 2.1 64.9 1.0
OG1 F:THR995 2.2 55.8 1.0
O2A F:TDL1204 2.3 53.6 1.0
O F:HOH1304 2.4 21.5 1.0
CG F:ASP967 3.2 72.0 1.0
PB F:TDL1204 3.3 61.1 1.0
C F:VAL997 3.3 68.2 1.0
PA F:TDL1204 3.4 55.0 1.0
O3A F:TDL1204 3.5 60.5 1.0
CB F:THR995 3.5 57.1 1.0
N F:ASP967 3.8 60.1 1.0
N F:SER999 3.8 76.9 1.0
OG F:SER999 3.8 87.7 1.0
O1B F:TDL1204 3.9 61.6 1.0
OD2 F:ASP967 3.9 70.2 1.0
N F:THR995 4.0 60.6 1.0
CG2 F:THR995 4.0 56.4 1.0
N F:VAL997 4.0 73.4 1.0
O7 F:TDL1204 4.1 55.6 1.0
CA F:TYR998 4.1 66.7 1.0
N F:TYR998 4.2 65.0 1.0
CA F:THR995 4.2 63.1 1.0
N F:GLY968 4.3 62.5 1.0
CB F:ASP967 4.3 70.9 1.0
CA F:VAL997 4.3 74.3 1.0
O F:LEU993 4.4 54.0 1.0
CB F:SER999 4.4 83.6 1.0
C F:THR995 4.5 59.3 1.0
CA F:ASP967 4.5 64.7 1.0
O2B F:TDL1204 4.5 57.8 1.0
C F:TYR998 4.5 69.7 1.0
CA F:GLY966 4.5 55.0 1.0
N F:GLU996 4.5 59.2 1.0
C F:GLY966 4.6 55.2 1.0
O1A F:TDL1204 4.6 53.7 1.0
CA F:SER999 4.8 80.8 1.0
CG2 F:VAL997 4.9 58.4 1.0
C F:ASP967 4.9 58.3 1.0
OE2 F:GLU814 4.9 53.7 1.0

Reference:

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
Page generated: Mon Sep 30 22:21:01 2024

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