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Magnesium in PDB 6cip: Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound

Protein crystallography data

The structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound, PDB code: 6cip 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) 97.45 / 3.19
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 342.005, 108.263, 240.437, 90.00, 109.32, 90.00
R / Rfree (%) 18.7 / 22.5

Other elements in 6cip:

The structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-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 Acetyl-Tpp Bound (pdb code 6cip). 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 Acetyl-Tpp Bound, PDB code: 6cip:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6cip

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

b:64.5
occ:1.00
 O23 A:HTL1204 2.1 0.6 1.0
OD1 A:ASP967 2.1 0.2 1.0
O A:HOH1301 2.1 63.7 1.0
O13 A:HTL1204 2.2 0.3 1.0
OG1 A:THR995 2.2 0.6 1.0
O A:VAL997 2.2 94.0 1.0
P2 A:HTL1204 3.2 0.7 1.0
CG A:ASP967 3.3 0.8 1.0
P1 A:HTL1204 3.3 97.2 1.0
C A:VAL997 3.5 100.0 1.0
O11 A:HTL1204 3.5 0.8 1.0
CB A:THR995 3.6 92.2 1.0
OG A:SER999 3.7 0.9 1.0
N A:SER999 3.9 0.1 1.0
OD2 A:ASP967 3.9 0.6 1.0
N A:ASP967 3.9 98.7 1.0
O21 A:HTL1204 3.9 99.4 1.0
N A:THR995 4.0 97.7 1.0
O5G A:HTL1204 4.1 95.8 1.0
CG2 A:THR995 4.1 85.5 1.0
N A:VAL997 4.2 0.5 1.0
CA A:THR995 4.2 98.8 1.0
CA A:TYR998 4.3 0.7 1.0
N A:TYR998 4.3 0.1 1.0
CB A:SER999 4.3 0.9 1.0
CB A:ASP967 4.4 0.6 1.0
O A:LEU993 4.4 97.1 1.0
N A:GLY968 4.4 98.9 1.0
O22 A:HTL1204 4.4 0.5 1.0
CA A:VAL997 4.5 0.9 1.0
O12 A:HTL1204 4.5 94.3 1.0
C A:THR995 4.5 95.7 1.0
N A:GLU996 4.6 99.4 1.0
CA A:ASP967 4.6 0.1 1.0
C A:TYR998 4.6 0.8 1.0
CA A:GLY966 4.7 69.6 1.0
CA A:SER999 4.8 0.5 1.0
C A:GLY966 4.8 99.0 1.0
OE2 A:GLU814 4.8 0.8 1.0
CG2 A:VAL997 5.0 0.1 1.0

Magnesium binding site 2 out of 6 in 6cip

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

b:66.6
occ:1.00
 O B:HOH1302 1.8 75.7 1.0
OD1 B:ASP967 2.0 0.4 1.0
O B:VAL997 2.0 0.0 1.0
O12 B:HTL1204 2.1 0.6 1.0
O21 B:HTL1204 2.2 0.1 1.0
OG1 B:THR995 2.2 0.8 1.0
CG B:ASP967 3.2 0.1 1.0
P1 B:HTL1204 3.2 0.1 1.0
P2 B:HTL1204 3.3 0.5 1.0
C B:VAL997 3.3 0.7 1.0
O11 B:HTL1204 3.4 0.8 1.0
CB B:THR995 3.6 0.3 1.0
N B:ASP967 3.8 0.3 1.0
OD2 B:ASP967 3.8 0.3 1.0
N B:SER999 3.9 0.6 1.0
O22 B:HTL1204 3.9 0.2 1.0
O5G B:HTL1204 3.9 0.2 1.0
N B:VAL997 4.0 0.9 1.0
N B:THR995 4.0 0.7 1.0
CA B:TYR998 4.1 0.2 1.0
N B:TYR998 4.1 0.4 1.0
CG2 B:THR995 4.1 0.5 1.0
OG B:SER999 4.1 97.1 1.0
CA B:THR995 4.2 0.5 1.0
CB B:ASP967 4.2 0.9 1.0
CA B:VAL997 4.3 0.1 1.0
N B:GLY968 4.3 97.5 1.0
O13 B:HTL1204 4.4 0.6 1.0
C B:THR995 4.5 0.5 1.0
O23 B:HTL1204 4.5 0.2 1.0
CA B:ASP967 4.5 0.7 1.0
O B:LEU993 4.5 91.0 1.0
C B:TYR998 4.5 0.2 1.0
N B:GLU996 4.6 0.1 1.0
CA B:GLY966 4.6 0.2 1.0
CB B:SER999 4.6 99.5 1.0
C B:GLY966 4.7 0.1 1.0
CA B:SER999 4.9 0.7 1.0
C B:ASP967 4.9 0.6 1.0
CG2 B:VAL997 5.0 0.3 1.0

Magnesium binding site 3 out of 6 in 6cip

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

b:49.0
occ:1.00
 O C:VAL997 1.9 1.0 1.0
O C:HOH1303 2.0 53.4 1.0
O13 C:HTL1204 2.1 96.5 1.0
OD1 C:ASP967 2.1 0.3 1.0
OG1 C:THR995 2.1 0.8 1.0
O23 C:HTL1204 2.4 86.1 1.0
C C:VAL997 3.1 98.3 1.0
P1 C:HTL1204 3.2 85.0 1.0
CG C:ASP967 3.2 0.1 1.0
P2 C:HTL1204 3.4 85.8 1.0
O11 C:HTL1204 3.4 84.5 1.0
CB C:THR995 3.5 0.0 1.0
N C:SER999 3.8 96.8 1.0
OD2 C:ASP967 3.9 0.6 1.0
N C:VAL997 3.9 0.1 1.0
N C:TYR998 3.9 98.0 1.0
O5G C:HTL1204 4.0 89.0 1.0
CA C:TYR998 4.0 97.6 1.0
O22 C:HTL1204 4.0 84.0 1.0
CG2 C:THR995 4.1 97.9 1.0
OG C:SER999 4.1 88.0 1.0
N C:ASP967 4.1 95.7 1.0
N C:THR995 4.2 0.6 1.0
CA C:VAL997 4.2 99.9 1.0
CA C:THR995 4.3 0.1 1.0
CB C:ASP967 4.4 92.2 1.0
O12 C:HTL1204 4.4 87.6 1.0
C C:TYR998 4.4 98.6 1.0
C C:THR995 4.5 0.2 1.0
N C:GLY968 4.5 78.5 1.0
N C:GLU996 4.6 0.0 1.0
CB C:SER999 4.6 92.2 1.0
O21 C:HTL1204 4.7 81.8 1.0
O C:LEU993 4.8 89.6 1.0
CA C:ASP967 4.8 87.6 1.0
CA C:SER999 4.8 97.4 1.0
CG2 C:VAL997 4.9 91.5 1.0
CD1 C:TYR998 5.0 94.2 1.0
CA C:GLY966 5.0 0.5 1.0

Magnesium binding site 4 out of 6 in 6cip

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Magnesium binding site 4 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-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 Acetyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1205

b:36.6
occ:1.00
 OD1 D:ASP967 2.0 95.1 1.0
O13 D:HTL1204 2.1 90.8 1.0
O23 D:HTL1204 2.1 91.4 1.0
O D:HOH1301 2.2 40.5 1.0
O D:VAL997 2.2 76.2 1.0
OG1 D:THR995 2.4 73.7 1.0
CG D:ASP967 3.1 88.7 1.0
P1 D:HTL1204 3.2 79.9 1.0
P2 D:HTL1204 3.2 82.3 1.0
O11 D:HTL1204 3.4 82.8 1.0
C D:VAL997 3.5 82.2 1.0
CB D:THR995 3.7 74.9 1.0
OD2 D:ASP967 3.7 89.2 1.0
N D:ASP967 3.8 80.4 1.0
O22 D:HTL1204 3.9 74.2 1.0
N D:SER999 3.9 0.2 1.0
OG D:SER999 3.9 0.7 1.0
O5G D:HTL1204 4.0 79.9 1.0
N D:THR995 4.0 81.6 1.0
CG2 D:THR995 4.1 83.3 1.0
CB D:ASP967 4.2 84.4 1.0
N D:VAL997 4.2 86.0 1.0
N D:GLY968 4.2 73.1 1.0
CA D:TYR998 4.2 92.1 1.0
O D:LEU993 4.3 74.7 1.0
N D:TYR998 4.3 88.0 1.0
CA D:THR995 4.3 81.5 1.0
O12 D:HTL1204 4.4 81.9 1.0
CA D:ASP967 4.4 81.0 1.0
CB D:SER999 4.5 0.9 1.0
CA D:VAL997 4.5 83.1 1.0
O21 D:HTL1204 4.5 84.4 1.0
CA D:GLY966 4.6 67.6 1.0
C D:TYR998 4.6 94.0 1.0
C D:THR995 4.6 77.2 1.0
C D:GLY966 4.6 68.3 1.0
N D:GLU996 4.7 77.3 1.0
CA D:SER999 4.8 0.1 1.0
C D:ASP967 4.8 76.1 1.0

Magnesium binding site 5 out of 6 in 6cip

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Magnesium binding site 5 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-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 Acetyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1205

b:43.7
occ:1.00
 OG1 E:THR995 2.0 83.6 1.0
O E:HOH1306 2.0 50.9 1.0
O21 E:HTL1204 2.1 86.6 1.0
O E:VAL997 2.1 0.4 1.0
OD1 E:ASP967 2.2 95.2 1.0
O12 E:HTL1204 2.2 84.4 1.0
P2 E:HTL1204 3.3 78.7 1.0
CG E:ASP967 3.3 88.7 1.0
C E:VAL997 3.3 0.5 1.0
P1 E:HTL1204 3.4 75.1 1.0
CB E:THR995 3.4 73.9 1.0
O11 E:HTL1204 3.5 77.5 1.0
OG E:SER999 3.8 0.1 1.0
N E:SER999 3.9 0.6 1.0
O22 E:HTL1204 3.9 74.3 1.0
N E:ASP967 3.9 72.3 1.0
OD2 E:ASP967 3.9 92.8 1.0
N E:THR995 4.0 73.4 1.0
CG2 E:THR995 4.0 65.8 1.0
N E:VAL997 4.0 89.7 1.0
CA E:THR995 4.1 76.5 1.0
O5G E:HTL1204 4.1 76.4 1.0
N E:TYR998 4.2 0.0 1.0
CA E:TYR998 4.2 0.3 1.0
CA E:VAL997 4.3 97.5 1.0
C E:THR995 4.4 74.3 1.0
CB E:ASP967 4.4 80.5 1.0
CB E:SER999 4.4 0.2 1.0
N E:GLY968 4.4 68.9 1.0
N E:GLU996 4.5 75.0 1.0
O23 E:HTL1204 4.5 88.2 1.0
O13 E:HTL1204 4.5 80.1 1.0
O E:LEU993 4.5 66.6 1.0
C E:TYR998 4.6 0.8 1.0
CA E:ASP967 4.6 74.7 1.0
CA E:GLY966 4.7 64.5 1.0
CA E:SER999 4.8 0.5 1.0
C E:GLY966 4.8 65.3 1.0
OE2 E:GLU814 4.8 66.1 1.0
CG2 E:VAL997 5.0 0.7 1.0
O E:THR995 5.0 76.7 1.0

Magnesium binding site 6 out of 6 in 6cip

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

b:33.5
occ:1.00
 O F:HOH1303 1.9 34.1 1.0
O12 F:HTL1204 2.0 76.1 1.0
OD1 F:ASP967 2.1 81.3 1.0
O F:VAL997 2.1 84.2 1.0
O23 F:HTL1204 2.2 75.8 1.0
OG1 F:THR995 2.4 78.9 1.0
P1 F:HTL1204 3.1 71.7 1.0
CG F:ASP967 3.1 76.0 1.0
P2 F:HTL1204 3.2 68.4 1.0
O11 F:HTL1204 3.2 72.6 1.0
C F:VAL997 3.4 80.7 1.0
OD2 F:ASP967 3.6 79.7 1.0
CB F:THR995 3.7 76.8 1.0
O21 F:HTL1204 3.8 54.8 1.0
N F:SER999 3.9 0.3 1.0
N F:ASP967 3.9 63.9 1.0
O5G F:HTL1204 3.9 74.0 1.0
CA F:TYR998 4.1 89.0 1.0
OG F:SER999 4.1 0.0 1.0
N F:THR995 4.1 74.0 1.0
N F:TYR998 4.2 82.0 1.0
CG2 F:THR995 4.2 74.5 1.0
N F:VAL997 4.2 73.8 1.0
N F:GLY968 4.2 54.0 1.0
O13 F:HTL1204 4.3 69.6 1.0
CB F:ASP967 4.3 68.2 1.0
CA F:THR995 4.4 76.0 1.0
CA F:VAL997 4.4 78.1 1.0
O22 F:HTL1204 4.5 70.5 1.0
O F:LEU993 4.5 59.0 1.0
C F:TYR998 4.5 96.0 1.0
CA F:ASP967 4.5 63.9 1.0
CB F:SER999 4.6 0.8 1.0
CA F:GLY966 4.7 59.4 1.0
C F:THR995 4.7 73.6 1.0
C F:GLY966 4.7 57.3 1.0
N F:GLU996 4.8 73.4 1.0
CA F:SER999 4.9 0.6 1.0
C F:ASP967 4.9 58.7 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 22:21:37 2024

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