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Magnesium in PDB 9iz4: Crystal Structure of Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate

Protein crystallography data

The structure of Crystal Structure of Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate, PDB code: 9iz4 was solved by A.Nakamura, S.Kojima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.55 / 3.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.115, 156.494, 172.971, 90, 90, 90
R / Rfree (%) 23.2 / 27.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate (pdb code 9iz4). 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 Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate, PDB code: 9iz4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 9iz4

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Magnesium binding site 1 out of 6 in the Crystal Structure of Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate


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 Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:72.8
occ:1.00
 OD1 B:ASN99 2.0 75.2 1.0
O2B B:TPP502 2.2 71.6 1.0
O1B B:TPP502 2.2 68.1 1.0
O1A B:TPP502 2.2 66.5 1.0
ND2 B:ASN99 2.6 74.9 1.0
CG B:ASN99 2.6 73.8 1.0
PB B:TPP502 2.6 70.6 1.0
OD1 B:ASP71 2.7 65.4 1.0
O B:MET101 3.2 68.8 1.0
PA B:TPP502 3.3 69.3 1.0
O3A B:TPP502 3.3 68.9 1.0
O B:LEU97 3.9 71.5 1.0
CG B:ASP71 3.9 63.9 1.0
O3B B:TPP502 4.0 73.7 1.0
CB B:ASN99 4.1 69.1 1.0
N B:ASP71 4.2 60.1 1.0
N B:ASN99 4.3 68.5 1.0
O7 B:TPP502 4.3 66.8 1.0
O2A B:TPP502 4.3 65.2 1.0
CA B:GLY70 4.4 62.6 1.0
C B:MET101 4.5 70.7 1.0
N B:GLU103 4.6 67.7 1.0
OD2 B:ASP71 4.6 63.4 1.0
CB B:GLU103 4.7 74.5 1.0
CA B:ASN99 4.7 66.8 1.0
C B:GLY70 4.8 61.3 1.0
N B:GLY72 4.8 63.3 1.0

Magnesium binding site 2 out of 6 in 9iz4

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Magnesium binding site 2 out of 6 in the Crystal Structure of Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate


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 Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:74.6
occ:1.00
 O1A D:TPP502 2.1 69.5 1.0
OD1 D:ASP71 2.2 68.6 1.0
O D:MET101 2.2 74.4 1.0
O3B D:TPP502 2.3 75.2 1.0
OD1 D:ASN99 2.3 78.9 1.0
O1B D:TPP502 2.7 66.5 1.0
PB D:TPP502 3.0 77.8 1.0
ND2 D:ASN99 3.0 78.1 1.0
CG D:ASN99 3.0 79.7 1.0
CG D:ASP71 3.0 72.1 1.0
OD2 D:ASP71 3.2 75.6 1.0
PA D:TPP502 3.3 68.5 1.0
C D:MET101 3.4 76.9 1.0
O3A D:TPP502 3.6 81.4 1.0
O7 D:TPP502 3.9 67.8 1.0
N D:GLU103 4.1 73.3 1.0
N D:ASP71 4.1 65.2 1.0
N D:GLY72 4.2 68.5 1.0
N D:MET101 4.2 78.6 1.0
CA D:HIS102 4.3 74.0 1.0
N D:HIS102 4.3 77.6 1.0
O2B D:TPP502 4.3 73.3 1.0
CB D:ASP71 4.4 69.2 1.0
CB D:ASN99 4.4 79.1 1.0
CA D:MET101 4.5 77.8 1.0
O2A D:TPP502 4.5 65.8 1.0
N D:ASN99 4.7 75.8 1.0
CA D:ASP71 4.7 65.7 1.0
CB D:GLU103 4.7 80.3 1.0
C D:HIS102 4.7 76.3 1.0
O D:LEU97 4.8 70.2 1.0
CA D:GLY70 4.9 62.4 1.0
C D:GLY70 4.9 61.8 1.0
N D:GLY100 4.9 72.7 1.0
OG1 D:THR110 4.9 76.5 1.0
CA D:ASN99 4.9 74.0 1.0
C D:ASP71 4.9 68.9 1.0

Magnesium binding site 3 out of 6 in 9iz4

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Magnesium binding site 3 out of 6 in the Crystal Structure of Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate


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 Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:77.5
occ:1.00
 OD1 F:ASN99 2.0 83.6 1.0
OD1 F:ASP71 2.1 75.0 1.0
O F:MET101 2.2 78.5 1.0
O1B F:TPP502 2.3 79.4 1.0
O2A F:TPP502 2.4 72.7 1.0
CG F:ASP71 2.9 76.8 1.0
OD2 F:ASP71 3.0 79.1 1.0
CG F:ASN99 3.0 82.6 1.0
O2B F:TPP502 3.0 74.5 1.0
PB F:TPP502 3.1 77.9 1.0
C F:MET101 3.4 81.2 1.0
ND2 F:ASN99 3.4 78.1 1.0
PA F:TPP502 3.5 73.9 1.0
O3A F:TPP502 3.6 78.2 1.0
N F:MET101 4.0 79.5 1.0
O7 F:TPP502 4.1 75.5 1.0
N F:ASN99 4.1 78.5 1.0
N F:ASP71 4.2 72.5 1.0
O F:LEU97 4.3 74.6 1.0
N F:GLY72 4.3 72.1 1.0
CB F:ASP71 4.3 74.4 1.0
CA F:MET101 4.3 81.1 1.0
N F:HIS102 4.3 79.1 1.0
N F:GLU103 4.4 79.0 1.0
CB F:ASN99 4.4 84.0 1.0
O3B F:TPP502 4.4 74.8 1.0
CA F:HIS102 4.5 76.0 1.0
N F:GLY100 4.6 81.2 1.0
CA F:ASN99 4.7 78.7 1.0
CA F:ASP71 4.7 75.1 1.0
O1A F:TPP502 4.8 71.9 1.0
C F:ASN99 4.9 80.5 1.0
CG F:MET101 5.0 83.4 1.0
C F:HIS102 5.0 77.9 1.0
CB F:GLU103 5.0 87.5 1.0
C F:ASP71 5.0 72.5 1.0

Magnesium binding site 4 out of 6 in 9iz4

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Magnesium binding site 4 out of 6 in the Crystal Structure of Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate


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 Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg501

b:80.1
occ:1.00
 O H:MET101 2.1 87.0 1.0
O1B H:TPP502 2.2 85.3 1.0
OD1 H:ASP71 2.2 77.2 1.0
O2A H:TPP502 2.3 76.6 1.0
ND2 H:ASN99 2.3 86.5 1.0
O3B H:TPP502 2.5 89.5 1.0
OD1 H:ASN99 2.5 86.8 1.0
CG H:ASN99 2.7 87.4 1.0
PB H:TPP502 2.8 92.0 1.0
CG H:ASP71 3.0 78.6 1.0
OD2 H:ASP71 3.2 80.1 1.0
C H:MET101 3.3 88.1 1.0
PA H:TPP502 3.3 79.1 1.0
O3A H:TPP502 3.5 85.9 1.0
N H:MET101 3.9 89.7 1.0
O7 H:TPP502 4.0 78.3 1.0
N H:GLY72 4.0 76.3 1.0
N H:ASP71 4.1 74.0 1.0
O2B H:TPP502 4.1 84.5 1.0
CA H:MET101 4.1 90.2 1.0
CB H:ASN99 4.2 85.9 1.0
N H:HIS102 4.2 85.7 1.0
N H:GLU103 4.2 86.0 1.0
CA H:HIS102 4.3 84.3 1.0
CB H:ASP71 4.4 75.6 1.0
N H:ASN99 4.5 82.4 1.0
O1A H:TPP502 4.6 78.2 1.0
CA H:ASP71 4.6 73.8 1.0
CB H:MET101 4.7 88.2 1.0
N H:GLY100 4.8 86.5 1.0
CA H:ASN99 4.8 83.0 1.0
O H:LEU97 4.8 78.4 1.0
C H:ASP71 4.8 75.1 1.0
CA H:GLY72 4.8 75.1 1.0
CA H:GLY70 4.9 72.0 1.0
C H:GLY70 4.9 72.6 1.0
C H:HIS102 4.9 86.8 1.0
C H:ASN99 4.9 85.8 1.0
CB H:GLU103 5.0 92.4 1.0

Magnesium binding site 5 out of 6 in 9iz4

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Magnesium binding site 5 out of 6 in the Crystal Structure of Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate


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 Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg501

b:73.8
occ:1.00
 OD1 J:ASN99 2.1 78.5 1.0
OD1 J:ASP71 2.2 72.2 1.0
O1B J:TPP502 2.3 72.0 1.0
O2B J:TPP502 2.3 74.0 1.0
O2A J:TPP502 2.3 71.7 1.0
O J:MET101 2.7 79.2 1.0
PB J:TPP502 2.7 72.2 1.0
CG J:ASN99 2.9 79.5 1.0
ND2 J:ASN99 3.0 77.5 1.0
CG J:ASP71 3.1 72.6 1.0
OD2 J:ASP71 3.3 73.3 1.0
PA J:TPP502 3.4 73.3 1.0
O3A J:TPP502 3.4 69.8 1.0
C J:MET101 3.9 78.9 1.0
O3B J:TPP502 4.1 76.2 1.0
O7 J:TPP502 4.1 73.7 1.0
N J:ASP71 4.3 67.5 1.0
CB J:ASN99 4.3 80.4 1.0
N J:ASN99 4.3 73.8 1.0
N J:GLU103 4.4 79.0 1.0
CB J:ASP71 4.5 70.2 1.0
N J:GLY72 4.5 69.7 1.0
N J:MET101 4.5 81.3 1.0
O J:LEU97 4.5 76.2 1.0
O1A J:TPP502 4.6 69.5 1.0
CA J:HIS102 4.7 73.6 1.0
N J:HIS102 4.7 79.2 1.0
CA J:ASN99 4.8 77.5 1.0
CB J:GLU103 4.8 83.4 1.0
CA J:ASP71 4.9 65.1 1.0
CA J:MET101 4.9 78.7 1.0
N J:GLY100 5.0 78.7 1.0

Magnesium binding site 6 out of 6 in 9iz4

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Magnesium binding site 6 out of 6 in the Crystal Structure of Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate


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 Phosphonopyruvate Decarboxylase Rhief From Bacillus Subtilis ATCC6633 in Complex with Thiamine Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg501

b:83.0
occ:1.00
 O1A L:TPP502 2.1 81.5 1.0
O L:MET101 2.1 87.3 1.0
OD1 L:ASN99 2.2 82.8 1.0
O1B L:TPP502 2.3 84.1 1.0
OD1 L:ASP71 2.5 76.6 1.0
O3B L:TPP502 2.6 85.0 1.0
PB L:TPP502 2.9 86.5 1.0
OD2 L:ASP71 3.0 81.0 1.0
CG L:ASP71 3.0 80.2 1.0
CG L:ASN99 3.1 84.3 1.0
PA L:TPP502 3.2 77.5 1.0
ND2 L:ASN99 3.3 86.0 1.0
C L:MET101 3.3 86.8 1.0
O3A L:TPP502 3.5 76.8 1.0
O7 L:TPP502 3.8 84.1 1.0
N L:GLY72 4.0 73.9 1.0
N L:MET101 4.0 84.2 1.0
N L:HIS102 4.2 84.4 1.0
CA L:HIS102 4.2 80.9 1.0
O2B L:TPP502 4.2 86.2 1.0
N L:GLU103 4.3 83.6 1.0
CA L:MET101 4.3 84.7 1.0
N L:ASP71 4.4 74.6 1.0
CB L:ASP71 4.4 75.4 1.0
O2A L:TPP502 4.5 81.2 1.0
CB L:ASN99 4.5 80.5 1.0
N L:ASN99 4.6 80.4 1.0
O L:LEU97 4.8 80.2 1.0
CA L:GLY72 4.8 71.8 1.0
CA L:ASP71 4.8 73.4 1.0
N L:GLY100 4.8 80.7 1.0
C L:HIS102 4.9 80.5 1.0
C L:ASP71 4.9 74.0 1.0
OG1 L:THR110 4.9 85.9 1.0
CA L:ASN99 5.0 80.7 1.0
CG L:MET101 5.0 84.7 1.0

Reference:

A.Nakamura, A.Shiina, T.Fukaya, Y.Seki, M.Momiyama, S.Kojima. Structural Analysis of Phosphonopyruvate Decarboxylase Rhief: First Insights Into An Ancestral Heterooligomeric Thiamine Pyrophosphate-Dependent Decarboxylase. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 39586109
DOI: 10.1021/ACS.BIOCHEM.4C00559
Page generated: Sat Aug 16 04:40:04 2025

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