Magnesium in PDB 8vzj: Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp

Protein crystallography data

The structure of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp, PDB code: 8vzj was solved by Y.Kim, P.Gade, M.Endres, S.Lee, Y.Yoshikuni, R.Gonzalez, K.Michalska, A.Joachimiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.53 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 324.22, 77.84, 229.55, 90, 134.53, 90
R / Rfree (%) 19.7 / 23.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp (pdb code 8vzj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp, PDB code: 8vzj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8vzj

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Magnesium binding site 1 out of 8 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp


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 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:54.4
occ:1.00
 O2A A:TPP601 2.0 54.7 1.0
OD1 A:ASN469 2.0 56.5 1.0
O A:GLY471 2.3 58.9 1.0
O2B A:TPP601 2.3 56.7 1.0
OD1 A:ASP441 2.5 52.6 1.0
CG A:ASN469 2.8 58.0 1.0
PA A:TPP601 3.1 54.3 1.0
ND2 A:ASN469 3.1 58.7 1.0
PB A:TPP601 3.1 60.5 1.0
O3A A:TPP601 3.2 57.3 1.0
O1B A:TPP601 3.4 57.8 1.0
C A:GLY471 3.5 59.0 1.0
O7 A:TPP601 3.5 56.8 1.0
CG A:ASP441 3.5 53.2 1.0
N A:GLY473 3.8 57.5 1.0
OD2 A:ASP441 3.9 54.8 1.0
CB A:ASN469 4.3 58.1 1.0
CA A:ILE472 4.3 60.1 1.0
N A:ILE472 4.3 61.4 1.0
N A:ASP441 4.3 49.0 1.0
N A:GLY471 4.4 59.8 1.0
O1A A:TPP601 4.4 55.0 1.0
N A:SER442 4.4 50.2 1.0
N A:ASN469 4.4 56.4 1.0
N A:GLY474 4.5 58.4 1.0
C A:ILE472 4.5 60.8 1.0
O3B A:TPP601 4.5 64.5 1.0
CA A:GLY471 4.5 60.3 1.0
CA A:GLY473 4.6 57.9 1.0
CB A:SER442 4.7 55.6 1.0
CA A:ASN469 4.7 58.0 1.0
CB A:ASP441 4.8 51.6 1.0
O A:ILE467 4.8 53.5 1.0
C7 A:TPP601 4.8 57.3 1.0
C A:ASN469 4.9 58.2 1.0
OH A:TYR367 4.9 59.9 1.0
CA A:ASP441 5.0 50.8 1.0
CA A:GLY440 5.0 59.0 1.0

Magnesium binding site 2 out of 8 in 8vzj

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Magnesium binding site 2 out of 8 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp


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 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:58.2
occ:1.00
 OD1 B:ASN469 1.9 62.6 1.0
O2A B:TPP601 2.0 58.5 1.0
OD1 B:ASP441 2.1 58.9 1.0
O1B B:TPP601 2.3 61.9 1.0
O B:GLY471 2.4 57.6 1.0
CG B:ASN469 3.0 62.4 1.0
PA B:TPP601 3.0 60.1 1.0
O3A B:TPP601 3.1 61.1 1.0
PB B:TPP601 3.1 64.2 1.0
CG B:ASP441 3.1 58.6 1.0
ND2 B:ASN469 3.5 64.6 1.0
OD2 B:ASP441 3.5 57.7 1.0
C B:GLY471 3.6 57.0 1.0
O2B B:TPP601 3.6 65.7 1.0
O7 B:TPP601 3.7 58.6 1.0
N B:ASP441 4.0 58.1 1.0
N B:ASN469 4.1 64.1 1.0
N B:GLY473 4.2 57.3 1.0
N B:GLY471 4.2 59.4 1.0
N B:SER442 4.3 55.2 1.0
CB B:ASN469 4.3 65.6 1.0
O1A B:TPP601 4.3 58.8 1.0
O B:ILE467 4.3 61.0 1.0
CB B:ASP441 4.4 57.6 1.0
N B:ILE472 4.5 57.3 1.0
O3B B:TPP601 4.5 66.7 1.0
CA B:GLY471 4.5 57.2 1.0
CA B:ILE472 4.6 55.4 1.0
CA B:ASN469 4.6 65.1 1.0
CA B:ASP441 4.6 57.6 1.0
CA B:GLY440 4.7 58.5 1.0
C B:GLY440 4.7 58.1 1.0
C B:ASN469 4.7 63.0 1.0
CB B:SER442 4.8 54.1 1.0
N B:GLY474 4.8 61.2 1.0
C B:ILE472 4.9 56.5 1.0
N B:ASN470 4.9 62.6 1.0
C B:ASP441 5.0 56.3 1.0

Magnesium binding site 3 out of 8 in 8vzj

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Magnesium binding site 3 out of 8 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp


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 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:75.7
occ:1.00
 O1B C:TPP601 2.0 77.9 1.0
O2A C:TPP601 2.2 76.7 1.0
OD1 C:ASN469 2.2 79.4 1.0
O C:HOH701 2.3 78.6 1.0
O C:GLY471 2.5 78.7 1.0
PB C:TPP601 2.7 81.4 1.0
OD1 C:ASP441 2.7 78.2 1.0
O3A C:TPP601 2.9 79.9 1.0
PA C:TPP601 2.9 76.4 1.0
CG C:ASN469 3.0 78.9 1.0
ND2 C:ASN469 3.1 78.5 1.0
O2B C:TPP601 3.1 84.3 1.0
O7 C:TPP601 3.3 78.7 1.0
CG C:ASP441 3.7 78.3 1.0
C C:GLY471 3.7 79.1 1.0
N C:GLY473 3.7 74.9 1.0
OD2 C:ASP441 3.9 79.1 1.0
O3B C:TPP601 4.2 84.9 1.0
CA C:ILE472 4.2 76.5 1.0
O1A C:TPP601 4.4 77.0 1.0
N C:ILE472 4.4 78.1 1.0
C C:ILE472 4.4 75.8 1.0
CB C:ASN469 4.4 80.9 1.0
N C:ASP441 4.4 74.2 1.0
N C:GLY474 4.4 78.2 1.0
N C:SER442 4.5 76.0 1.0
CA C:GLY473 4.5 74.9 1.0
N C:ASN469 4.5 79.0 1.0
C7 C:TPP601 4.6 76.7 1.0
CB C:SER442 4.6 76.8 1.0
N C:GLY471 4.7 81.7 1.0
O C:ILE467 4.8 81.1 1.0
CA C:GLY471 4.8 80.9 1.0
OH C:TYR367 4.8 86.7 1.0
CA C:ASN469 4.9 79.2 1.0
CA C:GLY440 4.9 77.9 1.0
C C:GLY473 5.0 75.5 1.0
CB C:ASP441 5.0 78.5 1.0

Magnesium binding site 4 out of 8 in 8vzj

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Magnesium binding site 4 out of 8 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp


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 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:72.1
occ:1.00
 O2B D:TPP601 2.0 76.1 1.0
OD1 D:ASN469 2.0 77.5 1.0
O2A D:TPP601 2.1 74.8 1.0
OD1 D:ASP441 2.3 74.2 1.0
O D:GLY471 2.7 75.3 1.0
PB D:TPP601 2.9 77.3 1.0
CG D:ASN469 2.9 77.0 1.0
O3A D:TPP601 3.1 75.4 1.0
PA D:TPP601 3.1 75.9 1.0
CG D:ASP441 3.3 75.6 1.0
ND2 D:ASN469 3.3 79.3 1.0
O1B D:TPP601 3.4 79.1 1.0
OD2 D:ASP441 3.6 76.5 1.0
O7 D:TPP601 3.7 75.0 1.0
C D:GLY471 3.9 76.0 1.0
N D:GLY473 4.0 80.5 1.0
N D:ASP441 4.0 73.2 1.0
N D:ASN469 4.2 78.0 1.0
CB D:ASN469 4.2 76.1 1.0
O3B D:TPP601 4.2 79.0 1.0
O D:ILE467 4.3 75.8 1.0
O1A D:TPP601 4.4 77.0 1.0
N D:SER442 4.5 78.0 1.0
CB D:ASP441 4.6 74.4 1.0
CA D:ILE472 4.6 71.7 1.0
CA D:ASN469 4.6 78.9 1.0
CA D:GLY440 4.7 75.2 1.0
N D:GLY471 4.7 80.3 1.0
N D:ILE472 4.7 72.3 1.0
C D:GLY440 4.8 74.4 1.0
CA D:ASP441 4.8 73.8 1.0
CA D:GLY473 4.8 80.9 1.0
C D:ILE472 4.8 75.5 1.0
OH D:TYR367 4.9 82.7 1.0
CA D:GLY471 5.0 78.1 1.0
C7 D:TPP601 5.0 74.6 1.0
C D:ASN469 5.0 79.8 1.0

Magnesium binding site 5 out of 8 in 8vzj

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Magnesium binding site 5 out of 8 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp


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 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:70.6
occ:1.00
 O2B E:TPP601 2.0 73.1 1.0
O2A E:TPP601 2.2 70.2 1.0
OD1 E:ASN469 2.3 76.2 1.0
O E:GLY471 2.3 74.1 1.0
OD1 E:ASP441 2.4 74.0 1.0
O E:HOH701 2.5 71.0 1.0
O3A E:TPP601 2.6 73.5 1.0
PB E:TPP601 2.9 74.3 1.0
PA E:TPP601 2.9 70.2 1.0
CG E:ASP441 3.2 75.9 1.0
CG E:ASN469 3.3 72.8 1.0
OD2 E:ASP441 3.4 77.6 1.0
C E:GLY471 3.5 72.9 1.0
ND2 E:ASN469 3.7 70.9 1.0
N E:GLY473 3.8 71.2 1.0
O1B E:TPP601 3.8 75.7 1.0
O3B E:TPP601 4.0 77.0 1.0
O1A E:TPP601 4.0 74.4 1.0
O7 E:TPP601 4.1 72.9 1.0
N E:ASP441 4.2 69.6 1.0
CA E:ILE472 4.3 67.7 1.0
N E:ILE472 4.3 70.1 1.0
N E:GLY471 4.4 80.5 1.0
N E:SER442 4.5 72.5 1.0
N E:ASN469 4.5 77.6 1.0
C E:ILE472 4.5 70.3 1.0
CA E:GLY471 4.5 76.5 1.0
CB E:ASP441 4.6 75.8 1.0
N E:GLY474 4.6 75.7 1.0
CB E:ASN469 4.7 71.2 1.0
CA E:GLY473 4.7 71.5 1.0
O E:ILE467 4.7 71.4 1.0
CA E:ASP441 4.9 71.9 1.0
CA E:GLY440 4.9 69.8 1.0
CB E:SER442 5.0 69.1 1.0
CA E:ASN469 5.0 76.3 1.0
OH E:TYR367 5.0 77.4 1.0
C E:GLY473 5.0 74.1 1.0

Magnesium binding site 6 out of 8 in 8vzj

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Magnesium binding site 6 out of 8 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp


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 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg604

b:82.8
occ:1.00
 OD1 F:ASN469 2.0 85.7 1.0
O1B F:TPP601 2.2 86.7 1.0
O F:GLY471 2.2 85.3 1.0
O2A F:TPP601 2.3 82.9 1.0
O F:HOH701 2.7 82.1 1.0
CG F:ASN469 2.7 86.2 1.0
ND2 F:ASN469 2.8 85.9 1.0
OD1 F:ASP441 2.9 85.4 1.0
PB F:TPP601 3.0 86.1 1.0
PA F:TPP601 3.2 80.8 1.0
O3A F:TPP601 3.2 83.0 1.0
O3B F:TPP601 3.4 83.4 1.0
N F:GLY473 3.4 85.0 1.0
C F:GLY471 3.4 85.2 1.0
O7 F:TPP601 3.5 80.4 1.0
CG F:ASP441 3.8 85.7 1.0
N F:GLY474 4.0 93.8 1.0
CA F:ILE472 4.0 80.7 1.0
OD2 F:ASP441 4.0 85.7 1.0
C F:ILE472 4.1 83.8 1.0
N F:ILE472 4.2 83.3 1.0
CB F:ASN469 4.2 87.5 1.0
CA F:GLY473 4.2 87.5 1.0
O2B F:TPP601 4.5 86.6 1.0
N F:GLY471 4.5 87.2 1.0
N F:ASN469 4.5 86.7 1.0
CA F:GLY471 4.6 85.5 1.0
O1A F:TPP601 4.6 81.0 1.0
C F:GLY473 4.6 91.4 1.0
CA F:ASN469 4.8 88.0 1.0
N F:ASP441 4.8 79.7 1.0
C7 F:TPP601 4.8 78.5 1.0
N F:SER442 4.9 81.0 1.0
OH F:TYR367 4.9 85.0 1.0
C F:ASN469 4.9 88.2 1.0
CA F:GLY474 5.0 93.7 1.0

Magnesium binding site 7 out of 8 in 8vzj

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Magnesium binding site 7 out of 8 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg604

b:80.7
occ:1.00
 O2A G:TPP601 2.1 78.4 1.0
O1B G:TPP601 2.2 82.8 1.0
OD1 G:ASN469 2.2 85.5 1.0
O G:GLY471 2.2 82.6 1.0
OD1 G:ASP441 2.3 82.9 1.0
O G:HOH701 2.6 82.3 1.0
CG G:ASN469 3.1 84.5 1.0
PA G:TPP601 3.2 77.0 1.0
PB G:TPP601 3.2 81.0 1.0
CG G:ASP441 3.2 84.4 1.0
O3A G:TPP601 3.3 78.9 1.0
ND2 G:ASN469 3.4 83.7 1.0
C G:GLY471 3.4 82.8 1.0
OD2 G:ASP441 3.5 86.2 1.0
O7 G:TPP601 3.6 78.0 1.0
N G:GLY473 3.7 81.1 1.0
O3B G:TPP601 4.0 82.3 1.0
CA G:ILE472 4.2 77.9 1.0
N G:ILE472 4.3 81.7 1.0
N G:ASP441 4.3 79.9 1.0
N G:GLY471 4.3 87.3 1.0
N G:GLY474 4.4 90.8 1.0
N G:ASN469 4.4 87.4 1.0
C G:ILE472 4.4 80.3 1.0
N G:SER442 4.5 77.0 1.0
O2B G:TPP601 4.5 85.2 1.0
CA G:GLY471 4.5 86.3 1.0
CA G:GLY473 4.5 85.3 1.0
CB G:ASN469 4.5 85.7 1.0
O1A G:TPP601 4.5 77.6 1.0
CB G:ASP441 4.6 83.8 1.0
O G:ILE467 4.8 87.8 1.0
CB G:SER442 4.8 74.6 1.0
CA G:ASP441 4.9 81.7 1.0
CA G:ASN469 4.9 87.2 1.0
C7 G:TPP601 4.9 76.8 1.0
OH G:TYR367 4.9 90.1 1.0
C G:GLY473 5.0 90.0 1.0
C G:ASN469 5.0 87.6 1.0

Magnesium binding site 8 out of 8 in 8vzj

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Magnesium binding site 8 out of 8 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Dhchacs From Dehalococcoidia Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg604

b:87.0
occ:1.00
 OD1 H:ASN469 1.9 94.7 1.0
O2A H:TPP601 2.0 85.0 1.0
O2B H:TPP601 2.2 90.8 1.0
OD1 H:ASP441 2.3 86.8 1.0
CG H:ASN469 2.8 96.7 1.0
O H:GLY471 2.8 85.8 1.0
PB H:TPP601 3.2 89.8 1.0
PA H:TPP601 3.2 84.3 1.0
ND2 H:ASN469 3.2 97.8 1.0
O3A H:TPP601 3.2 89.2 1.0
N H:ASP441 3.5 81.7 1.0
CG H:ASP441 3.5 87.4 1.0
O1B H:TPP601 3.7 89.8 1.0
N H:ASN469 3.8 97.1 1.0
O H:ILE467 3.9 91.4 1.0
O7 H:TPP601 4.0 83.6 1.0
C H:GLY471 4.1 86.9 1.0
CB H:ASN469 4.1 98.6 1.0
CA H:GLY440 4.1 83.9 1.0
C H:GLY440 4.2 82.5 1.0
CB H:ASP441 4.3 86.2 1.0
O1A H:TPP601 4.3 84.0 1.0
N H:SER442 4.3 79.7 1.0
CA H:ASP441 4.3 82.8 1.0
CA H:ASN469 4.4 98.3 1.0
OD2 H:ASP441 4.5 89.0 1.0
O3B H:TPP601 4.5 96.7 1.0
N H:GLY473 4.5 83.3 1.0
N H:GLY471 4.6 93.6 1.0
OH H:TYR367 4.7 104.9 1.0
C H:ASN469 4.7 97.5 1.0
C H:ASP441 4.8 82.3 1.0
C H:ASN468 4.8 97.3 1.0
CA H:ASN468 4.9 94.6 1.0
CA H:GLY471 4.9 90.0 1.0
N H:ASN470 4.9 96.6 1.0
N H:ILE472 5.0 83.2 1.0
C H:ILE467 5.0 91.8 1.0

Reference:

Y.Kim, S.H.Lee, P.Gade, M.Nattermann, N.Maltseva, M.Endres, J.Chen, P.Wichmann, Y.Hu, D.G.Marchal, Y.Yoshikuni, T.J.Erb, R.Gonzalez, K.Michalska, A.Joachimiak. Revealing Reaction Intermediates in One-Carbon Elongation By Thiamine Diphosphate/Coa-Dependent Enzyme Family. Commun Chem V. 7 160 2024.
ISSN: ESSN 2399-3669
PubMed: 39034323
DOI: 10.1038/S42004-024-01242-Y
Page generated: Thu Oct 31 22:16:21 2024

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