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Magnesium in PDB 8i07: Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde

Enzymatic activity of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde

All present enzymatic activity of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde:
4.1.1.47;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde, PDB code: 8i07 was solved by J.H.Kim, J.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.89 / 1.99
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 189.299, 189.299, 246.982, 90, 90, 90
R / Rfree (%) 20.8 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde (pdb code 8i07). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde, PDB code: 8i07:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8i07

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Magnesium binding site 1 out of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde


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 Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:20.6
occ:1.00
 OD1 A:ASN473 2.0 21.0 1.0
OD1 A:ASP446 2.1 21.2 1.0
O2A A:TPP604 2.1 18.6 1.0
O A:TYR475 2.2 18.9 1.0
O1B A:TPP604 2.2 19.9 1.0
O A:HOH821 2.3 18.8 1.0
CG A:ASN473 3.0 20.1 1.0
CG A:ASP446 3.2 18.7 1.0
PB A:TPP604 3.3 20.6 1.0
PA A:TPP604 3.3 19.1 1.0
C A:TYR475 3.3 19.0 1.0
ND2 A:ASN473 3.4 19.2 1.0
O3A A:TPP604 3.4 21.2 1.0
OD2 A:ASP446 3.7 18.8 1.0
N A:TYR475 3.8 19.1 1.0
N A:ASP446 3.8 18.5 1.0
O2B A:TPP604 3.9 20.4 1.0
O7 A:TPP604 4.0 18.9 1.0
CA A:TYR475 4.1 19.2 1.0
N A:ASN473 4.1 19.1 1.0
N A:GLY477 4.1 19.1 1.0
CB A:ASN473 4.3 19.3 1.0
N A:LEU476 4.4 19.0 1.0
CB A:ASP446 4.4 18.5 1.0
N A:PHE447 4.4 18.4 1.0
CB A:TYR475 4.5 19.4 1.0
CA A:GLY445 4.5 18.5 1.0
O3B A:TPP604 4.6 20.1 1.0
CA A:LEU476 4.6 19.0 1.0
C A:GLY445 4.6 18.4 1.0
O1A A:TPP604 4.6 19.2 1.0
CA A:ASN473 4.6 19.2 1.0
CA A:ASP446 4.6 18.4 1.0
O A:VAL471 4.6 18.8 1.0
N A:ALA474 4.6 19.1 1.0
C A:ASN473 4.7 19.3 1.0
C A:LEU476 4.9 19.1 1.0
C A:ALA474 5.0 19.2 1.0
CA A:GLY477 5.0 19.3 1.0

Magnesium binding site 2 out of 10 in 8i07

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Magnesium binding site 2 out of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde


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 Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:17.3
occ:0.39
 OE1 A:GLU454 2.2 17.2 0.9
O A:PHE451 2.5 17.4 1.0
CD A:GLU454 3.1 17.1 1.0
OE2 A:GLU454 3.6 17.1 1.0
C A:PHE451 3.6 17.5 1.0
CA A:LEU452 3.7 17.3 1.0
CD2 A:LEU452 3.9 17.1 1.0
N A:LEU452 4.1 17.4 1.0
N A:ILE453 4.3 17.4 1.0
C A:LEU452 4.3 17.3 1.0
CG A:GLU454 4.4 18.0 1.0
O A:GLN450 4.4 17.6 1.0
CD2 A:HIS50 4.7 16.9 1.0
N A:GLU454 4.7 17.3 1.0
CB A:LEU452 4.8 17.2 1.0
CB A:GLU454 4.9 17.6 1.0
CA A:PHE451 4.9 17.6 1.0
CG A:LEU452 4.9 17.2 1.0

Magnesium binding site 3 out of 10 in 8i07

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Magnesium binding site 3 out of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde


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 Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:21.2
occ:1.00
 O1A B:TPP604 2.0 21.5 1.0
OD1 B:ASP446 2.1 21.5 1.0
OD1 B:ASN473 2.1 23.5 1.0
O B:TYR475 2.2 20.5 1.0
O3B B:TPP604 2.2 23.9 1.0
O B:HOH786 2.2 20.4 1.0
CG B:ASN473 3.1 23.3 1.0
CG B:ASP446 3.2 19.0 1.0
PA B:TPP604 3.2 22.7 1.0
PB B:TPP604 3.3 23.6 1.0
O3A B:TPP604 3.3 23.9 1.0
C B:TYR475 3.3 23.9 1.0
ND2 B:ASN473 3.4 22.1 1.0
OD2 B:ASP446 3.7 19.0 1.0
N B:ASP446 3.7 18.8 1.0
N B:TYR475 3.8 21.5 1.0
O7 B:TPP604 4.0 21.8 1.0
O2B B:TPP604 4.0 24.1 1.0
CA B:TYR475 4.1 24.3 1.0
N B:GLY477 4.1 22.8 1.0
N B:ASN473 4.3 21.6 1.0
N B:PHE447 4.3 18.6 1.0
N B:LEU476 4.4 24.6 1.0
CB B:ASP446 4.4 19.0 1.0
CA B:GLY445 4.4 20.4 1.0
CB B:ASN473 4.5 21.5 1.0
O2A B:TPP604 4.5 19.2 1.0
CB B:TYR475 4.5 23.6 1.0
C B:GLY445 4.5 18.8 1.0
O1B B:TPP604 4.5 22.7 1.0
CA B:ASP446 4.5 18.9 1.0
O B:VAL471 4.6 19.5 1.0
CA B:LEU476 4.6 22.7 1.0
N B:ALA474 4.7 21.7 1.0
CA B:ASN473 4.7 22.0 1.0
C B:ASN473 4.9 23.6 1.0
C B:LEU476 4.9 22.9 1.0
C B:ASP446 5.0 18.9 1.0
CA B:GLY477 5.0 23.1 1.0

Magnesium binding site 4 out of 10 in 8i07

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Magnesium binding site 4 out of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde


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 Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:20.0
occ:0.49
 O B:PHE451 2.5 19.5 1.0
OE1 B:GLU454 2.6 20.4 0.8
CD B:GLU454 3.5 20.5 1.0
C B:PHE451 3.6 19.4 1.0
OE2 B:GLU454 3.8 20.4 1.0
CA B:LEU452 4.0 19.8 1.0
CD2 B:LEU452 4.1 19.6 1.0
N B:LEU452 4.2 19.6 1.0
O B:GLN450 4.4 19.6 1.0
CD2 B:HIS50 4.6 19.9 1.0
N B:ILE453 4.6 20.1 1.0
CG B:GLU454 4.6 20.9 1.0
C B:LEU452 4.7 20.1 1.0
CA B:PHE451 4.8 19.2 1.0

Magnesium binding site 5 out of 10 in 8i07

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Magnesium binding site 5 out of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde


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 Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:26.4
occ:1.00
 O1B C:TPP603 2.1 23.7 1.0
OD1 C:ASN473 2.1 26.3 1.0
O2A C:TPP603 2.1 25.2 1.0
O C:TYR475 2.2 24.8 1.0
OD1 C:ASP446 2.2 26.3 1.0
O C:HOH812 2.2 25.1 1.0
CG C:ASN473 3.0 26.2 1.0
PB C:TPP603 3.1 26.6 1.0
PA C:TPP603 3.2 27.2 1.0
O3A C:TPP603 3.2 26.9 1.0
ND2 C:ASN473 3.3 24.4 1.0
C C:TYR475 3.3 26.6 1.0
CG C:ASP446 3.3 26.7 1.0
O2B C:TPP603 3.8 27.3 1.0
O7 C:TPP603 3.9 26.0 1.0
OD2 C:ASP446 3.9 25.9 1.0
N C:TYR475 3.9 24.5 1.0
N C:ASP446 3.9 25.4 1.0
N C:GLY477 3.9 26.2 1.0
CA C:TYR475 4.1 26.6 1.0
N C:ASN473 4.3 25.6 1.0
N C:LEU476 4.3 28.1 1.0
CB C:TYR475 4.4 28.6 1.0
CB C:ASN473 4.4 25.8 1.0
O3B C:TPP603 4.4 25.9 1.0
CA C:LEU476 4.5 26.3 1.0
N C:PHE447 4.5 23.4 1.0
O1A C:TPP603 4.5 26.2 1.0
CA C:GLY445 4.6 26.6 1.0
CB C:ASP446 4.6 24.8 1.0
O C:VAL471 4.7 24.0 1.0
C C:GLY445 4.7 23.9 1.0
CA C:ASP446 4.7 25.2 1.0
CA C:ASN473 4.7 26.2 1.0
CA C:GLY477 4.7 25.3 1.0
N C:ALA474 4.8 24.6 1.0
C C:LEU476 4.8 27.0 1.0
C C:ASN473 4.9 26.7 1.0

Magnesium binding site 6 out of 10 in 8i07

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Magnesium binding site 6 out of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde


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 Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg606

b:27.1
occ:1.00
 OE1 E:GLU454 2.3 22.9 0.6
O C:PHE451 2.3 22.5 1.0
O E:PHE451 2.5 25.8 1.0
OE1 C:GLU454 2.6 25.6 0.9
CD E:GLU454 3.1 24.2 1.0
CD C:GLU454 3.3 25.4 1.0
C C:PHE451 3.4 25.1 1.0
OE2 E:GLU454 3.5 25.1 1.0
OE2 C:GLU454 3.5 25.1 1.0
C E:PHE451 3.6 25.6 1.0
CA C:LEU452 3.7 23.6 1.0
CA E:LEU452 3.7 24.7 1.0
CD2 E:LEU452 3.7 23.0 1.0
CD2 C:LEU452 3.8 22.8 1.0
N C:LEU452 3.9 24.5 1.0
N E:LEU452 4.1 24.3 1.0
C E:LEU452 4.3 25.1 1.0
N E:ILE453 4.4 26.2 1.0
C C:LEU452 4.4 25.5 1.0
O C:GLN450 4.4 24.4 1.0
N C:ILE453 4.4 25.3 1.0
CG E:GLU454 4.4 23.7 1.0
CD2 E:HIS50 4.5 25.1 1.0
O E:GLN450 4.5 24.2 1.0
CG C:GLU454 4.6 25.1 1.0
CB C:LEU452 4.7 22.2 1.0
CA C:PHE451 4.7 23.6 1.0
CG C:LEU452 4.7 23.5 1.0
CB E:LEU452 4.7 22.3 1.0
CG E:LEU452 4.7 23.5 1.0
CD2 C:HIS50 4.8 24.2 1.0
N E:GLU454 4.8 24.2 1.0
CA E:PHE451 4.9 23.7 1.0
N C:GLU454 5.0 23.7 1.0
CB E:GLU454 5.0 25.1 1.0

Magnesium binding site 7 out of 10 in 8i07

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Magnesium binding site 7 out of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde


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 Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:26.6
occ:1.00
 O1A D:TPP603 2.1 27.4 1.0
OD1 D:ASN473 2.1 29.1 1.0
O3B D:TPP603 2.1 29.0 1.0
O D:TYR475 2.1 27.7 1.0
OD1 D:ASP446 2.2 28.1 1.0
O D:HOH857 2.2 27.8 1.0
CG D:ASN473 3.1 30.2 1.0
PA D:TPP603 3.1 29.4 1.0
PB D:TPP603 3.2 30.7 1.0
O3A D:TPP603 3.2 27.6 1.0
CG D:ASP446 3.3 27.9 1.0
C D:TYR475 3.3 30.2 1.0
ND2 D:ASN473 3.4 28.0 1.0
N D:ASP446 3.8 25.3 1.0
OD2 D:ASP446 3.8 25.8 1.0
N D:TYR475 3.9 27.5 1.0
O2B D:TPP603 3.9 28.9 1.0
O7 D:TPP603 3.9 28.0 1.0
N D:GLY477 4.0 28.8 1.0
CA D:TYR475 4.1 28.6 1.0
N D:ASN473 4.3 29.5 1.0
N D:PHE447 4.3 24.4 1.0
N D:LEU476 4.4 30.7 1.0
CB D:TYR475 4.4 29.3 1.0
CB D:ASN473 4.5 28.1 1.0
O2A D:TPP603 4.5 26.5 1.0
O1B D:TPP603 4.5 29.4 1.0
CB D:ASP446 4.5 26.8 1.0
CA D:GLY445 4.5 26.4 1.0
CA D:LEU476 4.5 28.4 1.0
C D:GLY445 4.5 26.2 1.0
CA D:ASP446 4.6 25.9 1.0
N D:ALA474 4.6 29.1 1.0
O D:VAL471 4.7 29.2 1.0
CA D:ASN473 4.7 28.8 1.0
C D:LEU476 4.8 29.9 1.0
C D:ASN473 4.9 29.6 1.0
CA D:GLY477 4.9 28.0 1.0

Magnesium binding site 8 out of 10 in 8i07

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Magnesium binding site 8 out of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde


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 Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:27.5
occ:1.00
 OD1 E:ASN473 2.1 31.3 1.0
O1A E:TPP603 2.1 27.5 1.0
OD1 E:ASP446 2.1 28.9 1.0
O E:TYR475 2.2 29.6 1.0
O E:HOH816 2.2 28.4 1.0
O3B E:TPP603 2.2 29.4 1.0
CG E:ASN473 3.0 32.0 1.0
PA E:TPP603 3.2 29.9 1.0
PB E:TPP603 3.3 31.1 1.0
CG E:ASP446 3.3 30.9 1.0
O3A E:TPP603 3.3 28.6 1.0
C E:TYR475 3.3 30.4 1.0
ND2 E:ASN473 3.4 30.9 1.0
N E:TYR475 3.8 30.3 1.0
OD2 E:ASP446 3.8 31.1 1.0
N E:ASP446 3.8 26.3 1.0
O2B E:TPP603 3.9 27.9 1.0
O7 E:TPP603 4.0 26.5 1.0
CA E:TYR475 4.1 30.5 1.0
N E:GLY477 4.1 29.5 1.0
N E:ASN473 4.2 29.8 1.0
N E:LEU476 4.4 29.5 1.0
CB E:ASN473 4.4 30.3 1.0
N E:PHE447 4.4 26.4 1.0
CB E:TYR475 4.4 30.4 1.0
CB E:ASP446 4.5 27.6 1.0
O2A E:TPP603 4.5 29.1 1.0
CA E:GLY445 4.5 28.1 1.0
O1B E:TPP603 4.6 29.9 1.0
C E:GLY445 4.6 26.7 1.0
CA E:LEU476 4.6 29.7 1.0
N E:ALA474 4.6 29.8 1.0
CA E:ASP446 4.6 25.8 1.0
O E:VAL471 4.6 28.3 1.0
CA E:ASN473 4.7 31.3 1.0
C E:ASN473 4.8 31.5 1.0
CA E:GLY477 4.9 31.9 1.0
C E:LEU476 4.9 30.6 1.0
C E:ALA474 5.0 31.3 1.0

Magnesium binding site 9 out of 10 in 8i07

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Magnesium binding site 9 out of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:29.8
occ:1.00
 OD1 F:ASP446 2.1 29.8 1.0
O2A F:TPP604 2.1 29.4 1.0
O F:TYR475 2.2 30.2 1.0
O F:HOH780 2.2 27.7 1.0
OD1 F:ASN473 2.2 32.3 1.0
O2B F:TPP604 2.3 31.4 1.0
CG F:ASN473 3.1 32.4 1.0
CG F:ASP446 3.2 28.3 1.0
PA F:TPP604 3.2 30.5 1.0
PB F:TPP604 3.3 32.5 1.0
O3A F:TPP604 3.3 30.9 1.0
C F:TYR475 3.3 33.5 1.0
ND2 F:ASN473 3.5 31.4 1.0
OD2 F:ASP446 3.7 29.3 1.0
N F:ASP446 3.7 26.0 1.0
N F:TYR475 3.8 31.3 1.0
O7 F:TPP604 4.0 31.4 1.0
CA F:TYR475 4.0 32.8 1.0
N F:GLY477 4.1 31.9 1.0
O1B F:TPP604 4.1 31.6 1.0
N F:PHE447 4.2 27.0 1.0
N F:ASN473 4.3 29.2 1.0
N F:LEU476 4.4 34.2 1.0
CB F:ASP446 4.4 26.5 1.0
CB F:TYR475 4.4 31.5 1.0
O1A F:TPP604 4.5 27.1 1.0
CA F:GLY445 4.5 27.6 1.0
CB F:ASN473 4.5 28.3 1.0
C F:GLY445 4.5 27.0 1.0
CA F:ASP446 4.5 27.0 1.0
O3B F:TPP604 4.5 30.7 1.0
CA F:LEU476 4.6 33.3 1.0
O F:VAL471 4.7 26.4 1.0
N F:ALA474 4.7 29.3 1.0
CA F:ASN473 4.8 29.4 1.0
C F:ASN473 4.8 31.0 1.0
CA F:GLY477 4.9 32.2 1.0
C F:LEU476 4.9 31.8 1.0
C F:ASP446 4.9 25.9 1.0
C F:ALA474 4.9 33.0 1.0
CB F:PHE447 5.0 26.8 1.0

Magnesium binding site 10 out of 10 in 8i07

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Magnesium binding site 10 out of 10 in the Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Escherichia Coli Glyoxylate Carboligase Double Mutant in Complex with Glycolaldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:27.0
occ:1.00
 O F:PHE451 2.4 23.8 1.0
OE1 F:GLU454 2.4 23.8 0.8
OE1 D:GLU454 2.5 20.8 0.6
O D:PHE451 2.5 24.1 1.0
CD F:GLU454 3.2 25.1 1.0
CD D:GLU454 3.3 24.2 1.0
C F:PHE451 3.5 25.7 1.0
OE2 F:GLU454 3.5 26.2 1.0
C D:PHE451 3.6 25.0 1.0
OE2 D:GLU454 3.6 24.6 1.0
CA F:LEU452 3.6 24.8 1.0
CA D:LEU452 3.7 23.4 1.0
CD2 D:LEU452 3.9 20.6 1.0
CD2 F:LEU452 3.9 24.0 1.0
N F:LEU452 4.0 22.9 1.0
N D:LEU452 4.1 23.0 1.0
O F:GLN450 4.3 23.3 1.0
N F:ILE453 4.3 25.2 1.0
C F:LEU452 4.3 25.6 1.0
C D:LEU452 4.4 24.1 1.0
O D:GLN450 4.4 24.8 1.0
N D:ILE453 4.4 23.8 1.0
CD2 D:HIS50 4.5 23.0 1.0
CG F:GLU454 4.5 24.5 1.0
CG D:GLU454 4.5 23.6 1.0
CD2 F:HIS50 4.7 25.2 1.0
CB F:LEU452 4.7 22.2 1.0
CA F:PHE451 4.7 25.0 1.0
CG F:LEU452 4.8 25.3 1.0
CB D:LEU452 4.8 23.3 1.0
CG D:LEU452 4.8 24.0 1.0
CA D:PHE451 4.8 23.4 1.0
N F:GLU454 4.9 23.4 1.0
N D:GLU454 5.0 22.9 1.0

Reference:

J.H.Kim, H.Cheon, H.J.Jo, J.W.Kim, G.Y.Kim, H.R.Seo, P.W.Seo, J.S.Kim, J.B.Park. Engineering of Two Thiamine Diphosphate-Dependent Enzymes For the Regioselective Condensation of C1-Formaldehyde Into C4-Erythrulose Int.J.Biol.Macromol. V. 253 27674 2023.
ISSN: ISSN 0141-8130
DOI: 10.1016/J.IJBIOMAC.2023.127674
Page generated: Fri Oct 4 09:00:45 2024

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