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Magnesium in PDB 2pan: Crystal Structure of E. Coli Glyoxylate Carboligase

Enzymatic activity of Crystal Structure of E. Coli Glyoxylate Carboligase

All present enzymatic activity of Crystal Structure of E. Coli Glyoxylate Carboligase:
4.1.1.47;

Protein crystallography data

The structure of Crystal Structure of E. Coli Glyoxylate Carboligase, PDB code: 2pan was solved by A.Kaplun, D.M.Chipman, Z.Barak, M.Vyazmensky, B.Shaanan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 188.180, 188.180, 249.400, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 25.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Glyoxylate Carboligase (pdb code 2pan). 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 E. Coli Glyoxylate Carboligase, PDB code: 2pan:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 2pan

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Magnesium binding site 1 out of 10 in the Crystal Structure of E. Coli Glyoxylate Carboligase


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 E. Coli Glyoxylate Carboligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg851

b:30.4
occ:1.00
OD1 A:ASP446 2.1 23.3 1.0
O21 A:TDP801 2.2 21.7 1.0
O12 A:TDP801 2.2 20.9 1.0
O A:TYR475 2.2 23.3 1.0
OD1 A:ASN473 2.2 23.9 1.0
CG A:ASN473 3.2 23.2 1.0
CG A:ASP446 3.2 23.1 1.0
P1 A:TDP801 3.4 21.1 1.0
P2 A:TDP801 3.4 21.3 1.0
C A:TYR475 3.4 23.6 1.0
O11 A:TDP801 3.5 20.9 1.0
ND2 A:ASN473 3.5 22.0 1.0
OD2 A:ASP446 3.8 23.6 1.0
N A:TYR475 3.8 24.0 1.0
N A:ASP446 3.9 21.9 1.0
O5G A:TDP801 4.1 21.0 1.0
CA A:TYR475 4.1 24.0 1.0
O22 A:TDP801 4.1 22.9 1.0
N A:GLY477 4.2 23.7 1.0
N A:ASN473 4.3 23.5 1.0
CB A:ASN473 4.4 24.0 1.0
CB A:TYR475 4.5 24.3 1.0
CB A:ASP446 4.5 22.4 1.0
N A:LEU476 4.5 23.8 1.0
N A:PHE447 4.5 21.6 1.0
O23 A:TDP801 4.6 20.4 1.0
CA A:GLY445 4.6 21.8 1.0
N A:ALA474 4.6 23.9 1.0
CA A:ASP446 4.6 21.9 1.0
O13 A:TDP801 4.6 20.9 1.0
C A:GLY445 4.7 21.6 1.0
CA A:ASN473 4.7 24.0 1.0
O A:VAL471 4.7 22.3 1.0
CA A:LEU476 4.7 23.6 1.0
C A:ASN473 4.7 24.2 1.0
CA A:GLY477 4.9 24.0 1.0
C A:LEU476 5.0 23.9 1.0
C A:ALA474 5.0 24.1 1.0

Magnesium binding site 2 out of 10 in 2pan

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Magnesium binding site 2 out of 10 in the Crystal Structure of E. Coli Glyoxylate Carboligase


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 E. Coli Glyoxylate Carboligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1501

b:14.0
occ:0.50
OE1 A:GLU454 2.5 19.5 0.5
O A:PHE451 2.5 21.5 1.0
CD A:GLU454 3.3 22.0 1.0
OE2 A:GLU454 3.4 23.7 1.0
C A:PHE451 3.6 21.2 1.0
CD2 A:LEU452 3.6 22.4 1.0
CA A:LEU452 3.7 21.2 1.0
N A:LEU452 4.1 21.1 1.0
ND1 A:HIS50 4.4 22.1 1.0
C A:LEU452 4.5 21.1 1.0
O A:GLN450 4.5 21.1 1.0
N A:ILE453 4.5 21.1 1.0
CG A:LEU452 4.6 21.6 1.0
CB A:LEU452 4.6 21.4 1.0
CG A:GLU454 4.6 22.1 1.0
CA A:PHE451 4.9 21.2 1.0

Magnesium binding site 3 out of 10 in 2pan

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Magnesium binding site 3 out of 10 in the Crystal Structure of E. Coli Glyoxylate Carboligase


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 E. Coli Glyoxylate Carboligase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg851

b:16.5
occ:1.00
O21 B:TDP801 2.1 20.9 1.0
OD1 B:ASP446 2.2 25.3 1.0
OD1 B:ASN473 2.2 26.6 1.0
O12 B:TDP801 2.2 19.9 1.0
O B:TYR475 2.3 25.8 1.0
CG B:ASN473 3.1 26.1 1.0
P2 B:TDP801 3.2 20.1 1.0
P1 B:TDP801 3.2 20.3 1.0
O11 B:TDP801 3.3 21.4 1.0
CG B:ASP446 3.4 26.3 1.0
C B:TYR475 3.4 26.4 1.0
ND2 B:ASN473 3.4 25.0 1.0
O22 B:TDP801 3.9 20.8 1.0
N B:ASP446 3.9 24.6 1.0
N B:TYR475 3.9 27.3 1.0
OD2 B:ASP446 3.9 28.6 1.0
O5G B:TDP801 3.9 21.2 1.0
CA B:TYR475 4.1 27.1 1.0
N B:GLY477 4.2 25.7 1.0
N B:ASN473 4.2 26.7 1.0
CB B:ASN473 4.4 27.2 1.0
CB B:TYR475 4.5 27.2 1.0
O23 B:TDP801 4.5 20.6 1.0
N B:LEU476 4.5 26.4 1.0
O13 B:TDP801 4.5 20.6 1.0
CA B:GLY445 4.6 24.2 1.0
CB B:ASP446 4.6 25.6 1.0
N B:PHE447 4.6 24.3 1.0
O B:VAL471 4.6 25.2 1.0
C B:GLY445 4.6 24.1 1.0
N B:ALA474 4.7 27.5 1.0
CA B:ASN473 4.7 27.4 1.0
CA B:ASP446 4.7 24.9 1.0
CA B:LEU476 4.7 25.8 1.0
C B:ASN473 4.8 27.6 1.0
CA B:GLY477 4.9 25.9 1.0
C B:LEU476 5.0 26.0 1.0

Magnesium binding site 4 out of 10 in 2pan

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Magnesium binding site 4 out of 10 in the Crystal Structure of E. Coli Glyoxylate Carboligase


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 E. Coli Glyoxylate Carboligase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1501

b:21.6
occ:0.50
OE1 B:GLU454 2.4 21.8 0.5
O B:PHE451 2.6 23.6 1.0
CD B:GLU454 3.1 23.5 1.0
OE2 B:GLU454 3.2 23.8 1.0
C B:PHE451 3.6 23.3 1.0
CA B:LEU452 3.7 23.1 1.0
CD2 B:LEU452 3.8 23.9 1.0
N B:LEU452 4.1 23.2 1.0
O B:GLN450 4.4 23.7 1.0
C B:LEU452 4.4 23.4 1.0
N B:ILE453 4.4 23.7 1.0
CG B:GLU454 4.5 24.6 1.0
ND1 B:HIS50 4.5 23.1 1.0
CB B:LEU452 4.7 22.9 1.0
CG B:LEU452 4.8 22.9 1.0
CA B:PHE451 4.8 23.1 1.0

Magnesium binding site 5 out of 10 in 2pan

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Magnesium binding site 5 out of 10 in the Crystal Structure of E. Coli Glyoxylate Carboligase


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 E. Coli Glyoxylate Carboligase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg851

b:25.0
occ:1.00
OD1 C:ASN473 2.1 37.4 1.0
OD1 C:ASP446 2.1 36.6 1.0
O C:TYR475 2.2 37.0 1.0
O12 C:TDP801 2.3 34.9 1.0
O21 C:TDP801 2.4 34.4 1.0
CG C:ASN473 3.1 37.2 1.0
CG C:ASP446 3.2 36.3 1.0
C C:TYR475 3.3 37.4 1.0
P1 C:TDP801 3.5 35.0 1.0
ND2 C:ASN473 3.5 36.4 1.0
P2 C:TDP801 3.5 32.7 1.0
O11 C:TDP801 3.6 34.3 1.0
N C:TYR475 3.7 37.9 1.0
OD2 C:ASP446 3.7 36.5 1.0
N C:ASP446 3.9 35.6 1.0
CA C:TYR475 4.0 37.9 1.0
O22 C:TDP801 4.1 34.1 1.0
N C:ASN473 4.2 37.2 1.0
O5G C:TDP801 4.2 35.4 1.0
N C:GLY477 4.2 37.3 1.0
CB C:TYR475 4.3 38.1 1.0
CB C:ASN473 4.4 37.8 1.0
N C:LEU476 4.4 37.6 1.0
CB C:ASP446 4.5 36.1 1.0
N C:ALA474 4.5 37.8 1.0
CA C:ASN473 4.6 37.7 1.0
N C:PHE447 4.6 35.5 1.0
C C:ASN473 4.6 38.0 1.0
CA C:ASP446 4.7 35.7 1.0
CA C:GLY445 4.7 35.4 1.0
O C:VAL471 4.7 35.9 1.0
O23 C:TDP801 4.7 33.3 1.0
O13 C:TDP801 4.7 35.3 1.0
CA C:LEU476 4.7 37.4 1.0
C C:GLY445 4.7 35.3 1.0
C C:ALA474 4.9 38.1 1.0
CA C:GLY477 4.9 37.6 1.0

Magnesium binding site 6 out of 10 in 2pan

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Magnesium binding site 6 out of 10 in the Crystal Structure of E. Coli Glyoxylate Carboligase


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 E. Coli Glyoxylate Carboligase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg851

b:33.6
occ:1.00
OD1 D:ASP446 2.1 38.9 1.0
OD1 D:ASN473 2.1 40.4 1.0
O12 D:TDP801 2.1 39.1 1.0
O21 D:TDP801 2.2 38.5 1.0
O D:TYR475 2.4 40.4 1.0
CG D:ASN473 3.1 40.2 1.0
P1 D:TDP801 3.3 38.6 1.0
CG D:ASP446 3.3 40.1 1.0
P2 D:TDP801 3.3 38.4 1.0
O11 D:TDP801 3.4 39.3 1.0
ND2 D:ASN473 3.5 39.5 1.0
C D:TYR475 3.5 41.1 1.0
N D:ASP446 3.8 38.4 1.0
OD2 D:ASP446 3.9 41.7 1.0
N D:TYR475 4.0 41.8 1.0
O5G D:TDP801 4.0 39.4 1.0
O22 D:TDP801 4.1 38.3 1.0
N D:GLY477 4.2 40.4 1.0
N D:ASN473 4.2 40.4 1.0
CA D:TYR475 4.2 41.8 1.0
CB D:ASN473 4.4 41.1 1.0
CA D:GLY445 4.5 37.7 1.0
O23 D:TDP801 4.5 38.5 1.0
CB D:ASP446 4.5 39.5 1.0
O D:VAL471 4.5 38.5 1.0
CB D:TYR475 4.5 41.9 1.0
O13 D:TDP801 4.5 39.5 1.0
C D:GLY445 4.6 37.8 1.0
N D:PHE447 4.6 38.4 1.0
N D:LEU476 4.6 41.3 1.0
CA D:ASP446 4.7 38.6 1.0
CA D:ASN473 4.7 41.2 1.0
N D:ALA474 4.7 41.6 1.0
C D:ASN473 4.8 41.7 1.0
CA D:LEU476 4.8 40.8 1.0
CA D:GLY477 4.9 40.6 1.0

Magnesium binding site 7 out of 10 in 2pan

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Magnesium binding site 7 out of 10 in the Crystal Structure of E. Coli Glyoxylate Carboligase


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 E. Coli Glyoxylate Carboligase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg851

b:41.5
occ:1.00
OD1 E:ASN473 2.1 40.6 1.0
O21 E:TDP801 2.1 37.4 1.0
O E:TYR475 2.2 40.4 1.0
OD1 E:ASP446 2.2 39.9 1.0
O12 E:TDP801 2.3 36.7 1.0
CG E:ASN473 3.1 40.9 1.0
CG E:ASP446 3.3 39.8 1.0
C E:TYR475 3.3 40.7 1.0
P2 E:TDP801 3.3 37.1 1.0
P1 E:TDP801 3.4 37.1 1.0
O11 E:TDP801 3.5 38.2 1.0
ND2 E:ASN473 3.6 40.8 1.0
OD2 E:ASP446 3.6 39.9 1.0
N E:TYR475 3.7 41.1 1.0
CA E:TYR475 4.0 41.1 1.0
O22 E:TDP801 4.0 37.8 1.0
O5G E:TDP801 4.0 37.9 1.0
N E:ASP446 4.0 39.1 1.0
N E:GLY477 4.1 41.0 1.0
N E:ASN473 4.3 41.1 1.0
CB E:TYR475 4.3 41.6 1.0
N E:LEU476 4.4 40.8 1.0
CB E:ASN473 4.4 41.8 1.0
CB E:ASP446 4.6 39.5 1.0
O23 E:TDP801 4.6 36.3 1.0
N E:ALA474 4.6 41.2 1.0
CA E:LEU476 4.6 40.5 1.0
CA E:ASN473 4.7 41.6 1.0
N E:PHE447 4.7 38.4 1.0
C E:ASN473 4.7 41.6 1.0
O13 E:TDP801 4.7 36.4 1.0
CA E:GLY445 4.7 39.4 1.0
O E:VAL471 4.8 40.1 1.0
CA E:ASP446 4.8 39.0 1.0
CA E:GLY477 4.8 41.5 1.0
C E:GLY445 4.8 38.9 1.0
C E:LEU476 4.9 41.1 1.0
C E:ALA474 4.9 41.2 1.0

Magnesium binding site 8 out of 10 in 2pan

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Magnesium binding site 8 out of 10 in the Crystal Structure of E. Coli Glyoxylate Carboligase


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 E. Coli Glyoxylate Carboligase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1501

b:31.1
occ:1.00
O C:PHE451 2.4 35.5 1.0
OE1 C:GLU454 2.5 33.7 0.5
OE1 E:GLU454 2.5 35.7 0.5
O E:PHE451 2.6 37.0 1.0
CD E:GLU454 3.2 37.1 1.0
OE2 E:GLU454 3.2 38.3 1.0
CD C:GLU454 3.4 35.4 1.0
C C:PHE451 3.5 35.3 1.0
OE2 C:GLU454 3.6 36.1 1.0
CD2 C:LEU452 3.6 36.2 1.0
CD2 E:LEU452 3.6 37.6 1.0
C E:PHE451 3.6 37.0 1.0
CA C:LEU452 3.7 35.2 1.0
CA E:LEU452 3.7 37.0 1.0
N C:LEU452 4.0 35.2 1.0
ND1 E:HIS50 4.1 37.8 1.0
N E:LEU452 4.1 37.0 1.0
ND1 C:HIS50 4.2 37.3 1.0
C C:LEU452 4.5 35.2 1.0
O C:GLN450 4.5 35.1 1.0
C E:LEU452 4.5 37.1 1.0
CG E:GLU454 4.5 37.2 1.0
CG C:LEU452 4.6 35.4 1.0
N C:ILE453 4.6 35.2 1.0
CB C:LEU452 4.6 35.1 1.0
O E:GLN450 4.6 36.9 1.0
N E:ILE453 4.6 37.1 1.0
CG E:LEU452 4.6 37.2 1.0
CB E:LEU452 4.6 37.1 1.0
CG C:GLU454 4.7 35.9 1.0
CE1 E:HIS50 4.8 37.2 1.0
CA C:PHE451 4.8 35.2 1.0
CE1 C:HIS50 4.9 37.0 1.0
CA E:PHE451 4.9 37.0 1.0

Magnesium binding site 9 out of 10 in 2pan

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Magnesium binding site 9 out of 10 in the Crystal Structure of E. Coli Glyoxylate Carboligase


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 E. Coli Glyoxylate Carboligase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg851

b:37.2
occ:1.00
O21 F:TDP801 2.1 37.5 1.0
O12 F:TDP801 2.1 38.9 1.0
OD1 F:ASP446 2.2 38.8 1.0
OD1 F:ASN473 2.2 40.4 1.0
O F:TYR475 2.3 39.5 1.0
CG F:ASN473 3.2 40.3 1.0
P2 F:TDP801 3.2 37.0 1.0
P1 F:TDP801 3.2 38.7 1.0
O11 F:TDP801 3.3 39.1 1.0
CG F:ASP446 3.4 39.0 1.0
C F:TYR475 3.5 39.9 1.0
ND2 F:ASN473 3.6 38.8 1.0
N F:ASP446 3.9 38.5 1.0
O22 F:TDP801 3.9 37.0 1.0
N F:TYR475 4.0 40.6 1.0
OD2 F:ASP446 4.0 39.4 1.0
O5G F:TDP801 4.0 39.0 1.0
N F:GLY477 4.2 40.0 1.0
CA F:TYR475 4.2 40.5 1.0
N F:ASN473 4.3 40.8 1.0
O23 F:TDP801 4.5 38.2 1.0
CA F:GLY445 4.5 38.5 1.0
CB F:ASN473 4.5 41.4 1.0
CB F:TYR475 4.5 40.9 1.0
O13 F:TDP801 4.5 39.2 1.0
N F:LEU476 4.5 39.9 1.0
CB F:ASP446 4.6 38.9 1.0
N F:PHE447 4.6 37.7 1.0
C F:GLY445 4.6 38.2 1.0
O F:VAL471 4.6 39.6 1.0
CA F:ASP446 4.7 38.4 1.0
N F:ALA474 4.7 41.0 1.0
CA F:ASN473 4.7 41.4 1.0
CA F:LEU476 4.8 39.6 1.0
C F:ASN473 4.8 41.4 1.0
CA F:GLY477 4.9 40.4 1.0
C F:LEU476 5.0 40.0 1.0

Magnesium binding site 10 out of 10 in 2pan

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Magnesium binding site 10 out of 10 in the Crystal Structure of E. Coli Glyoxylate Carboligase


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 E. Coli Glyoxylate Carboligase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1501

b:35.4
occ:1.00
OE1 F:GLU454 2.4 34.3 0.5
O F:PHE451 2.5 36.3 1.0
OE1 D:GLU454 2.5 36.5 0.5
O D:PHE451 2.6 38.0 1.0
CD F:GLU454 3.0 36.5 1.0
OE2 F:GLU454 3.1 36.9 1.0
CD D:GLU454 3.2 37.6 1.0
OE2 D:GLU454 3.2 37.5 1.0
C F:PHE451 3.5 36.3 1.0
CA F:LEU452 3.5 36.3 1.0
C D:PHE451 3.7 37.5 1.0
CD2 F:LEU452 3.7 36.9 1.0
CA D:LEU452 3.8 37.0 1.0
N F:LEU452 3.9 36.4 1.0
CD2 D:LEU452 4.0 37.8 1.0
N D:LEU452 4.2 37.2 1.0
C F:LEU452 4.2 36.5 1.0
N F:ILE453 4.3 36.6 1.0
O F:GLN450 4.4 36.3 1.0
ND1 F:HIS50 4.4 38.4 1.0
CG F:GLU454 4.4 37.2 1.0
ND1 D:HIS50 4.5 38.8 1.0
O D:GLN450 4.5 38.0 1.0
CG D:GLU454 4.5 38.4 1.0
CB F:LEU452 4.5 36.3 1.0
N D:ILE453 4.5 37.4 1.0
C D:LEU452 4.6 37.1 1.0
CG F:LEU452 4.7 36.4 1.0
CA F:PHE451 4.8 36.2 1.0
CB D:LEU452 4.8 36.6 1.0
N F:GLU454 4.9 37.1 1.0
CA D:PHE451 4.9 37.6 1.0
CG D:LEU452 5.0 36.9 1.0

Reference:

A.Kaplun, E.Binshtein, M.Vyazmensky, A.Steinmetz, Z.Barak, D.M.Chipman, K.Tittmann, B.Shaanan. Glyoxylate Carboligase Lacks the Canonical Active Site Glutamate of Thiamine-Dependent Enzymes. Nat.Chem.Biol. V. 4 113 2008.
ISSN: ISSN 1552-4450
PubMed: 18176558
DOI: 10.1038/NCHEMBIO.62
Page generated: Wed Aug 14 02:06:10 2024

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