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Magnesium in PDB 3v5c: Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg

Protein crystallography data

The structure of Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg, PDB code: 3v5c was solved by A.A.Fedorov, E.V.Fedorov, F.Groninger-Poe, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.47 / 1.53
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.271, 65.863, 151.218, 90.00, 94.17, 90.00
R / Rfree (%) 18.5 / 21.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg (pdb code 3v5c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg, PDB code: 3v5c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3v5c

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Magnesium binding site 1 out of 7 in the Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg


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 the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg393

b:11.6
occ:1.00
 OD1 A:ASP261 2.0 8.8 1.0
OE2 A:GLU238 2.1 10.9 1.0
O A:HOH1443 2.1 13.2 1.0
O A:HOH1441 2.1 10.8 1.0
O A:HOH1450 2.2 12.9 1.0
O A:HOH1446 2.2 11.2 1.0
CG A:ASP261 3.0 10.9 1.0
CD A:GLU238 3.2 12.5 1.0
OD2 A:ASP261 3.4 10.6 1.0
OE1 A:GLU238 3.6 10.8 1.0
O A:HOH485 4.0 23.4 1.0
N A:GLY262 4.1 10.1 1.0
O A:GLU263 4.1 13.7 1.0
OD1 A:ASN210 4.3 11.2 1.0
ND1 A:HIS237 4.3 13.3 1.0
N A:GLU238 4.3 9.9 1.0
ND2 A:ASN210 4.3 17.0 1.0
CB A:ASP261 4.4 8.1 1.0
CG A:GLU238 4.5 13.1 1.0
O A:HOH458 4.5 15.7 1.0
O A:HOH424 4.5 13.5 1.0
CB A:GLU238 4.6 10.2 1.0
N A:GLU263 4.7 11.4 1.0
CE1 A:HIS237 4.7 14.1 1.0
CG A:ASN210 4.7 13.3 1.0
CA A:HIS237 4.8 11.8 1.0
CA A:ASP261 4.8 7.3 1.0
CA A:GLY262 4.9 10.7 1.0
CB A:ALA234 4.9 10.4 1.0
O A:PHE236 4.9 10.2 1.0
C A:ASP261 5.0 9.9 1.0
C A:GLY262 5.0 12.3 1.0

Magnesium binding site 2 out of 7 in 3v5c

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Magnesium binding site 2 out of 7 in the Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg


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 the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg393

b:13.9
occ:1.00
 OD1 B:ASP261 2.1 11.2 1.0
OE2 B:GLU238 2.1 13.2 1.0
O B:HOH1442 2.1 13.5 1.0
O B:HOH1447 2.1 13.7 1.0
O B:HOH1451 2.2 15.6 1.0
O B:HOH1449 2.2 13.4 1.0
CG B:ASP261 3.0 13.0 1.0
CD B:GLU238 3.1 14.8 1.0
OD2 B:ASP261 3.3 13.6 1.0
OE1 B:GLU238 3.5 13.9 1.0
O B:HOH497 4.0 27.2 1.0
N B:GLY262 4.1 15.9 1.0
O B:GLU263 4.2 15.8 1.0
OD1 B:ASN210 4.2 13.0 1.0
ND1 B:HIS237 4.2 16.2 1.0
N B:GLU238 4.3 12.4 1.0
ND2 B:ASN210 4.4 18.5 1.0
CB B:ASP261 4.4 12.4 1.0
CG B:GLU238 4.5 14.9 1.0
O B:HOH493 4.5 19.2 1.0
O B:HOH491 4.6 22.7 1.0
CB B:GLU238 4.6 13.5 1.0
CE1 B:HIS237 4.7 18.7 1.0
N B:GLU263 4.7 13.9 1.0
CG B:ASN210 4.7 14.4 1.0
CA B:HIS237 4.8 13.2 1.0
CB B:ALA234 4.8 14.6 1.0
CA B:ASP261 4.8 13.0 1.0
CA B:GLY262 4.9 16.9 1.0
O B:PHE236 5.0 13.4 1.0
CA B:ALA234 5.0 13.6 1.0
C B:ASP261 5.0 17.8 1.0

Magnesium binding site 3 out of 7 in 3v5c

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Magnesium binding site 3 out of 7 in the Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg


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 the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg394

b:29.6
occ:1.00
 O B:HOH1468 2.2 27.5 1.0
O B:HOH426 2.2 29.2 1.0
OD2 B:ASP207 2.3 14.2 1.0
O B:HOH425 2.3 22.8 1.0
O B:HOH430 2.3 24.8 1.0
OE2 B:GLU233 2.4 22.0 1.0
O B:HOH1479 3.0 33.5 1.0
CG B:ASP207 3.1 11.9 1.0
OD1 B:ASP207 3.3 13.3 1.0
CD B:GLU233 3.4 14.7 1.0
CG B:GLU233 4.0 14.5 1.0
O B:HOH469 4.0 23.9 1.0
NZ B:LYS168 4.0 17.6 1.0
ND2 B:ASN209 4.3 20.4 1.0
NZ B:LYS170 4.3 18.3 1.0
CB B:ASP207 4.4 12.3 1.0
OE1 B:GLU233 4.4 15.8 1.0
O B:HOH493 4.6 19.2 1.0
O B:HOH491 4.6 22.7 1.0
CE B:LYS168 4.7 15.9 1.0
O B:HOH473 4.7 21.2 1.0
CD2 B:HIS311 4.8 21.6 1.0
CG B:ASN209 4.9 16.6 1.0
OD1 B:ASN209 4.9 15.2 1.0
CB B:GLU263 5.0 19.0 1.0

Magnesium binding site 4 out of 7 in 3v5c

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Magnesium binding site 4 out of 7 in the Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg


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 the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg395

b:29.9
occ:1.00
 O B:HOH435 2.3 25.5 1.0
OD2 B:ASP371 2.3 31.8 1.0
O B:HOH952 2.3 29.4 1.0
O B:HOH543 2.4 22.6 1.0
O B:HOH1533 2.4 32.6 1.0
O B:HOH1095 2.5 36.3 1.0
CG B:ASP371 3.3 20.0 1.0
O B:HOH1317 3.8 37.0 1.0
CB B:ASP371 3.9 15.2 1.0
O B:HOH645 4.2 29.2 1.0
OD1 B:ASP371 4.2 22.0 1.0
O B:HOH1017 4.3 24.6 1.0
N B:ASP371 4.3 15.1 1.0
OE2 B:GLU372 4.3 16.4 1.0
OE1 B:GLU372 4.4 19.6 1.0
O B:PHE369 4.4 18.6 1.0
CA B:ASP371 4.8 18.8 1.0
CD B:GLU372 4.8 14.6 1.0

Magnesium binding site 5 out of 7 in 3v5c

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Magnesium binding site 5 out of 7 in the Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg


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 the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg393

b:13.9
occ:1.00
 OD1 C:ASP261 2.0 13.4 1.0
OE2 C:GLU238 2.1 13.1 1.0
O C:HOH1448 2.1 13.5 1.0
O C:HOH1453 2.2 14.3 1.0
O C:HOH1444 2.2 16.0 1.0
O C:HOH1455 2.2 16.2 1.0
CG C:ASP261 3.1 14.2 1.0
CD C:GLU238 3.1 15.3 1.0
OD2 C:ASP261 3.4 12.9 1.0
OE1 C:GLU238 3.5 14.6 1.0
O C:HOH600 4.0 26.6 1.0
O C:GLU263 4.1 16.1 1.0
N C:GLY262 4.1 13.0 1.0
ND1 C:HIS237 4.3 19.7 1.0
N C:GLU238 4.3 15.7 1.0
OD1 C:ASN210 4.3 17.3 1.0
ND2 C:ASN210 4.3 18.0 1.0
CB C:ASP261 4.4 12.3 1.0
O C:HOH487 4.4 19.8 1.0
CG C:GLU238 4.5 14.7 1.0
O C:HOH415 4.6 16.3 1.0
N C:GLU263 4.6 12.8 1.0
CE1 C:HIS237 4.7 18.4 1.0
CB C:GLU238 4.7 16.1 1.0
CA C:HIS237 4.8 16.2 1.0
CG C:ASN210 4.8 17.4 1.0
CA C:ASP261 4.8 10.1 1.0
CA C:GLY262 4.8 13.5 1.0
CB C:ALA234 4.9 14.2 1.0
C C:GLY262 5.0 14.8 1.0
C C:ASP261 5.0 11.8 1.0

Magnesium binding site 6 out of 7 in 3v5c

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Magnesium binding site 6 out of 7 in the Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg


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 the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg393

b:18.2
occ:1.00
 OD1 D:ASP261 2.1 17.4 1.0
OE2 D:GLU238 2.2 16.0 1.0
O D:HOH1456 2.2 17.9 1.0
O D:HOH1454 2.2 16.7 1.0
O D:HOH1457 2.2 20.7 1.0
O D:HOH1452 2.2 19.1 1.0
CG D:ASP261 3.0 17.1 1.0
CD D:GLU238 3.2 16.3 1.0
OD2 D:ASP261 3.3 18.2 1.0
OE1 D:GLU238 3.5 17.5 1.0
O D:HOH442 4.0 31.4 1.0
N D:GLY262 4.2 19.2 1.0
OD1 D:ASN210 4.2 17.5 1.0
O D:GLU263 4.2 22.4 1.0
ND1 D:HIS237 4.2 18.7 1.0
N D:GLU238 4.3 15.2 1.0
CB D:ASP261 4.4 19.2 1.0
ND2 D:ASN210 4.4 21.2 1.0
CG D:GLU238 4.5 17.8 1.0
O D:HOH429 4.5 23.9 1.0
N D:GLU263 4.6 21.0 1.0
CB D:GLU238 4.6 16.9 1.0
CE1 D:HIS237 4.7 18.7 1.0
O D:HOH421 4.7 24.4 1.0
CG D:ASN210 4.7 20.0 1.0
CA D:HIS237 4.8 15.4 1.0
CB D:ALA234 4.8 16.7 1.0
CA D:ASP261 4.8 17.6 1.0
CA D:GLY262 4.9 20.8 1.0

Magnesium binding site 7 out of 7 in 3v5c

Go back to Magnesium Binding Sites List in 3v5c
Magnesium binding site 7 out of 7 in the Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg


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 the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg394

b:32.0
occ:1.00
 O D:HOH408 2.3 23.4 1.0
OD2 D:ASP207 2.3 19.6 1.0
O D:HOH1131 2.3 34.8 1.0
O D:HOH1506 2.3 34.9 1.0
OE2 D:GLU233 2.3 25.0 1.0
O D:HOH905 2.5 27.3 1.0
CG D:ASP207 3.1 17.2 1.0
O D:HOH1114 3.3 33.9 1.0
CD D:GLU233 3.4 21.8 1.0
OD1 D:ASP207 3.4 16.6 1.0
CG D:GLU233 4.0 21.7 1.0
NZ D:LYS168 4.0 20.6 1.0
NZ D:LYS170 4.1 25.9 1.0
O D:HOH571 4.1 30.5 1.0
ND2 D:ASN209 4.2 21.3 1.0
OE1 D:GLU233 4.3 20.2 1.0
CB D:ASP207 4.4 15.9 1.0
O D:HOH429 4.6 23.9 1.0
O D:HOH854 4.7 29.1 1.0
O D:HOH421 4.7 24.4 1.0
CE D:LYS168 4.7 18.4 1.0
CD2 D:HIS311 4.7 28.5 1.0
CG D:ASN209 4.8 17.2 1.0
OD1 D:ASN209 4.9 18.6 1.0
O D:HOH405 4.9 21.9 1.0
CB D:GLU263 5.0 24.1 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, F.Groninger-Poe, J.A.Gerlt, S.C.Almo. Crystal Structure of the Mutant E234A of Galacturonate Dehydratase From Geobacillus Sp. Complexed with Mg To Be Published.
Page generated: Mon Aug 11 04:23:39 2025

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