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Magnesium in PDB 3qpe: Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate

Protein crystallography data

The structure of Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate, PDB code: 3qpe was solved by A.A.Fedorov, E.V.Fedorov, F.Mills-Groninger, 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) 39.03 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.019, 66.265, 154.609, 90.00, 95.73, 90.00
R / Rfree (%) 22.1 / 27

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate (pdb code 3qpe). 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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate, PDB code: 3qpe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3qpe

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Magnesium binding site 1 out of 8 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate


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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg393

b:26.0
occ:1.00
 OE2 A:GLU233 2.1 23.0 1.0
O A:HOH743 2.2 18.5 1.0
OAD A:DGU401 2.2 20.7 1.0
OD2 A:ASP207 2.2 18.7 1.0
OE2 A:GLU263 2.2 23.6 1.0
OAC A:DGU401 2.4 28.8 1.0
CAJ A:DGU401 3.0 30.3 1.0
CD A:GLU233 3.1 19.1 1.0
CD A:GLU263 3.1 26.0 1.0
CG A:ASP207 3.1 24.5 1.0
CAI A:DGU401 3.1 32.0 1.0
OE1 A:GLU263 3.4 29.2 1.0
OD1 A:ASP207 3.4 21.4 1.0
CG A:GLU233 3.6 20.0 1.0
OE1 A:GLU233 4.0 21.4 1.0
O A:HOH406 4.1 19.8 1.0
ND2 A:ASN209 4.2 19.9 1.0
OE1 A:GLU234 4.2 23.4 1.0
OAM A:DGU401 4.2 29.9 1.0
NZ A:LYS168 4.2 21.7 1.0
O A:HOH436 4.4 25.7 1.0
CG A:GLU263 4.4 27.3 1.0
CB A:ASP207 4.4 22.6 1.0
NZ A:LYS170 4.4 28.0 1.0
CAH A:DGU401 4.5 29.5 1.0
CE A:LYS168 4.6 20.6 1.0
CD2 A:HIS311 4.6 23.0 1.0
OAL A:DGU401 4.8 38.5 1.0
CG A:GLU234 4.8 18.8 1.0
CD A:GLU234 4.8 24.8 1.0
CG A:ASN209 4.9 21.7 1.0
CB A:GLU233 5.0 22.9 1.0

Magnesium binding site 2 out of 8 in 3qpe

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Magnesium binding site 2 out of 8 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate


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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg394

b:23.1
occ:1.00
 OE2 A:GLU234 2.2 21.6 1.0
OD1 A:ASP261 2.2 19.1 1.0
OE2 A:GLU238 2.2 23.6 1.0
O A:HOH751 2.2 22.0 1.0
O A:HOH749 2.2 20.1 1.0
O A:HOH750 2.3 21.6 1.0
CD A:GLU238 3.1 20.5 1.0
CG A:ASP261 3.1 21.4 1.0
CD A:GLU234 3.2 24.8 1.0
OE1 A:GLU238 3.4 21.1 1.0
OD2 A:ASP261 3.4 20.9 1.0
CG A:GLU234 3.6 18.8 1.0
O A:HOH559 3.9 27.8 1.0
N A:GLY262 4.2 19.5 1.0
ND1 A:HIS237 4.2 24.1 1.0
OD1 A:ASN210 4.2 23.1 1.0
ND2 A:ASN210 4.2 20.5 1.0
OE1 A:GLU234 4.3 23.4 1.0
N A:GLU238 4.3 22.9 1.0
O A:GLU263 4.4 20.6 1.0
CG A:GLU238 4.5 20.1 1.0
CB A:ASP261 4.5 20.0 1.0
CB A:GLU234 4.5 23.7 1.0
CG A:ASN210 4.7 23.3 1.0
CE1 A:HIS237 4.7 27.1 1.0
CB A:GLU238 4.7 22.6 1.0
CA A:HIS237 4.8 20.6 1.0
CA A:GLY262 4.9 19.0 1.0
CA A:ASP261 4.9 17.8 1.0
N A:GLU263 4.9 22.0 1.0
O A:PHE236 4.9 21.0 1.0

Magnesium binding site 3 out of 8 in 3qpe

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Magnesium binding site 3 out of 8 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate


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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg393

b:30.0
occ:1.00
 OE2 B:GLU233 2.1 27.5 1.0
O B:HOH744 2.2 25.8 1.0
OD2 B:ASP207 2.3 29.1 1.0
OE2 B:GLU263 2.3 27.5 1.0
OAC B:D54401 2.3 32.0 1.0
OAL B:D54401 2.4 31.5 1.0
CAI B:D54401 3.0 38.2 1.0
CAJ B:D54401 3.1 37.8 1.0
CD B:GLU233 3.1 26.6 1.0
CD B:GLU263 3.1 29.2 1.0
CG B:ASP207 3.2 25.9 1.0
OE1 B:GLU263 3.4 30.9 1.0
OD1 B:ASP207 3.5 27.4 1.0
CG B:GLU233 3.6 27.8 1.0
O B:HOH414 3.9 27.7 1.0
NZ B:LYS170 4.0 26.4 1.0
OE1 B:GLU233 4.1 24.8 1.0
NZ B:LYS168 4.1 30.0 1.0
OE1 B:GLU234 4.1 25.4 1.0
O B:HOH470 4.2 30.4 1.0
ND2 B:ASN209 4.3 23.8 1.0
OAD B:D54401 4.3 34.9 1.0
CG B:GLU263 4.4 27.1 1.0
CD2 B:HIS311 4.5 29.9 1.0
CB B:ASP207 4.5 25.6 1.0
CAH B:D54401 4.5 33.8 1.0
CE B:LYS168 4.8 26.2 1.0
CD B:GLU234 4.8 23.8 1.0
CG B:GLU234 4.8 23.7 1.0
CB B:GLU233 4.9 24.2 1.0
CG B:ASN209 4.9 26.8 1.0
OD1 B:ASN209 5.0 25.2 1.0

Magnesium binding site 4 out of 8 in 3qpe

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Magnesium binding site 4 out of 8 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate


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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg394

b:26.4
occ:1.00
 OE2 B:GLU234 2.2 22.2 1.0
OD1 B:ASP261 2.2 24.8 1.0
O B:HOH752 2.2 22.1 1.0
OE2 B:GLU238 2.2 23.2 1.0
O B:HOH753 2.2 25.4 1.0
O B:HOH565 2.3 24.2 1.0
CG B:ASP261 3.2 31.1 1.0
CD B:GLU238 3.2 27.3 1.0
CD B:GLU234 3.2 23.8 1.0
OD2 B:ASP261 3.4 28.3 1.0
OE1 B:GLU238 3.5 27.2 1.0
O B:HOH452 3.6 28.0 1.0
CG B:GLU234 3.7 23.7 1.0
N B:GLY262 4.2 25.9 1.0
OD1 B:ASN210 4.2 24.3 1.0
ND2 B:ASN210 4.3 24.8 1.0
N B:GLU238 4.3 26.1 1.0
ND1 B:HIS237 4.3 24.0 1.0
OE1 B:GLU234 4.3 25.4 1.0
O B:GLU263 4.4 26.0 1.0
CB B:ASP261 4.5 29.1 1.0
CG B:GLU238 4.5 22.9 1.0
CB B:GLU234 4.6 25.6 1.0
CG B:ASN210 4.7 25.2 1.0
CB B:GLU238 4.7 25.4 1.0
CA B:HIS237 4.8 25.6 1.0
CE1 B:HIS237 4.9 28.1 1.0
CA B:GLY262 4.9 28.5 1.0
O B:PHE236 5.0 25.3 1.0
CA B:ASP261 5.0 26.6 1.0
N B:GLU263 5.0 28.7 1.0

Magnesium binding site 5 out of 8 in 3qpe

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Magnesium binding site 5 out of 8 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate


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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg393

b:22.6
occ:1.00
 O C:HOH741 2.1 24.1 1.0
OE2 C:GLU233 2.2 28.7 1.0
OAL C:D54401 2.3 23.1 1.0
OD2 C:ASP207 2.3 26.1 1.0
OE2 C:GLU263 2.3 26.1 1.0
OAC C:D54401 2.4 27.3 1.0
CAJ C:D54401 3.0 34.4 1.0
CAI C:D54401 3.1 32.5 1.0
CD C:GLU263 3.1 32.4 1.0
CD C:GLU233 3.1 25.8 1.0
CG C:ASP207 3.2 23.1 1.0
OE1 C:GLU263 3.3 29.4 1.0
OD1 C:ASP207 3.4 21.5 1.0
CG C:GLU233 3.6 23.5 1.0
OE1 C:GLU234 4.0 24.8 1.0
NZ C:LYS170 4.1 34.7 1.0
OE1 C:GLU233 4.1 27.1 1.0
O C:HOH434 4.2 26.6 1.0
ND2 C:ASN209 4.2 26.9 1.0
OAD C:D54401 4.3 31.0 1.0
NZ C:LYS168 4.3 27.9 1.0
O C:HOH475 4.3 29.7 1.0
CG C:GLU263 4.4 27.3 1.0
CB C:ASP207 4.5 24.1 1.0
CAH C:D54401 4.6 33.7 1.0
CD2 C:HIS311 4.6 28.8 1.0
CD C:GLU234 4.7 23.1 1.0
CG C:ASN209 4.8 26.1 1.0
CG C:GLU234 4.8 23.5 1.0
OD1 C:ASN209 4.9 23.9 1.0

Magnesium binding site 6 out of 8 in 3qpe

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Magnesium binding site 6 out of 8 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate


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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg394

b:27.9
occ:1.00
 OE2 C:GLU238 2.2 25.0 1.0
OE2 C:GLU234 2.2 27.9 1.0
O C:HOH745 2.2 20.2 1.0
O C:HOH566 2.3 24.7 1.0
OD1 C:ASP261 2.3 23.4 1.0
O C:HOH746 2.3 24.4 1.0
CG C:ASP261 3.2 26.8 1.0
CD C:GLU234 3.2 23.1 1.0
CD C:GLU238 3.2 25.4 1.0
OD2 C:ASP261 3.4 25.1 1.0
CG C:GLU234 3.5 23.5 1.0
OE1 C:GLU238 3.5 26.5 1.0
O C:HOH427 3.8 27.2 1.0
OD1 C:ASN210 4.1 23.7 1.0
ND1 C:HIS237 4.2 23.3 1.0
N C:GLU238 4.2 25.0 1.0
ND2 C:ASN210 4.2 22.9 1.0
OE1 C:GLU234 4.3 24.8 1.0
N C:GLY262 4.3 25.1 1.0
O C:GLU263 4.4 23.8 1.0
CB C:GLU234 4.5 21.7 1.0
CG C:GLU238 4.5 25.7 1.0
CB C:ASP261 4.5 24.1 1.0
CG C:ASN210 4.6 24.1 1.0
CA C:HIS237 4.6 27.1 1.0
CE1 C:HIS237 4.7 24.6 1.0
CB C:GLU238 4.8 21.9 1.0
C C:HIS237 4.9 24.6 1.0
O C:PHE236 5.0 24.8 1.0

Magnesium binding site 7 out of 8 in 3qpe

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Magnesium binding site 7 out of 8 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate


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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg393

b:23.3
occ:1.00
 O D:HOH742 2.1 22.3 1.0
OE2 D:GLU233 2.2 24.3 1.0
OE2 D:GLU263 2.2 21.9 1.0
OD2 D:ASP207 2.3 21.8 1.0
OAC D:D54401 2.3 25.7 1.0
OAL D:D54401 2.5 27.2 1.0
CAI D:D54401 3.0 33.3 1.0
CD D:GLU263 3.1 28.4 1.0
CD D:GLU233 3.1 20.4 1.0
CG D:ASP207 3.1 24.9 1.0
CAJ D:D54401 3.1 35.4 1.0
OE1 D:GLU263 3.4 29.3 1.0
OD1 D:ASP207 3.4 24.1 1.0
CG D:GLU233 3.7 20.5 1.0
NZ D:LYS170 4.0 25.8 1.0
ND2 D:ASN209 4.1 24.3 1.0
OE1 D:GLU234 4.1 26.1 1.0
OE1 D:GLU233 4.1 19.6 1.0
O D:HOH404 4.2 22.9 1.0
NZ D:LYS168 4.3 22.1 1.0
CG D:GLU263 4.3 24.8 1.0
O D:HOH448 4.3 22.6 1.0
OAD D:D54401 4.4 27.1 1.0
CB D:ASP207 4.4 22.3 1.0
CAH D:D54401 4.5 34.7 1.0
CD2 D:HIS311 4.7 25.7 1.0
CG D:GLU234 4.7 21.6 1.0
CD D:GLU234 4.8 25.7 1.0
CG D:ASN209 4.8 23.2 1.0
OD1 D:ASN209 4.9 24.2 1.0
CE D:LYS168 4.9 22.8 1.0
CB D:GLU233 4.9 21.3 1.0

Magnesium binding site 8 out of 8 in 3qpe

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Magnesium binding site 8 out of 8 in the Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate


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 Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg394

b:25.2
occ:1.00
 OE2 D:GLU238 2.1 21.8 1.0
O D:HOH747 2.1 17.2 1.0
OD1 D:ASP261 2.2 20.4 1.0
OE2 D:GLU234 2.2 23.4 1.0
O D:HOH567 2.3 23.1 1.0
O D:HOH748 2.4 20.3 1.0
CG D:ASP261 3.1 26.3 1.0
CD D:GLU238 3.1 21.8 1.0
CD D:GLU234 3.2 25.7 1.0
OD2 D:ASP261 3.4 19.5 1.0
OE1 D:GLU238 3.5 20.6 1.0
CG D:GLU234 3.6 21.6 1.0
O D:HOH447 3.9 27.0 1.0
N D:GLU238 4.2 20.4 1.0
OD1 D:ASN210 4.2 20.5 1.0
ND2 D:ASN210 4.2 23.4 1.0
N D:GLY262 4.2 19.7 1.0
OE1 D:GLU234 4.3 26.1 1.0
ND1 D:HIS237 4.4 23.6 1.0
CG D:GLU238 4.4 24.2 1.0
CB D:ASP261 4.4 23.6 1.0
O D:GLU263 4.5 24.0 1.0
CB D:GLU234 4.5 22.4 1.0
CG D:ASN210 4.7 25.4 1.0
CB D:GLU238 4.7 22.9 1.0
CA D:HIS237 4.7 21.0 1.0
CA D:ASP261 4.9 17.7 1.0
CE1 D:HIS237 4.9 26.1 1.0
CA D:GLU234 5.0 18.6 1.0
O D:PHE236 5.0 22.0 1.0
C D:HIS237 5.0 23.8 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, F.Mills-Groninger, J.A.Gerlt, S.C.Almo. Crystal Structure of Galacturonate Dehydratase From Geobacillus Sp. Complexed with D-Galacturonate and 5-Keto-4-Deoxy-D-Galacturonate To Be Published.
Page generated: Thu Aug 15 10:06:15 2024

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