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Magnesium in PDB 3jr2: X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961

Protein crystallography data

The structure of X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961, PDB code: 3jr2 was solved by B.Nocek, N.Maltseva, J.Stam, W.Anderson, A.Joachimiak, Csgid, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.305, 95.711, 125.577, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961 (pdb code 3jr2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961, PDB code: 3jr2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3jr2

Go back to Magnesium Binding Sites List in 3jr2
Magnesium binding site 1 out of 7 in the X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:16.6
occ:0.80
 O A:HOH284 1.9 24.5 1.0
OE2 A:GLU33 2.0 17.0 1.0
OD2 A:ASP62 2.0 18.3 1.0
O A:HOH285 2.1 21.9 1.0
O A:HOH249 2.1 15.7 1.0
O A:HOH258 2.3 19.2 1.0
CG A:ASP62 2.9 17.1 1.0
CD A:GLU33 3.0 16.7 1.0
OE1 A:GLU33 3.3 16.0 1.0
OE2 A:GLU112 3.6 27.3 1.0
CB A:ASP62 3.7 14.8 1.0
OD1 A:ASP62 3.8 16.2 1.0
NZ A:LYS64 4.1 19.8 1.0
CG A:GLU33 4.3 13.6 1.0
O A:HOH370 4.3 30.9 1.0
O A:HOH299 4.4 21.1 1.0
O A:HOH738 4.5 30.1 1.0
CD A:GLU112 4.7 21.0 1.0
CB A:ALA9 4.9 13.4 1.0
CE A:LYS64 4.9 19.9 1.0
CA A:GLY35 4.9 12.4 1.0
O A:HOH226 5.0 16.2 1.0

Magnesium binding site 2 out of 7 in 3jr2

Go back to Magnesium Binding Sites List in 3jr2
Magnesium binding site 2 out of 7 in the X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:40.5
occ:1.00
 O A:HOH791 2.1 35.3 1.0
O A:HOH792 2.1 20.5 1.0
O A:HOH275 2.1 16.9 1.0
O A:HOH790 2.2 22.8 1.0
O A:HOH794 2.3 26.1 1.0
O A:HOH793 2.5 23.6 1.0
OE2 A:GLU181 4.2 15.7 1.0
O A:HOH330 4.3 18.1 1.0
OE1 A:GLU181 4.4 12.7 1.0
O A:HOH782 4.5 25.5 1.0
CD A:GLU181 4.7 15.2 1.0

Magnesium binding site 3 out of 7 in 3jr2

Go back to Magnesium Binding Sites List in 3jr2
Magnesium binding site 3 out of 7 in the X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:14.5
occ:0.80
 OD2 B:ASP62 1.9 17.3 1.0
O B:HOH239 2.0 19.1 1.0
OE2 B:GLU33 2.0 17.6 1.0
O B:HOH249 2.0 18.3 1.0
O B:HOH302 2.2 19.6 1.0
O B:HOH304 2.2 21.9 1.0
CG B:ASP62 2.9 15.0 1.0
CD B:GLU33 3.0 18.4 1.0
OE1 B:GLU33 3.4 15.3 1.0
OE2 B:GLU112 3.6 25.9 1.0
CB B:ASP62 3.6 13.4 1.0
OD1 B:ASP62 3.8 14.7 1.0
NZ B:LYS64 4.0 18.5 1.0
O B:HOH538 4.2 34.7 1.0
CG B:GLU33 4.3 14.1 1.0
O B:HOH626 4.6 30.1 1.0
O B:HOH259 4.7 19.5 1.0
CD B:GLU112 4.8 20.8 1.0
CA B:GLY35 4.8 12.5 1.0
O B:HOH516 4.8 26.9 1.0
CB B:ALA9 4.9 12.7 1.0
O B:HOH262 5.0 13.4 1.0

Magnesium binding site 4 out of 7 in 3jr2

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Magnesium binding site 4 out of 7 in the X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:27.2
occ:0.80
 O C:HOH266 2.0 33.1 1.0
O B:HOH774 2.1 39.2 1.0
O B:HOH531 2.1 42.1 1.0
O C:HOH505 2.1 32.7 1.0
O B:HOH775 2.1 45.3 1.0
NE2 B:HIS52 2.2 20.0 1.0
CE1 B:HIS52 3.0 19.3 1.0
CD2 B:HIS52 3.4 20.7 1.0
ND1 B:HIS52 4.2 18.8 1.0
OE2 C:GLU165 4.3 29.4 1.0
O C:HOH290 4.3 22.5 1.0
O C:HOH535 4.4 38.5 1.0
CG B:HIS52 4.4 16.6 1.0
O B:HOH371 4.6 25.5 1.0
CD C:GLU165 4.7 28.2 1.0
OE1 C:GLU165 4.7 35.1 1.0
OG1 C:THR131 4.8 20.2 1.0

Magnesium binding site 5 out of 7 in 3jr2

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Magnesium binding site 5 out of 7 in the X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:21.7
occ:0.80
 O C:HOH276 2.0 30.5 1.0
O C:HOH274 2.0 28.7 1.0
O C:HOH272 2.1 23.2 1.0
O C:HOH273 2.1 23.1 1.0
O C:HOH269 2.2 27.9 1.0
NE2 C:HIS136 2.3 23.4 1.0
CE1 C:HIS136 3.1 25.3 1.0
CD2 C:HIS136 3.3 21.5 1.0
OE2 C:GLU142 4.1 23.2 1.0
OE1 C:GLU142 4.2 26.3 1.0
ND1 C:HIS136 4.3 24.0 1.0
O1 C:SO4502 4.4 41.0 1.0
C1 D:GOL1002 4.4 27.4 1.0
CG C:HIS136 4.5 22.4 1.0
CD C:GLU142 4.5 28.4 1.0
NH1 C:ARG139 4.7 28.5 1.0
CA C:GLY170 4.9 17.8 1.0

Magnesium binding site 6 out of 7 in 3jr2

Go back to Magnesium Binding Sites List in 3jr2
Magnesium binding site 6 out of 7 in the X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:15.8
occ:0.80
 OD2 C:ASP62 2.0 17.7 1.0
OE2 C:GLU33 2.0 20.6 1.0
O C:HOH258 2.0 19.6 1.0
O C:HOH255 2.1 17.4 1.0
O C:HOH230 2.1 20.1 1.0
O C:HOH271 2.1 15.4 1.0
CG C:ASP62 3.0 19.1 1.0
CD C:GLU33 3.0 19.1 1.0
OE1 C:GLU33 3.3 18.8 1.0
OE2 C:GLU112 3.7 27.0 1.0
CB C:ASP62 3.7 16.1 1.0
OD1 C:ASP62 3.9 17.6 1.0
NZ C:LYS64 4.1 17.9 1.0
CG C:GLU33 4.3 15.5 1.0
O C:HOH359 4.3 23.8 1.0
O C:HOH301 4.4 23.2 1.0
O C:HOH631 4.6 31.6 1.0
O C:HOH218 4.7 15.0 1.0
CD C:GLU112 4.8 22.2 1.0

Magnesium binding site 7 out of 7 in 3jr2

Go back to Magnesium Binding Sites List in 3jr2
Magnesium binding site 7 out of 7 in the X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of X-Ray Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:19.4
occ:0.90
 OE2 D:GLU33 2.0 19.0 1.0
OD2 D:ASP62 2.0 19.3 1.0
O D:HOH251 2.0 22.5 1.0
O D:HOH248 2.0 20.1 1.0
O D:HOH250 2.1 28.4 1.0
O D:HOH249 2.2 23.5 1.0
CD D:GLU33 3.0 18.9 1.0
CG D:ASP62 3.0 20.0 1.0
OE1 D:GLU33 3.4 22.6 1.0
OE2 D:GLU112 3.7 28.0 1.0
CB D:ASP62 3.8 17.2 1.0
O D:HOH253 3.8 36.8 1.0
OD1 D:ASP62 3.9 18.4 1.0
NZ D:LYS64 4.0 19.4 1.0
CG D:GLU33 4.3 18.0 1.0
O D:HOH565 4.4 27.3 1.0
CB D:ALA9 4.8 15.5 1.0
CA D:GLY35 4.9 13.7 1.0
CD D:GLU112 4.9 23.6 1.0
O D:HOH228 4.9 19.3 1.0
OD1 D:ASP11 5.0 33.0 1.0

Reference:

B.Nocek, N.Maltseva, J.Stam, W.Anderson, A.Joachimiak, Csgid. Crystal Structure of the Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961 To Be Published.
Page generated: Wed Aug 14 17:11:35 2024

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