Atomistry » Magnesium » PDB 3jay-3jwr » 3jr2
Atomistry »
  Magnesium »
    PDB 3jay-3jwr »
      3jr2 »

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

Go back to Magnesium Binding Sites List in 3jr2
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

Go back to Magnesium Binding Sites List in 3jr2
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy