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Magnesium in PDB 3uj2: Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate

Enzymatic activity of Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate

All present enzymatic activity of Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate:
4.2.1.11;

Protein crystallography data

The structure of Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate, PDB code: 3uj2 was solved by M.W.Vetting, R.Toro, R.Bhosle, B.Hillerich, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.03 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 282.350, 282.210, 119.180, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 23.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate (pdb code 3uj2). 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 An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate, PDB code: 3uj2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3uj2

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Magnesium binding site 1 out of 8 in the Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate


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 An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg431

b:27.4
occ:1.00
 O A:HOH1536 2.1 31.6 1.0
OD2 A:ASP244 2.1 25.5 1.0
O A:HOH442 2.1 13.4 1.0
O A:HOH470 2.1 22.9 1.0
OD2 A:ASP316 2.1 19.0 1.0
OE2 A:GLU289 2.3 19.9 1.0
CG A:ASP244 3.0 19.9 1.0
OD1 A:ASP244 3.2 19.1 1.0
CG A:ASP316 3.3 29.2 1.0
O A:HOH798 3.5 40.3 1.0
CD A:GLU289 3.5 26.2 1.0
CB A:ASP316 3.8 20.4 1.0
NE2 A:GLN165 4.1 31.2 1.0
OE2 A:GLU166 4.2 21.2 1.0
OD2 A:ASP290 4.3 20.9 1.0
NZ A:LYS392 4.3 22.2 1.0
CG A:GLU289 4.3 25.1 1.0
OD1 A:ASP316 4.3 21.2 1.0
CB A:ASP244 4.4 18.5 1.0
O A:HOH533 4.4 33.6 1.0
OE1 A:GLU289 4.4 25.9 1.0
NZ A:LYS341 4.6 21.4 1.0
CD2 A:LEU339 4.8 5.7 1.0
CB A:ALA246 4.8 8.3 1.0
CD A:GLU166 5.0 26.6 1.0

Magnesium binding site 2 out of 8 in 3uj2

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Magnesium binding site 2 out of 8 in the Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate


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 An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg431

b:34.7
occ:1.00
 O B:HOH1542 2.1 45.9 1.0
O B:HOH962 2.1 23.6 1.0
OD2 B:ASP244 2.1 29.7 1.0
O B:HOH1543 2.1 34.4 1.0
OD2 B:ASP316 2.1 23.4 1.0
OE2 B:GLU289 2.2 27.6 1.0
CG B:ASP244 3.0 26.7 1.0
CG B:ASP316 3.2 24.1 1.0
OD1 B:ASP244 3.3 24.7 1.0
CD B:GLU289 3.4 32.2 1.0
CB B:ASP316 3.8 26.3 1.0
NE2 B:GLN165 4.0 44.6 1.0
NZ B:LYS392 4.1 32.0 1.0
O B:HOH1284 4.1 44.3 1.0
CG B:GLU289 4.2 19.5 1.0
OE1 B:GLU289 4.3 25.6 1.0
OD1 B:ASP316 4.3 20.4 1.0
CB B:ASP244 4.3 16.8 1.0
OE2 B:GLU166 4.4 37.8 1.0
OD2 B:ASP290 4.4 34.5 1.0
CD2 B:LEU339 4.7 4.1 1.0
NZ B:LYS341 4.7 21.9 1.0
CD B:GLU166 4.9 29.8 1.0
CB B:ALA246 4.9 16.1 1.0

Magnesium binding site 3 out of 8 in 3uj2

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Magnesium binding site 3 out of 8 in the Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate


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 An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg431

b:36.5
occ:1.00
 OD2 C:ASP316 2.1 22.4 1.0
O C:HOH482 2.1 36.9 1.0
O C:HOH968 2.1 29.9 1.0
O C:HOH958 2.1 25.6 1.0
OD2 C:ASP244 2.2 22.6 1.0
OE2 C:GLU289 2.3 24.1 1.0
CG C:ASP316 3.2 25.7 1.0
CG C:ASP244 3.3 25.7 1.0
CD C:GLU289 3.5 20.3 1.0
OD1 C:ASP244 3.7 28.3 1.0
CB C:ASP316 3.8 19.9 1.0
NE2 C:GLN165 3.9 42.2 1.0
OE2 C:GLU166 4.1 27.7 1.0
NZ C:LYS392 4.2 30.2 1.0
OD1 C:ASP316 4.3 23.8 1.0
OE1 C:GLU289 4.3 19.4 1.0
OD2 C:ASP290 4.3 30.3 1.0
CG C:GLU289 4.4 17.9 1.0
CB C:ASP244 4.5 22.9 1.0
CD2 C:LEU339 4.6 16.1 1.0
NZ C:LYS341 4.6 31.9 1.0
O C:HOH1570 4.7 43.0 1.0
CD C:GLU166 4.9 26.1 1.0

Magnesium binding site 4 out of 8 in 3uj2

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Magnesium binding site 4 out of 8 in the Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate


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 An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg430

b:44.6
occ:1.00
 O D:HOH431 2.0 37.5 1.0
O D:HOH1584 2.1 57.1 1.0
OD2 D:ASP244 2.1 50.6 1.0
O D:HOH453 2.1 39.8 1.0
OD2 D:ASP316 2.2 42.7 1.0
OE2 D:GLU289 2.4 46.4 1.0
CG D:ASP244 3.0 33.7 1.0
OD1 D:ASP244 3.2 34.7 1.0
CG D:ASP316 3.4 36.2 1.0
CD D:GLU289 3.6 39.2 1.0
NE2 D:GLN165 3.7 59.3 1.0
CB D:ASP316 4.0 34.6 1.0
OE2 D:GLU166 4.2 41.1 1.0
NZ D:LYS392 4.4 30.0 1.0
CB D:ASP244 4.4 32.0 1.0
OE1 D:GLU289 4.4 27.9 1.0
OD1 D:ASP316 4.4 28.5 1.0
CG D:GLU289 4.5 32.3 1.0
CB D:ALA246 4.7 30.4 1.0
NZ D:LYS341 4.8 40.4 1.0
OD2 D:ASP290 4.8 42.7 1.0
CD D:GLN165 4.8 52.6 1.0
CD D:GLU166 4.8 40.6 1.0
CD2 D:LEU339 4.9 30.4 1.0

Magnesium binding site 5 out of 8 in 3uj2

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Magnesium binding site 5 out of 8 in the Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate


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 An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg430

b:37.6
occ:1.00
 O E:HOH1233 2.1 34.3 1.0
O E:HOH1612 2.1 41.7 1.0
O E:HOH443 2.1 33.0 1.0
OD2 E:ASP244 2.1 32.9 1.0
OD2 E:ASP316 2.2 27.8 1.0
OE2 E:GLU289 2.3 27.3 1.0
CG E:ASP244 3.2 36.9 1.0
CG E:ASP316 3.4 29.2 1.0
OD1 E:ASP244 3.5 31.2 1.0
CD E:GLU289 3.6 37.6 1.0
NE2 E:GLN165 3.6 53.6 1.0
CB E:ASP316 4.1 31.9 1.0
OE2 E:GLU166 4.1 29.3 1.0
NZ E:LYS392 4.3 37.1 1.0
CG E:GLU289 4.4 26.1 1.0
OD1 E:ASP316 4.4 27.8 1.0
OE1 E:GLU289 4.5 30.2 1.0
CB E:ASP244 4.5 34.4 1.0
CB E:ALA246 4.6 28.4 1.0
OD2 E:ASP290 4.7 36.5 1.0
CD E:GLN165 4.7 50.0 1.0
CD E:GLU166 4.9 38.6 1.0
NZ E:LYS341 4.9 31.6 1.0

Magnesium binding site 6 out of 8 in 3uj2

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Magnesium binding site 6 out of 8 in the Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate


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 An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg430

b:41.8
occ:1.00
 OD2 F:ASP244 2.0 32.7 1.0
O F:HOH961 2.1 31.4 1.0
O F:HOH432 2.1 45.8 1.0
O F:HOH1621 2.1 49.9 1.0
OD2 F:ASP316 2.1 36.9 1.0
OE2 F:GLU289 2.2 36.4 1.0
CG F:ASP244 3.0 26.7 1.0
CG F:ASP316 3.3 25.7 1.0
CD F:GLU289 3.3 37.5 1.0
OD1 F:ASP244 3.4 22.4 1.0
NE2 F:GLN165 3.8 58.6 1.0
CB F:ASP316 3.9 20.6 1.0
OE1 F:GLU289 4.1 34.0 1.0
NZ F:LYS392 4.1 30.4 1.0
OE2 F:GLU166 4.1 24.7 1.0
CG F:GLU289 4.3 29.4 1.0
OD1 F:ASP316 4.3 20.7 1.0
CB F:ASP244 4.4 20.4 1.0
NZ F:LYS341 4.5 27.6 1.0
OD2 F:ASP290 4.6 31.2 1.0
CD2 F:LEU339 4.7 20.2 1.0
CB F:ALA246 4.8 40.4 1.0
CD F:GLU166 4.9 30.8 1.0

Magnesium binding site 7 out of 8 in 3uj2

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Magnesium binding site 7 out of 8 in the Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate


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 An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg431

b:32.3
occ:1.00
 O G:HOH1220 2.1 22.9 1.0
O G:HOH439 2.1 26.6 1.0
OD2 G:ASP244 2.1 39.7 1.0
O G:HOH1228 2.1 31.7 1.0
OE2 G:GLU289 2.1 26.9 1.0
OD2 G:ASP316 2.3 35.5 1.0
CG G:ASP244 3.0 35.1 1.0
OD1 G:ASP244 3.2 31.6 1.0
CD G:GLU289 3.3 33.3 1.0
CG G:ASP316 3.3 36.0 1.0
CB G:ASP316 3.7 26.6 1.0
NE2 G:GLN165 4.0 48.8 1.0
OE1 G:GLU289 4.2 22.1 1.0
CG G:GLU289 4.2 27.3 1.0
NZ G:LYS392 4.3 44.4 1.0
OE2 G:GLU166 4.3 33.9 1.0
CB G:ASP244 4.3 23.1 1.0
OD2 G:ASP290 4.4 30.4 1.0
OD1 G:ASP316 4.4 27.9 1.0
CD2 G:LEU339 4.5 29.1 1.0
NZ G:LYS341 4.6 33.7 1.0
CD G:GLU166 4.9 35.3 1.0
CB G:ALA246 4.9 27.6 1.0

Magnesium binding site 8 out of 8 in 3uj2

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Magnesium binding site 8 out of 8 in the Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate


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 An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg430

b:59.0
occ:1.00
 OD2 H:ASP244 2.1 43.4 1.0
O H:HOH980 2.1 34.0 1.0
O H:HOH1649 2.1 49.1 1.0
OD2 H:ASP316 2.3 41.1 1.0
OE2 H:GLU289 2.4 43.4 1.0
CG H:ASP244 3.1 38.1 1.0
NE2 H:GLN165 3.4 63.8 1.0
OD1 H:ASP244 3.4 39.6 1.0
CG H:ASP316 3.5 42.4 1.0
CD H:GLU289 3.7 49.2 1.0
OE2 H:GLU166 4.0 44.9 1.0
CB H:ASP316 4.2 35.6 1.0
CB H:ASP244 4.4 25.4 1.0
OD1 H:ASP316 4.5 46.6 1.0
NZ H:LYS392 4.5 35.7 1.0
OE1 H:GLU289 4.5 45.3 1.0
CG H:GLU289 4.6 46.8 1.0
OD2 H:ASP290 4.6 47.0 1.0
CB H:ALA246 4.7 37.4 1.0
CD H:GLN165 4.7 58.9 1.0
NZ H:LYS341 4.7 43.9 1.0
CD H:GLU166 4.8 51.6 1.0

Reference:

M.W.Vetting, R.Toro, R.Bhosle, B.Hillerich, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of An Enolase From Anaerostipes Caccae (Efi Target Efi-502054) with Bound Mg and Sulfate To Be Published.
Page generated: Thu Aug 15 12:31:31 2024

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