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Magnesium in PDB 2xh4: Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1

Enzymatic activity of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1

All present enzymatic activity of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1:
4.2.1.11;

Protein crystallography data

The structure of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1, PDB code: 2xh4 was solved by B.Schreier, B.Hocker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.69 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 62.421, 62.606, 100.948, 87.95, 76.07, 76.43
R / Rfree (%) 23.3 / 27.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1 (pdb code 2xh4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1, PDB code: 2xh4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 2xh4

Go back to Magnesium Binding Sites List in 2xh4
Magnesium binding site 1 out of 7 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1439

b:2.0
occ:1.00
 OD2 A:ASP246 2.0 14.9 1.0
O2 A:2PG1440 2.1 2.0 1.0
OE2 A:GLU295 2.1 6.2 1.0
O1 A:2PG1440 2.2 11.3 1.0
O A:HOH2402 2.2 5.2 1.0
C1 A:2PG1440 2.3 3.9 1.0
OD2 A:ASP320 2.3 12.3 1.0
CG A:ASP246 3.0 11.7 1.0
CD A:GLU295 3.2 10.1 1.0
OD1 A:ASP246 3.3 12.5 1.0
CG A:ASP320 3.4 9.5 1.0
O A:HOH2098 3.6 17.3 1.0
NZ A:LYS396 3.7 8.1 1.0
C2 A:2PG1440 3.8 10.8 1.0
OE1 A:GLU295 3.9 9.3 1.0
CB A:ASP320 3.9 9.7 1.0
NZ A:LYS345 4.1 5.3 1.0
NE2 A:GLN167 4.2 10.0 1.0
CG A:GLU295 4.2 6.2 1.0
OD2 A:ASP296 4.2 14.3 1.0
CD2 A:LEU343 4.2 10.2 1.0
OE2 A:GLU168 4.4 10.3 1.0
CB A:ASP246 4.4 12.9 1.0
OD1 A:ASP320 4.4 10.7 1.0
C3 A:2PG1440 4.5 9.9 1.0
CE A:LYS345 4.5 4.8 1.0
CE A:LYS396 4.7 7.3 1.0
O1P A:2PG1440 4.7 11.6 1.0

Magnesium binding site 2 out of 7 in 2xh4

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Magnesium binding site 2 out of 7 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1439

b:7.2
occ:1.00
 OD2 B:ASP320 2.1 16.1 1.0
OE2 B:GLU295 2.1 18.0 1.0
O B:HOH2275 2.1 19.1 1.0
O2 B:2PG1440 2.1 19.6 1.0
OD2 B:ASP246 2.3 23.9 1.0
O1 B:2PG1440 2.4 20.4 1.0
C1 B:2PG1440 2.6 20.2 1.0
CD B:GLU295 3.1 18.7 1.0
CG B:ASP320 3.2 18.5 1.0
CG B:ASP246 3.2 20.4 1.0
OD1 B:ASP246 3.4 23.1 1.0
CB B:ASP320 3.6 19.7 1.0
O B:HOH2376 3.7 29.8 1.0
NZ B:LYS396 3.8 15.3 1.0
OE1 B:GLU295 3.9 17.3 1.0
CD2 B:LEU343 4.0 18.1 1.0
C2 B:2PG1440 4.1 19.8 1.0
OD2 B:ASP296 4.1 23.3 1.0
CG B:GLU295 4.1 16.6 1.0
NZ B:LYS345 4.2 27.0 1.0
OD1 B:ASP320 4.3 20.7 1.0
MG B:MG1441 4.3 27.4 1.0
NE2 B:GLN167 4.4 22.1 1.0
CB B:ASP246 4.5 20.5 1.0
OE2 B:GLU168 4.5 20.5 1.0
CE B:LYS345 4.7 26.1 1.0
CE B:LYS396 4.8 14.4 1.0
CG B:ASP296 4.8 23.1 1.0
O1P B:2PG1440 4.9 19.8 1.0
C3 B:2PG1440 4.9 20.9 1.0

Magnesium binding site 3 out of 7 in 2xh4

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Magnesium binding site 3 out of 7 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1441

b:27.4
occ:1.00
 O B:HOH2377 1.9 26.3 1.0
O B:HOH2376 2.1 29.8 1.0
O B:HOH2186 2.3 30.9 1.0
O4P B:2PG1440 2.4 20.3 1.0
O1 B:2PG1440 2.5 20.4 1.0
NZ B:LYS345 3.4 27.0 1.0
P B:2PG1440 3.5 20.8 1.0
C1 B:2PG1440 3.5 20.2 1.0
O1P B:2PG1440 3.7 19.8 1.0
OD2 B:ASP320 3.9 16.1 1.0
O3P B:2PG1440 3.9 19.3 1.0
C2 B:2PG1440 4.0 19.8 1.0
O B:HOH2246 4.0 35.0 1.0
O B:HOH2294 4.1 37.9 1.0
O B:HOH2275 4.2 19.1 1.0
MG B:MG1439 4.3 7.2 1.0
O2 B:2PG1440 4.5 19.6 1.0
NH2 B:ARG374 4.6 20.5 1.0
NE2 B:GLN167 4.6 22.1 1.0
OE1 B:GLN167 4.6 25.3 1.0
O2P B:2PG1440 4.8 17.4 1.0
CG B:ASP320 4.8 18.5 1.0
CE B:LYS345 4.9 26.1 1.0
OD1 B:ASP320 4.9 20.7 1.0
OE1 B:GLU251 4.9 37.5 1.0

Magnesium binding site 4 out of 7 in 2xh4

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Magnesium binding site 4 out of 7 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1442

b:16.0
occ:1.00
 O B:HOH2366 2.1 28.4 1.0
O B:HOH2079 2.2 22.7 1.0
O B:HOH2189 2.3 24.8 1.0
O B:HOH2368 2.3 19.3 1.0
OE1 B:GLU428 2.3 27.8 1.0
O B:HOH2364 2.4 25.2 1.0
CD B:GLU428 3.3 28.3 1.0
OE2 B:GLU428 3.6 30.8 1.0
O B:HOH2362 4.2 41.3 1.0
O B:THR174 4.3 21.4 1.0
O B:ALA176 4.3 20.5 1.0
O B:HOH2363 4.4 24.6 1.0
O B:HOH2078 4.4 33.7 1.0
N B:GLU428 4.4 21.2 1.0
O B:HOH2192 4.6 48.8 1.0
CG B:GLU428 4.7 25.5 1.0
CA B:GLY427 4.7 18.2 1.0

Magnesium binding site 5 out of 7 in 2xh4

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Magnesium binding site 5 out of 7 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1439

b:2.0
occ:1.00
 OD2 C:ASP320 1.8 2.5 1.0
OE2 C:GLU295 1.8 16.1 1.0
O C:HOH2381 2.1 20.2 1.0
O2 C:2PG1440 2.2 3.4 1.0
OD2 C:ASP246 2.4 7.5 1.0
O1 C:2PG1440 2.5 13.7 1.0
C1 C:2PG1440 2.7 5.4 1.0
CG C:ASP320 2.8 12.3 1.0
CD C:GLU295 3.0 11.6 1.0
CG C:ASP246 3.1 12.9 1.0
OD1 C:ASP246 3.2 13.1 1.0
CB C:ASP320 3.2 9.5 1.0
O C:HOH2089 3.6 18.7 1.0
OE1 C:GLU295 3.7 11.7 1.0
NZ C:LYS396 3.8 9.2 1.0
CG C:GLU295 3.9 10.2 1.0
OD1 C:ASP320 3.9 11.8 1.0
NZ C:LYS345 4.0 16.7 1.0
OD2 C:ASP296 4.1 6.8 1.0
CD2 C:LEU343 4.2 13.5 1.0
C2 C:2PG1440 4.3 5.0 1.0
CB C:ASP246 4.4 11.3 1.0
NE2 C:GLN167 4.5 12.4 1.0
CG C:ASP296 4.7 10.9 1.0
CA C:ASP320 4.8 9.5 1.0
OE2 C:GLU168 4.8 7.9 1.0
CE C:LYS396 5.0 8.9 1.0
CE C:LYS345 5.0 16.7 1.0
O1P C:2PG1440 5.0 8.2 1.0

Magnesium binding site 6 out of 7 in 2xh4

Go back to Magnesium Binding Sites List in 2xh4
Magnesium binding site 6 out of 7 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1439

b:8.5
occ:1.00
 O D:HOH2211 1.8 17.0 1.0
OE2 D:GLU295 2.1 20.1 1.0
OD2 D:ASP320 2.1 21.9 1.0
OD2 D:ASP246 2.2 21.2 1.0
O1 D:2PG1440 2.3 18.2 1.0
O2 D:2PG1440 2.3 17.3 1.0
C1 D:2PG1440 2.6 17.7 1.0
CG D:ASP246 3.1 21.2 1.0
CG D:ASP320 3.2 21.2 1.0
CD D:GLU295 3.2 19.2 1.0
OD1 D:ASP246 3.3 24.8 1.0
CB D:ASP320 3.6 20.5 1.0
O D:HOH2255 3.8 32.3 1.0
NZ D:LYS396 3.8 15.2 1.0
OE1 D:GLU295 3.9 17.6 1.0
NZ D:LYS345 4.1 26.6 1.0
C2 D:2PG1440 4.1 17.0 1.0
OD2 D:ASP296 4.2 22.4 1.0
CG D:GLU295 4.2 17.9 1.0
OD1 D:ASP320 4.2 23.3 1.0
NE2 D:GLN167 4.3 16.7 1.0
CD2 D:LEU343 4.3 18.9 1.0
O D:HOH2312 4.3 32.0 1.0
CB D:ASP246 4.5 20.0 1.0
OE2 D:GLU168 4.7 21.5 1.0
CG D:ASP296 4.8 22.7 1.0
O1P D:2PG1440 4.9 19.0 1.0
CE D:LYS345 4.9 27.0 1.0
CB D:ALA248 5.0 21.4 1.0

Magnesium binding site 7 out of 7 in 2xh4

Go back to Magnesium Binding Sites List in 2xh4
Magnesium binding site 7 out of 7 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39A D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1441

b:8.9
occ:1.00
 O D:HOH2301 1.8 23.7 1.0
OE1 D:GLU428 1.9 29.7 1.0
O D:HOH2072 2.0 27.5 1.0
O D:HOH2154 2.1 18.6 1.0
O D:HOH2300 2.2 19.4 1.0
O D:HOH2299 2.2 29.9 1.0
CD D:GLU428 3.0 29.7 1.0
OE2 D:GLU428 3.4 29.9 1.0
O D:HOH2159 4.0 40.1 1.0
O D:HOH2155 4.0 25.5 1.0
N D:GLU428 4.1 21.5 1.0
O D:THR174 4.2 20.6 1.0
O D:HOH2298 4.3 33.9 1.0
CG D:GLU428 4.3 25.6 1.0
O D:ALA176 4.5 21.9 1.0
O D:HOH2143 4.5 48.4 1.0
CA D:GLY427 4.5 18.9 1.0
O D:HOH2297 4.6 32.8 1.0
CB D:GLU428 4.6 23.5 1.0
O D:HOH2305 4.6 28.9 1.0
C D:GLY427 4.8 19.8 1.0
O D:HOH2073 4.9 34.4 1.0
CA D:GLU428 5.0 22.1 1.0

Reference:

B.Schreier, B.Hoecker. Engineering the Enolase Magnesium II Binding Site - Implications For Its Evolution. Biochemistry V. 49 7582 2010.
ISSN: ISSN 0006-2960
PubMed: 20690637
DOI: 10.1021/BI100954F
Page generated: Mon Dec 14 07:46:39 2020

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