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Magnesium in PDB 2xh7: Engineering the Enolase Active Site Pocket: Crystal Structure of the D321A Mutant of Yeast Enolase 1

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

All present enzymatic activity of Engineering the Enolase Active Site Pocket: Crystal Structure of the 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 D321A Mutant of Yeast Enolase 1, PDB code: 2xh7 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) 43.69 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.973, 62.000, 64.320, 67.89, 78.33, 80.60
R / Rfree (%) 17.5 / 21.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Engineering the Enolase Active Site Pocket: Crystal Structure of the D321A Mutant of Yeast Enolase 1 (pdb code 2xh7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Engineering the Enolase Active Site Pocket: Crystal Structure of the D321A Mutant of Yeast Enolase 1, PDB code: 2xh7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 2xh7

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Magnesium binding site 1 out of 10 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the D321A Mutant of Yeast Enolase 1


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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 D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1439

b:5.5
occ:1.00
 OE2 A:GLU295 2.0 14.0 1.0
O A:HOH2268 2.1 13.5 1.0
OD2 A:ASP246 2.1 16.4 1.0
OD2 A:ASP320 2.2 14.4 1.0
O2 A:2PG1440 2.3 16.8 1.0
O1 A:2PG1440 2.6 16.7 1.0
C1 A:2PG1440 2.8 16.5 1.0
CG A:ASP246 3.0 15.8 1.0
CD A:GLU295 3.1 14.6 1.0
CG A:ASP320 3.2 14.5 1.0
OD1 A:ASP246 3.2 15.1 1.0
CB A:ASP320 3.6 13.6 1.0
O A:HOH2059 3.7 20.9 1.0
NZ A:LYS396 3.7 17.2 1.0
OE1 A:GLU295 3.8 14.8 1.0
CG A:GLU295 4.0 13.6 1.0
O A:HOH2327 4.0 22.4 1.0
NE2 A:GLN167 4.1 21.2 1.0
CD2 A:LEU343 4.1 12.8 1.0
MG A:MG1441 4.1 3.1 1.0
NZ A:LYS345 4.2 19.9 1.0
OD2 A:ASP296 4.2 13.4 1.0
C2 A:2PG1440 4.3 15.7 1.0
OD1 A:ASP320 4.3 15.2 1.0
CB A:ASP246 4.3 15.7 1.0
OE2 A:GLU168 4.4 22.6 1.0
CE A:LYS396 4.8 16.7 1.0
CG A:ASP296 4.9 12.1 1.0

Magnesium binding site 2 out of 10 in 2xh7

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Magnesium binding site 2 out of 10 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the D321A Mutant of Yeast Enolase 1


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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 D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1441

b:3.1
occ:1.00
 O4P A:2PG1440 2.0 12.4 1.0
O A:SER39 2.2 16.2 1.0
OG A:SER39 2.3 17.2 1.0
O A:HOH2059 2.3 20.9 1.0
O1 A:2PG1440 2.3 16.7 1.0
O A:HOH2327 2.3 22.4 1.0
C A:SER39 3.1 16.9 1.0
CB A:SER39 3.1 17.1 1.0
P A:2PG1440 3.2 12.3 1.0
C1 A:2PG1440 3.2 16.5 1.0
O1P A:2PG1440 3.3 14.1 1.0
CA A:SER39 3.5 17.1 1.0
C2 A:2PG1440 3.7 15.7 1.0
NZ A:LYS345 3.8 19.9 1.0
O3P A:2PG1440 3.8 13.1 1.0
OD2 A:ASP320 3.9 14.4 1.0
N A:SER39 4.0 17.3 1.0
MG A:MG1439 4.1 5.5 1.0
O2 A:2PG1440 4.2 16.8 1.0
N A:THR40 4.2 16.8 1.0
O A:HOH2268 4.2 13.5 1.0
NE2 A:GLN167 4.2 21.2 1.0
OE1 A:GLN167 4.3 21.3 1.0
O A:HOH2270 4.3 24.4 1.0
NH2 A:ARG374 4.4 11.6 1.0
O2P A:2PG1440 4.4 11.0 1.0
CA A:THR40 4.7 17.0 1.0
CD A:GLN167 4.7 20.7 1.0
CG A:ASP320 4.9 14.5 1.0

Magnesium binding site 3 out of 10 in 2xh7

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Magnesium binding site 3 out of 10 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the 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 D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1442

b:9.1
occ:1.00
 OD1 A:ASP135 2.2 17.2 1.0
O A:HOH2200 2.2 17.4 1.0
O A:HOH2182 2.4 20.0 1.0
O A:HOH2184 2.4 23.9 1.0
CG A:ASP135 3.2 16.3 1.0
OD2 A:ASP135 3.5 16.4 1.0
O A:LYS131 4.0 13.0 1.0
O A:HOH2201 4.2 24.9 1.0
OH A:TYR144 4.4 16.1 1.0
CB A:ASP135 4.5 14.6 1.0
O A:HOH2190 4.5 26.2 1.0
CG2 A:THR141 4.7 24.5 1.0
N A:ASP135 4.7 14.0 1.0
CA A:ASP135 4.8 14.8 1.0
C A:LYS131 4.9 13.4 1.0

Magnesium binding site 4 out of 10 in 2xh7

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Magnesium binding site 4 out of 10 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the 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 D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1443

b:15.9
occ:1.00
 OD1 A:ASP280 2.2 21.4 1.0
O A:HOH2147 2.4 32.8 1.0
O A:HOH2275 2.5 38.0 1.0
O A:HOH2280 2.5 37.5 1.0
O A:HOH2281 2.7 44.5 1.0
CG A:ASP280 3.2 21.0 1.0
OD2 A:ASP280 3.5 23.5 1.0
O A:HOH2279 4.1 30.7 1.0
O A:PRO276 4.2 23.8 1.0
O A:HOH2148 4.4 28.6 1.0
O A:HOH2159 4.4 48.9 1.0
CB A:ASP280 4.6 19.4 1.0
N A:ASP280 4.7 18.8 1.0
CA A:ASP280 4.8 19.3 1.0

Magnesium binding site 5 out of 10 in 2xh7

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Magnesium binding site 5 out of 10 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the 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 D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1444

b:9.8
occ:1.00
 OE2 A:GLU354 2.1 18.0 1.0
O A:HOH2335 2.3 19.5 1.0
O A:HOH2334 2.3 21.2 1.0
O A:HOH2333 2.3 28.7 1.0
O A:HOH2164 2.3 24.2 1.0
O A:HOH2332 2.4 24.1 1.0
CD A:GLU354 3.2 18.8 1.0
CG A:GLU354 3.7 16.4 1.0
O A:HOH2314 3.8 25.5 1.0
O A:HOH2178 4.2 20.2 1.0
O A:HOH2149 4.3 18.8 1.0
OE1 A:GLU354 4.3 18.5 1.0
O A:HOH2163 4.3 24.3 1.0
O A:HOH2180 4.4 45.2 1.0
O A:HOH2144 4.5 21.3 1.0
NZ A:LYS102 4.6 15.9 1.0
CB A:GLU354 4.8 14.2 1.0
CD1 A:ILE349 4.8 15.3 1.0
CD1 A:ILE94 4.9 19.2 1.0

Magnesium binding site 6 out of 10 in 2xh7

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Magnesium binding site 6 out of 10 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the 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 D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1439

b:4.7
occ:1.00
 OE2 B:GLU295 2.0 16.3 1.0
OD2 B:ASP320 2.2 15.6 1.0
OD2 B:ASP246 2.2 17.3 1.0
O B:HOH2272 2.2 17.0 1.0
O2 B:2PG1440 2.2 15.9 1.0
O1 B:2PG1440 2.5 15.1 1.0
C1 B:2PG1440 2.7 16.5 1.0
CG B:ASP246 3.0 18.3 1.0
CD B:GLU295 3.1 15.8 1.0
CG B:ASP320 3.2 14.7 1.0
OD1 B:ASP246 3.3 16.5 1.0
CB B:ASP320 3.6 13.2 1.0
NZ B:LYS396 3.7 14.0 1.0
OE1 B:GLU295 3.8 15.6 1.0
O B:HOH2046 3.8 27.3 1.0
CG B:GLU295 4.0 14.8 1.0
CD2 B:LEU343 4.0 13.0 1.0
MG B:MG1441 4.1 7.9 1.0
NZ B:LYS345 4.1 19.6 1.0
O B:HOH2303 4.1 22.7 1.0
C2 B:2PG1440 4.2 15.9 1.0
OD2 B:ASP296 4.2 15.3 1.0
NE2 B:GLN167 4.2 25.5 1.0
OD1 B:ASP320 4.3 16.2 1.0
CB B:ASP246 4.3 17.8 1.0
OE2 B:GLU168 4.5 25.3 1.0
CE B:LYS396 4.7 15.6 1.0
CG B:ASP296 4.9 14.9 1.0
C3 B:2PG1440 4.9 17.4 1.0
CE B:LYS345 5.0 18.6 1.0
O1P B:2PG1440 5.0 15.3 1.0

Magnesium binding site 7 out of 10 in 2xh7

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Magnesium binding site 7 out of 10 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the 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 D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1441

b:7.9
occ:1.00
 O B:HOH2303 2.1 22.7 1.0
O B:SER39 2.1 20.2 1.0
O4P B:2PG1440 2.1 15.5 1.0
O1 B:2PG1440 2.4 15.1 1.0
OG B:SER39 2.4 20.4 1.0
O B:HOH2046 2.5 27.3 1.0
C B:SER39 3.1 20.6 1.0
C1 B:2PG1440 3.2 16.5 1.0
P B:2PG1440 3.3 14.6 1.0
CB B:SER39 3.3 20.5 1.0
O1P B:2PG1440 3.4 15.3 1.0
C2 B:2PG1440 3.6 15.9 1.0
NZ B:LYS345 3.7 19.6 1.0
CA B:SER39 3.7 20.4 1.0
OD2 B:ASP320 3.7 15.6 1.0
O3P B:2PG1440 3.9 14.8 1.0
MG B:MG1439 4.1 4.7 1.0
O2 B:2PG1440 4.2 15.9 1.0
N B:SER39 4.2 20.1 1.0
N B:THR40 4.2 21.0 1.0
O B:HOH2246 4.2 20.8 1.0
O B:HOH2272 4.3 17.0 1.0
NH2 B:ARG374 4.3 14.5 1.0
O2P B:2PG1440 4.5 13.5 1.0
NE2 B:GLN167 4.5 25.5 1.0
CA B:THR40 4.6 21.4 1.0
OE1 B:GLN167 4.6 23.6 1.0
CG B:ASP320 4.7 14.7 1.0
OD1 B:ASP320 5.0 16.2 1.0
CE B:LYS345 5.0 18.6 1.0

Magnesium binding site 8 out of 10 in 2xh7

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Magnesium binding site 8 out of 10 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the 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 8 of Engineering the Enolase Active Site Pocket: Crystal Structure of the D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1442

b:6.1
occ:1.00
 OD1 B:ASP135 2.0 15.3 1.0
O B:HOH2169 2.1 19.6 1.0
O B:HOH2162 2.2 18.7 1.0
O B:HOH2170 2.4 21.4 1.0
CG B:ASP135 3.1 15.1 1.0
OD2 B:ASP135 3.4 16.9 1.0
O B:LYS131 3.9 12.3 1.0
CB B:ASP135 4.4 13.7 1.0
OH B:TYR144 4.4 14.9 1.0
O B:HOH2174 4.5 25.9 1.0
CG2 B:THR141 4.5 23.9 1.0
N B:ASP135 4.6 13.2 1.0
CA B:ASP135 4.6 13.7 1.0
C B:LYS131 4.8 12.4 1.0

Magnesium binding site 9 out of 10 in 2xh7

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Magnesium binding site 9 out of 10 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the 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 9 of Engineering the Enolase Active Site Pocket: Crystal Structure of the D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1443

b:25.1
occ:1.00
 O B:HOH2159 2.3 26.6 1.0
O B:HOH2313 2.3 32.1 1.0
OE2 B:GLU354 2.3 17.9 1.0
O B:HOH2314 2.4 22.6 1.0
O B:HOH2311 2.7 30.7 1.0
O B:HOH2312 2.8 27.2 1.0
CD B:GLU354 3.3 16.2 1.0
CG B:GLU354 3.7 15.2 1.0
O B:HOH2160 3.9 19.5 1.0
OE1 B:GLU354 4.4 16.5 1.0
O B:HOH2158 4.5 45.9 1.0
O B:HOH2129 4.6 19.9 1.0
CD1 B:ILE94 4.7 16.9 1.0
O B:HOH2143 4.8 44.8 1.0
CB B:GLU354 4.9 14.6 1.0
NZ B:LYS102 5.0 20.4 1.0

Magnesium binding site 10 out of 10 in 2xh7

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Magnesium binding site 10 out of 10 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the 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 10 of Engineering the Enolase Active Site Pocket: Crystal Structure of the D321A Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1444

b:30.4
occ:1.00
 O B:HOH2252 2.4 31.6 1.0
OD1 B:ASP280 2.4 28.7 1.0
O B:HOH2126 2.7 54.7 1.0
O B:HOH2259 2.7 67.4 1.0
O B:HOH2256 3.0 54.6 1.0
O B:HOH2042 3.1 38.5 1.0
CG B:ASP280 3.5 26.9 1.0
OD2 B:ASP280 4.0 28.6 1.0
O B:HOH2255 4.2 41.6 1.0
O B:HOH2130 4.3 36.4 1.0
O B:PRO276 4.4 32.6 1.0
N B:ASP280 4.7 25.5 1.0
CB B:ASP280 4.7 25.7 1.0
CA B:ASP280 4.8 25.5 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: Wed Aug 14 07:08:16 2024

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