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Magnesium in PDB 2xgz: Engineering the Enolase Active Site Pocket: Crystal Structure of the S39N D321R Mutant of Yeast Enolase 1

Enzymatic activity of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39N D321R Mutant of Yeast Enolase 1

All present enzymatic activity of Engineering the Enolase Active Site Pocket: Crystal Structure of the S39N D321R 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 S39N D321R Mutant of Yeast Enolase 1, PDB code: 2xgz 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) 37.90 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 62.380, 63.050, 64.430, 73.01, 79.28, 81.22
R / Rfree (%) 16.4 / 20.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39N D321R Mutant of Yeast Enolase 1 (pdb code 2xgz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39N D321R Mutant of Yeast Enolase 1, PDB code: 2xgz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2xgz

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Magnesium binding site 1 out of 5 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39N D321R 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 S39N D321R Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1439

b:2.7
occ:1.00
 OE2 A:GLU295 2.0 12.6 1.0
O A:HOH2298 2.1 11.1 1.0
OD2 A:ASP246 2.1 13.3 1.0
OD2 A:ASP320 2.2 10.7 1.0
O1 A:PEP1440 2.3 15.1 1.0
O2' A:PEP1440 2.3 14.6 1.0
C1 A:PEP1440 2.6 15.2 1.0
CG A:ASP246 3.0 14.0 1.0
CD A:GLU295 3.1 10.3 1.0
CG A:ASP320 3.2 12.3 1.0
OD1 A:ASP246 3.3 11.8 1.0
NZ A:LYS396 3.7 14.5 1.0
CB A:ASP320 3.7 12.1 1.0
OE1 A:GLU295 3.8 10.7 1.0
CG A:GLU295 4.0 11.8 1.0
C2 A:PEP1440 4.1 15.9 1.0
CD2 A:LEU343 4.2 9.7 1.0
OD2 A:ASP296 4.2 16.1 1.0
NZ A:LYS345 4.2 12.0 1.0
NH1 A:ARG321 4.3 25.2 1.0
OD1 A:ASP320 4.3 12.8 1.0
CB A:ASP246 4.3 14.2 1.0
OE2 A:GLU168 4.5 26.1 1.0
O A:HOH2233 4.5 37.1 1.0
CE A:LYS396 4.9 14.1 1.0
C3 A:PEP1440 4.9 16.6 1.0
O2 A:PEP1440 4.9 14.5 1.0
CG A:ASP296 4.9 13.1 1.0

Magnesium binding site 2 out of 5 in 2xgz

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Magnesium binding site 2 out of 5 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39N D321R 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 S39N D321R Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1441

b:7.3
occ:1.00
 O A:HOH2195 2.0 11.6 1.0
O A:HOH2201 2.1 22.4 1.0
OD1 A:ASP135 2.2 14.8 1.0
O A:HOH2213 2.2 20.7 1.0
O A:HOH2202 2.2 15.2 1.0
CG A:ASP135 3.3 12.8 1.0
OD2 A:ASP135 3.7 13.6 1.0
O A:HOH2217 4.0 18.2 1.0
O A:LYS131 4.1 9.3 1.0
CG2 A:THR141 4.3 16.8 1.0
OH A:TYR144 4.4 10.5 1.0
O A:HOH2203 4.4 30.9 1.0
O A:HOH2211 4.5 16.0 1.0
CB A:ASP135 4.5 11.4 1.0
OG1 A:THR141 4.6 20.1 1.0
N A:ASP135 4.6 11.2 1.0
CA A:ASP135 4.7 11.0 1.0
CB A:THR141 5.0 18.1 1.0

Magnesium binding site 3 out of 5 in 2xgz

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Magnesium binding site 3 out of 5 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39N D321R 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 S39N D321R Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1442

b:15.4
occ:1.00
 O A:HOH2110 2.2 19.6 1.0
O A:HOH2109 2.4 18.4 1.0
O A:HOH2062 2.4 34.5 1.0
O A:HOH2163 2.6 25.4 1.0
O A:HOH2105 4.0 27.6 1.0
OD1 A:ASN67 4.0 13.6 1.0
O A:LYS104 4.3 15.1 1.0
ND2 A:ASN67 4.5 13.3 1.0
O A:HOH2107 4.5 43.6 1.0
O A:HOH2111 4.6 23.4 1.0
CG A:ASN67 4.7 14.2 1.0
O A:HOH2159 4.7 29.0 1.0
CE A:LYS104 4.7 23.9 1.0
NZ A:LYS104 4.8 26.2 1.0

Magnesium binding site 4 out of 5 in 2xgz

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Magnesium binding site 4 out of 5 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39N D321R 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 S39N D321R Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1439

b:3.5
occ:1.00
 O B:HOH2293 2.0 10.7 1.0
OE2 B:GLU295 2.0 13.6 1.0
OD2 B:ASP246 2.1 17.3 1.0
OD2 B:ASP320 2.2 14.6 1.0
O1 B:PEP1440 2.3 38.7 1.0
O2' B:PEP1440 2.5 39.6 1.0
O B:HOH2392 2.5 24.7 1.0
C1 B:PEP1440 2.6 37.1 1.0
CG B:ASP246 2.9 15.8 1.0
CD B:GLU295 3.1 12.5 1.0
CG B:ASP320 3.2 13.9 1.0
OD1 B:ASP246 3.2 17.4 1.0
CB B:ASP320 3.6 13.0 1.0
C2 B:PEP1440 3.9 36.5 1.0
CG B:GLU295 3.9 11.3 1.0
OE1 B:GLU295 4.0 14.2 1.0
O B:HOH2317 4.0 39.5 1.0
OD2 B:ASP296 4.2 15.0 1.0
NZ B:LYS396 4.2 13.3 1.0
CB B:ASP246 4.2 14.9 1.0
OD1 B:ASP320 4.3 13.9 1.0
OE2 B:GLU168 4.3 18.4 1.0
CD2 B:LEU343 4.6 9.1 1.0
O2 B:PEP1440 4.6 35.1 1.0
NE2 B:GLN167 4.6 19.3 1.0
CG B:ASP296 4.8 12.9 1.0
C3 B:PEP1440 4.8 35.4 1.0
CD B:GLU168 4.9 17.0 1.0

Magnesium binding site 5 out of 5 in 2xgz

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Magnesium binding site 5 out of 5 in the Engineering the Enolase Active Site Pocket: Crystal Structure of the S39N D321R 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 S39N D321R Mutant of Yeast Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1441

b:5.5
occ:1.00
 OD1 B:ASP135 2.1 12.0 1.0
O B:HOH2090 2.1 17.9 1.0
O B:HOH2208 2.3 15.1 1.0
O B:HOH2194 2.3 16.3 1.0
O B:HOH2193 2.4 26.3 1.0
CG B:ASP135 3.1 10.5 1.0
OD2 B:ASP135 3.5 13.3 1.0
O B:LYS131 4.1 11.8 1.0
O B:HOH2209 4.2 18.2 1.0
O B:HOH2203 4.3 26.3 1.0
OH B:TYR144 4.4 7.6 1.0
CB B:ASP135 4.4 10.3 1.0
CG2 B:THR141 4.5 16.8 1.0
O B:HOH2197 4.5 15.6 1.0
N B:ASP135 4.6 9.8 1.0
CA B:ASP135 4.7 10.3 1.0
OG1 B:THR141 4.8 19.6 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 07:07:12 2024

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