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Magnesium in PDB 3b97: Crystal Structure of Human Enolase 1

Enzymatic activity of Crystal Structure of Human Enolase 1

All present enzymatic activity of Crystal Structure of Human Enolase 1:
4.2.1.11;

Protein crystallography data

The structure of Crystal Structure of Human Enolase 1, PDB code: 3b97 was solved by H.J.Kang, S.K.Jung, S.J.Kim, S.J.Chung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 192.796, 192.796, 65.170, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Enolase 1 (pdb code 3b97). 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 Human Enolase 1, PDB code: 3b97:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3b97

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Magnesium binding site 1 out of 8 in the Crystal Structure of Human Enolase 1


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 Human Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg434

b:18.7
occ:1.00
 O A:HOH614 2.1 8.1 1.0
OD2 A:ASP317 2.2 7.4 1.0
O A:HOH439 2.3 8.0 1.0
OD2 A:ASP244 2.3 13.2 1.0
OE2 A:GLU292 2.3 15.8 1.0
MG A:MG435 3.1 19.1 1.0
CG A:ASP244 3.2 17.1 1.0
CG A:ASP317 3.4 16.1 1.0
OD1 A:ASP244 3.5 13.8 1.0
CD A:GLU292 3.5 10.4 1.0
NZ A:LYS342 3.5 9.8 1.0
O A:HOH438 3.6 8.0 1.0
OE1 A:GLN165 3.7 17.1 1.0
O A:HOH437 3.7 10.4 1.0
NZ A:LYS393 3.8 7.4 1.0
CB A:ASP317 4.0 8.5 1.0
O1 A:SO4436 4.1 9.8 1.0
OE1 A:GLU292 4.2 9.9 1.0
CD2 A:LEU340 4.3 8.8 1.0
OD2 A:ASP293 4.3 12.6 1.0
OD1 A:ASP317 4.3 14.4 1.0
O2 A:SO4436 4.4 11.5 1.0
CG A:GLU292 4.5 7.3 1.0
OE2 A:GLU166 4.5 14.5 1.0
CB A:ASP244 4.6 10.4 1.0
CE A:LYS342 4.6 12.0 1.0
CD A:GLN165 4.7 13.9 1.0
OG A:SER39 4.8 11.7 1.0
CE A:LYS393 4.9 8.0 1.0
S A:SO4436 4.9 12.9 1.0
O A:HOH463 4.9 13.1 1.0
CB A:ALA246 4.9 12.1 1.0

Magnesium binding site 2 out of 8 in 3b97

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Magnesium binding site 2 out of 8 in the Crystal Structure of Human Enolase 1


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 Human Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg435

b:19.1
occ:1.00
 O A:HOH437 2.2 10.4 1.0
O A:HOH438 2.3 8.0 1.0
O2 A:SO4436 2.3 11.5 1.0
O A:SER39 2.3 19.2 1.0
OG A:SER39 2.4 11.7 1.0
MG A:MG434 3.1 18.7 1.0
CB A:SER39 3.3 14.3 1.0
S A:SO4436 3.3 12.9 1.0
C A:SER39 3.4 15.1 1.0
O1 A:SO4436 3.4 9.8 1.0
OD2 A:ASP317 3.5 7.4 1.0
NZ A:LYS342 3.7 9.8 1.0
O A:HOH439 3.8 8.0 1.0
CA A:SER39 3.8 12.3 1.0
OE1 A:GLN165 3.9 17.1 1.0
O3 A:SO4436 4.0 12.7 1.0
NE2 A:GLN165 4.1 9.1 1.0
O A:HOH614 4.1 8.1 1.0
OD2 A:ASP318 4.1 11.7 1.0
OD1 A:ASP318 4.2 11.7 1.0
N A:SER39 4.3 10.6 1.0
NH2 A:ARG371 4.4 7.3 1.0
CD A:GLN165 4.5 13.9 1.0
O4 A:SO4436 4.5 10.3 1.0
CG A:ASP318 4.6 12.9 1.0
N A:THR40 4.6 17.5 1.0
CG A:ASP317 4.7 16.1 1.0
OD2 A:ASP244 4.9 13.2 1.0
CB A:ALA246 4.9 12.1 1.0

Magnesium binding site 3 out of 8 in 3b97

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Magnesium binding site 3 out of 8 in the Crystal Structure of Human Enolase 1


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 Human Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg434

b:22.7
occ:1.00
 O B:HOH438 2.1 14.8 1.0
OD2 B:ASP317 2.2 14.9 1.0
O B:HOH437 2.3 14.5 1.0
OE2 B:GLU292 2.3 28.3 1.0
OD2 B:ASP244 2.4 21.2 1.0
MG B:MG435 2.9 23.3 1.0
CG B:ASP244 3.3 20.8 1.0
CG B:ASP317 3.3 17.1 1.0
OD1 B:ASP244 3.5 21.2 1.0
NZ B:LYS342 3.5 13.3 1.0
CD B:GLU292 3.5 22.5 1.0
OE1 B:GLN165 3.6 17.4 1.0
O B:HOH439 3.7 14.2 1.0
NZ B:LYS393 3.8 11.0 1.0
O B:HOH444 3.9 16.1 1.0
O1 B:SO4436 3.9 17.3 1.0
CB B:ASP317 4.0 13.7 1.0
OE1 B:GLU292 4.1 18.2 1.0
OD1 B:ASP317 4.3 17.4 1.0
CD2 B:LEU340 4.3 12.4 1.0
O2 B:SO4436 4.4 15.8 1.0
OE2 B:GLU166 4.4 19.0 1.0
OD2 B:ASP293 4.4 22.7 1.0
CG B:GLU292 4.6 20.5 1.0
CD B:GLN165 4.7 15.1 1.0
CE B:LYS342 4.7 12.9 1.0
CB B:ASP244 4.7 16.8 1.0
OG B:SER39 4.7 11.5 1.0
S B:SO4436 4.8 16.8 1.0
O B:HOH448 4.9 16.9 1.0
CB B:ALA246 5.0 15.2 1.0

Magnesium binding site 4 out of 8 in 3b97

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Magnesium binding site 4 out of 8 in the Crystal Structure of Human Enolase 1


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 Human Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg435

b:23.3
occ:1.00
 O B:HOH444 2.3 16.1 1.0
O B:HOH439 2.3 14.2 1.0
O2 B:SO4436 2.3 15.8 1.0
OG B:SER39 2.4 11.5 1.0
O B:SER39 2.4 21.2 1.0
MG B:MG434 2.9 22.7 1.0
O1 B:SO4436 3.1 17.3 1.0
S B:SO4436 3.2 16.8 1.0
CB B:SER39 3.4 14.7 1.0
OD2 B:ASP317 3.4 14.9 1.0
C B:SER39 3.4 18.7 1.0
NZ B:LYS342 3.6 13.3 1.0
O B:HOH437 3.7 14.5 1.0
O3 B:SO4436 3.8 17.5 1.0
OE1 B:GLN165 3.8 17.4 1.0
CA B:SER39 3.9 16.1 1.0
O B:HOH438 4.0 14.8 1.0
NE2 B:GLN165 4.0 8.0 1.0
OD1 B:ASP318 4.3 16.3 1.0
N B:SER39 4.3 17.6 1.0
CD B:GLN165 4.3 15.1 1.0
OD2 B:ASP318 4.4 17.9 1.0
NH2 B:ARG371 4.5 12.6 1.0
O4 B:SO4436 4.5 15.2 1.0
CG B:ASP317 4.6 17.1 1.0
N B:THR40 4.6 18.8 1.0
CG B:ASP318 4.7 21.4 1.0
OD2 B:ASP244 4.7 21.2 1.0
CB B:ALA246 4.9 15.2 1.0

Magnesium binding site 5 out of 8 in 3b97

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Magnesium binding site 5 out of 8 in the Crystal Structure of Human Enolase 1


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 Human Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg434

b:29.7
occ:1.00
 O C:HOH557 2.2 16.8 1.0
OD2 C:ASP317 2.3 18.6 1.0
OD2 C:ASP244 2.3 23.4 1.0
O C:HOH437 2.4 22.8 1.0
OE2 C:GLU292 2.7 24.9 1.0
MG C:MG435 2.7 26.0 1.0
CG C:ASP244 3.3 23.8 1.0
OE1 C:GLN165 3.3 26.5 1.0
NZ C:LYS342 3.5 19.2 1.0
CG C:ASP317 3.5 19.4 1.0
OD1 C:ASP244 3.6 22.8 1.0
O C:HOH457 3.6 16.9 1.0
O1 C:SO4436 3.8 13.0 1.0
CD C:GLU292 3.8 16.0 1.0
NZ C:LYS393 4.0 12.0 1.0
O2 C:SO4436 4.1 15.7 1.0
CB C:ASP317 4.3 15.2 1.0
CD C:GLN165 4.4 21.6 1.0
OD1 C:ASP317 4.4 14.1 1.0
OG C:SER39 4.4 16.4 1.0
OE2 C:GLU166 4.5 21.6 1.0
OE1 C:GLU292 4.5 21.3 1.0
OD2 C:ASP293 4.5 17.2 1.0
S C:SO4436 4.6 18.3 1.0
CE C:LYS342 4.6 21.4 1.0
CD2 C:LEU340 4.6 10.8 1.0
CB C:ASP244 4.7 17.4 1.0
NE2 C:GLN165 4.7 17.3 1.0
CB C:ALA246 4.7 24.2 1.0
CG C:GLU292 4.8 13.4 1.0
O C:HOH450 5.0 23.4 1.0

Magnesium binding site 6 out of 8 in 3b97

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Magnesium binding site 6 out of 8 in the Crystal Structure of Human Enolase 1


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 Human Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg435

b:26.0
occ:1.00
 O C:HOH457 2.3 16.9 1.0
O2 C:SO4436 2.4 15.7 1.0
OG C:SER39 2.4 16.4 1.0
O C:SER39 2.5 25.1 1.0
MG C:MG434 2.7 29.7 1.0
CB C:SER39 3.3 18.4 1.0
S C:SO4436 3.3 18.3 1.0
O1 C:SO4436 3.4 13.0 1.0
C C:SER39 3.5 21.8 1.0
OD2 C:ASP317 3.5 18.6 1.0
NZ C:LYS342 3.7 19.2 1.0
O C:HOH437 3.7 22.8 1.0
CA C:SER39 3.9 19.7 1.0
O3 C:SO4436 3.9 18.3 1.0
OE1 C:GLN165 4.0 26.5 1.0
NE2 C:GLN165 4.0 17.3 1.0
OD2 C:ASP318 4.1 23.3 1.0
O C:HOH557 4.1 16.8 1.0
OD1 C:ASP318 4.4 18.7 1.0
N C:SER39 4.4 19.6 1.0
NH2 C:ARG371 4.4 14.2 1.0
CD C:GLN165 4.5 21.6 1.0
CG C:ASP317 4.6 19.4 1.0
CG C:ASP318 4.6 23.6 1.0
O4 C:SO4436 4.6 16.4 1.0
N C:THR40 4.6 21.3 1.0
OD2 C:ASP244 4.8 23.4 1.0
CB C:ALA246 4.9 24.2 1.0
OD1 C:ASP317 5.0 14.1 1.0

Magnesium binding site 7 out of 8 in 3b97

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Magnesium binding site 7 out of 8 in the Crystal Structure of Human Enolase 1


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 Human Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg434

b:32.5
occ:1.00
 OD2 D:ASP317 2.3 16.5 1.0
O D:HOH524 2.3 21.9 1.0
O D:HOH445 2.4 23.1 1.0
OD2 D:ASP244 2.4 25.4 1.0
MG D:MG435 2.6 30.5 1.0
OE2 D:GLU292 2.7 38.4 1.0
O D:HOH525 3.3 25.8 1.0
CG D:ASP244 3.3 32.0 1.0
OE1 D:GLN165 3.4 23.9 1.0
O D:HOH481 3.5 19.3 1.0
CG D:ASP317 3.5 21.5 1.0
OD1 D:ASP244 3.5 27.4 1.0
NZ D:LYS342 3.6 10.2 1.0
CD D:GLU292 3.8 33.1 1.0
O1 D:SO4436 3.9 21.5 1.0
NZ D:LYS393 4.1 13.8 1.0
OG D:SER39 4.3 19.3 1.0
O2 D:SO4436 4.3 20.6 1.0
CB D:ASP317 4.3 21.5 1.0
OD1 D:ASP317 4.4 20.9 1.0
CD D:GLN165 4.4 22.1 1.0
OE1 D:GLU292 4.5 33.7 1.0
OD2 D:ASP293 4.5 28.1 1.0
OE2 D:GLU166 4.6 26.5 1.0
CD2 D:LEU340 4.6 18.2 1.0
CB D:ALA246 4.7 27.5 1.0
S D:SO4436 4.7 24.0 1.0
CB D:ASP244 4.8 25.8 1.0
NE2 D:GLN165 4.8 15.3 1.0
CE D:LYS342 4.8 12.4 1.0
CG D:GLU292 4.8 31.9 1.0
O D:HOH438 4.9 17.1 1.0
O D:SER39 5.0 29.6 1.0

Magnesium binding site 8 out of 8 in 3b97

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Magnesium binding site 8 out of 8 in the Crystal Structure of Human Enolase 1


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 Human Enolase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg435

b:30.5
occ:1.00
 OG D:SER39 2.3 19.3 1.0
O D:HOH525 2.3 25.8 1.0
O D:HOH481 2.3 19.3 1.0
O2 D:SO4436 2.5 20.6 1.0
O D:SER39 2.5 29.6 1.0
MG D:MG434 2.6 32.5 1.0
O1 D:SO4436 3.2 21.5 1.0
S D:SO4436 3.3 24.0 1.0
CB D:SER39 3.4 23.6 1.0
C D:SER39 3.5 24.5 1.0
OD2 D:ASP317 3.5 16.5 1.0
NZ D:LYS342 3.7 10.2 1.0
O D:HOH445 3.7 23.1 1.0
OE1 D:GLN165 3.8 23.9 1.0
O D:HOH524 3.9 21.9 1.0
O3 D:SO4436 3.9 18.7 1.0
CA D:SER39 4.0 23.9 1.0
NE2 D:GLN165 4.0 15.3 1.0
OD2 D:ASP318 4.1 27.5 1.0
OD1 D:ASP318 4.3 22.9 1.0
N D:SER39 4.4 24.0 1.0
NH2 D:ARG371 4.4 12.3 1.0
CD D:GLN165 4.4 22.1 1.0
CG D:ASP318 4.6 26.4 1.0
O4 D:SO4436 4.6 25.1 1.0
CG D:ASP317 4.6 21.5 1.0
N D:THR40 4.7 23.8 1.0
OD2 D:ASP244 4.7 25.4 1.0
CB D:ALA246 4.9 27.5 1.0

Reference:

H.J.Kang, S.K.Jung, S.J.Kim, S.J.Chung. Structure of Human Alpha-Enolase (HENO1), A Multifunctional Glycolytic Enzyme. Acta Crystallogr.,Sect.D V. 64 651 2008.
ISSN: ISSN 0907-4449
PubMed: 18560153
DOI: 10.1107/S0907444908008561
Page generated: Wed Aug 14 08:53:52 2024

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