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Magnesium in PDB 3ucd: Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep

Enzymatic activity of Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep

All present enzymatic activity of Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep:
4.2.1.11;

Protein crystallography data

The structure of Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep, PDB code: 3ucd was solved by J.Qin, G.Chai, J.Brewer, L.Lovelace, L.Lebioda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.58 / 1.41
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.708, 118.623, 67.579, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep (pdb code 3ucd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep, PDB code: 3ucd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3ucd

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Magnesium binding site 1 out of 4 in the Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg599

b:7.4
occ:1.00
OE1 A:GLU292 2.0 8.9 1.0
OD1 A:ASP317 2.0 8.3 1.0
O A:HOH800 2.0 7.4 1.0
O2 A:2PG601 2.1 7.4 1.0
OD1 A:ASP244 2.1 7.8 1.0
O1 A:2PG601 2.5 7.5 1.0
C1 A:2PG601 2.6 7.6 1.0
CG A:ASP244 3.0 9.0 1.0
CD A:GLU292 3.1 7.1 1.0
CG A:ASP317 3.1 7.1 1.0
OD2 A:ASP244 3.3 8.0 1.0
CB A:ASP317 3.6 7.4 1.0
NZ A:LYS393 3.7 8.7 1.0
O A:HOH801 3.9 8.2 1.0
OE2 A:GLU292 3.9 9.5 1.0
CG A:GLU292 4.0 7.0 1.0
O A:HOH802 4.1 8.7 1.0
C2 A:2PG601 4.1 8.3 1.0
OD2 A:ASP293 4.1 8.7 1.0
MG A:MG600 4.1 7.9 1.0
NZ A:LYS342 4.1 13.4 1.0
NE2 A:GLN165 4.1 9.8 1.0
CD2 A:LEU340 4.2 7.6 1.0
OD2 A:ASP317 4.2 8.8 1.0
CB A:ASP244 4.3 8.8 1.0
OE2 A:GLU166 4.6 10.8 1.0
CE A:LYS393 4.8 9.1 1.0
C3 A:2PG601 4.8 9.0 1.0
CG A:ASP293 4.9 7.5 1.0
O1P A:2PG601 4.9 7.6 1.0

Magnesium binding site 2 out of 4 in 3ucd

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Magnesium binding site 2 out of 4 in the Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg600

b:7.9
occ:1.00
O3P A:2PG601 2.0 8.0 1.0
O A:HOH802 2.1 8.7 1.0
O A:SER39 2.1 7.6 1.0
O1 A:2PG601 2.1 7.5 1.0
O A:HOH801 2.2 8.2 1.0
OG A:SER39 2.2 7.6 1.0
C A:SER39 3.1 7.5 1.0
CB A:SER39 3.1 7.9 1.0
C1 A:2PG601 3.2 7.6 1.0
P A:2PG601 3.2 7.3 1.0
O1P A:2PG601 3.5 7.6 1.0
CA A:SER39 3.5 7.2 1.0
C2 A:2PG601 3.7 8.3 1.0
OD1 A:ASP317 3.9 8.3 1.0
O2P A:2PG601 3.9 7.1 1.0
NZ A:LYS342 3.9 13.4 1.0
N A:SER39 4.0 6.9 1.0
MG A:MG599 4.1 7.4 1.0
OD1 A:ASP318 4.1 10.7 1.0
O2 A:2PG601 4.1 7.4 1.0
OD2 A:ASP318 4.2 12.3 1.0
NH2 A:ARG371 4.2 7.7 1.0
O A:HOH800 4.2 7.4 1.0
N A:THR40 4.3 8.5 1.0
NE2 A:GLN165 4.3 9.8 1.0
OE1 A:GLN165 4.3 8.1 1.0
O4P A:2PG601 4.5 6.5 1.0
CG A:ASP318 4.5 10.5 1.0
CA A:THR40 4.7 8.8 1.0
CD A:GLN165 4.8 8.5 1.0
CG A:ASP317 4.9 7.1 1.0

Magnesium binding site 3 out of 4 in 3ucd

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Magnesium binding site 3 out of 4 in the Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg599

b:7.0
occ:1.00
OE1 B:GLU292 2.0 8.2 1.0
OD1 B:ASP317 2.0 7.7 1.0
OD1 B:ASP244 2.0 7.3 1.0
O B:HOH800 2.0 6.0 1.0
O2' B:PEP601 2.1 6.6 1.0
O1 B:PEP601 2.5 6.4 1.0
C1 B:PEP601 2.6 6.3 1.0
CG B:ASP244 3.0 6.4 1.0
CD B:GLU292 3.1 7.2 1.0
CG B:ASP317 3.1 6.5 1.0
OD2 B:ASP244 3.3 7.7 1.0
CB B:ASP317 3.6 7.4 1.0
NZ B:LYS393 3.7 7.6 1.0
O B:HOH801 3.9 8.7 1.0
OE2 B:GLU292 3.9 9.7 1.0
CG B:GLU292 3.9 6.5 1.0
OD2 B:ASP293 4.0 7.3 1.0
O B:HOH802 4.0 7.4 1.0
C2 B:PEP601 4.1 9.1 1.0
NZ B:LYS342 4.1 11.5 1.0
MG B:MG600 4.1 6.8 1.0
OD2 B:ASP317 4.2 7.5 1.0
NE2 B:GLN165 4.2 11.3 1.0
CD2 B:LEU340 4.2 8.0 1.0
CB B:ASP244 4.3 7.5 1.0
OE2 B:GLU166 4.8 12.4 1.0
CE B:LYS393 4.8 7.9 1.0
CG B:ASP293 4.8 6.6 1.0
C3 B:PEP601 4.9 11.4 1.0
O2 B:PEP601 5.0 7.9 1.0

Magnesium binding site 4 out of 4 in 3ucd

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Magnesium binding site 4 out of 4 in the Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Asymmetric Complex of Human Neuron Specific Enolase-2-Pga/Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg600

b:6.8
occ:1.00
O3P B:PEP601 2.0 7.7 1.0
O B:SER39 2.1 7.2 1.0
O B:HOH801 2.1 8.7 1.0
O1 B:PEP601 2.1 6.4 1.0
O B:HOH802 2.1 7.4 1.0
OG B:SER39 2.1 7.5 1.0
C B:SER39 3.0 6.6 1.0
CB B:SER39 3.1 8.0 1.0
C1 B:PEP601 3.1 6.3 1.0
P B:PEP601 3.2 6.8 1.0
O2 B:PEP601 3.4 7.9 1.0
CA B:SER39 3.5 7.8 1.0
C2 B:PEP601 3.7 9.1 1.0
OD1 B:ASP317 3.9 7.7 1.0
O2P B:PEP601 3.9 7.3 1.0
N B:SER39 4.0 7.0 1.0
NZ B:LYS342 4.1 11.5 1.0
OD2 B:ASP318 4.1 9.4 1.0
O2' B:PEP601 4.1 6.6 1.0
MG B:MG599 4.1 7.0 1.0
NH2 B:ARG371 4.2 7.4 1.0
OD1 B:ASP318 4.2 7.3 1.0
O B:HOH800 4.2 6.0 1.0
N B:THR40 4.2 8.1 1.0
OE1 B:GLN165 4.3 9.2 1.0
NE2 B:GLN165 4.3 11.3 1.0
O1P B:PEP601 4.4 6.8 1.0
CG B:ASP318 4.5 7.8 1.0
CA B:THR40 4.7 7.5 1.0
CD B:GLN165 4.8 8.2 1.0
CG B:ASP317 4.9 6.5 1.0

Reference:

J.Qin, G.Chai, J.M.Brewer, L.L.Lovelace, L.Lebioda. Structures of Asymmetric Complexes of Human Neuron Specific Enolase with Resolved Substrate and Product and An Analogous Complex with Two Inhibitors Indicate Subunit Interaction and Inhibitor Cooperativity. J.Inorg.Biochem. V. 111 187 2012.
ISSN: ISSN 0162-0134
PubMed: 22437160
DOI: 10.1016/J.JINORGBIO.2012.02.011
Page generated: Mon Dec 14 08:56:22 2020

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