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Magnesium in PDB 2akz: Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex

Enzymatic activity of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex

All present enzymatic activity of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex:
4.2.1.11;

Protein crystallography data

The structure of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex, PDB code: 2akz was solved by J.Qin, G.Chai, J.M.Brewer, L.L.Lovelace, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.36
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 109.007, 118.515, 67.189, 90.00, 90.00, 90.00
R / Rfree (%) 11.2 / 14.4

Other elements in 2akz:

The structure of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex (pdb code 2akz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex, PDB code: 2akz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2akz

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Magnesium binding site 1 out of 4 in the Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg440

b:11.4
occ:1.00
 F A:F444 1.9 10.2 1.0
OD1 A:ASP317 2.0 12.0 1.0
OD1 A:ASP244 2.1 13.9 1.0
OE1 A:GLU292 2.1 15.0 1.0
F A:F445 2.1 14.4 1.0
O A:HOH461 2.1 10.5 1.0
CG A:ASP244 3.0 14.4 1.0
CG A:ASP317 3.1 9.9 1.0
CD A:GLU292 3.3 12.9 1.0
OD2 A:ASP244 3.3 11.8 1.0
MG A:MG441 3.6 10.5 1.0
NZ A:LYS342 3.7 13.3 1.0
NE2 A:GLN165 3.7 11.3 1.0
O A:HOH463 3.8 10.0 1.0
CB A:ASP317 3.8 11.3 1.0
O A:HOH462 3.8 10.4 1.0
NZ A:LYS393 3.8 13.2 1.0
OE2 A:GLU292 4.0 15.2 1.0
OD2 A:ASP317 4.1 13.6 1.0
CD2 A:LEU340 4.2 13.3 1.0
CG A:GLU292 4.2 11.9 1.0
OD2 A:ASP293 4.3 12.8 1.0
CB A:ASP244 4.3 11.1 1.0
O4 A:PO4442 4.4 10.7 1.0
O1 A:PO4442 4.5 9.6 1.0
OE2 A:GLU166 4.6 15.8 1.0
CD A:GLN165 4.8 9.3 1.0
CB A:ALA246 4.9 12.4 1.0
OG A:SER39 4.9 10.1 1.0
CE A:LYS342 4.9 11.2 1.0
CE A:LYS393 4.9 13.1 1.0

Magnesium binding site 2 out of 4 in 2akz

Go back to Magnesium Binding Sites List in 2akz
Magnesium binding site 2 out of 4 in the Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg441

b:10.5
occ:1.00
 F A:F444 2.0 10.2 1.0
O A:HOH463 2.0 10.0 1.0
O A:SER39 2.0 10.5 1.0
O A:HOH462 2.1 10.4 1.0
OG A:SER39 2.1 10.1 1.0
O1 A:PO4442 2.1 9.6 1.0
CB A:SER39 3.0 10.2 1.0
C A:SER39 3.0 9.3 1.0
P A:PO4442 3.2 9.0 1.0
CA A:SER39 3.5 11.2 1.0
O4 A:PO4442 3.6 10.7 1.0
MG A:MG440 3.6 11.4 1.0
OD1 A:ASP317 3.7 12.0 1.0
O3 A:PO4442 3.8 10.6 1.0
N A:SER39 4.0 12.6 1.0
O A:HOH461 4.0 10.5 1.0
OD1 A:ASP318 4.0 13.6 1.0
NZ A:LYS342 4.1 13.3 1.0
OD2 A:ASP318 4.1 13.9 1.0
NH2 A:ARG371 4.1 10.2 1.0
F A:F445 4.2 14.4 1.0
NE2 A:GLN165 4.2 11.3 1.0
N A:THR40 4.2 10.5 1.0
OE1 A:GLN165 4.2 10.9 1.0
O2 A:PO4442 4.4 10.2 1.0
CG A:ASP318 4.4 13.8 1.0
CD A:GLN165 4.6 9.3 1.0
CA A:THR40 4.7 11.0 1.0
CG A:ASP317 4.7 9.9 1.0
O A:HOH519 5.0 17.3 1.0

Magnesium binding site 3 out of 4 in 2akz

Go back to Magnesium Binding Sites List in 2akz
Magnesium binding site 3 out of 4 in the Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1440

b:9.7
occ:1.00
 OD1 B:ASP1317 1.9 11.6 1.0
F B:F1444 2.0 9.7 1.0
F B:F1445 2.0 13.9 1.0
OE1 B:GLU1292 2.1 14.4 1.0
OD1 B:ASP1244 2.1 13.8 1.0
O B:HOH1446 2.1 10.3 1.0
CG B:ASP1244 3.0 11.0 1.0
CG B:ASP1317 3.1 9.7 1.0
CD B:GLU1292 3.3 12.9 1.0
OD2 B:ASP1244 3.3 10.2 1.0
MG B:MG1441 3.6 9.2 1.0
NZ B:LYS1342 3.7 13.0 1.0
CB B:ASP1317 3.7 10.8 1.0
O B:HOH1448 3.8 8.7 1.0
NZ B:LYS1393 3.8 15.2 1.0
NE2 B:GLN1165 3.8 10.8 1.0
O B:HOH1447 3.8 10.2 1.0
OE2 B:GLU1292 4.0 14.4 1.0
OD2 B:ASP1317 4.1 10.7 1.0
CG B:GLU1292 4.2 10.5 1.0
OD2 B:ASP1293 4.3 9.4 1.0
CD2 B:LEU1340 4.3 12.8 1.0
CB B:ASP1244 4.3 11.0 1.0
O4 B:PO41442 4.4 10.9 1.0
OE2 B:GLU1166 4.5 14.3 1.0
O1 B:PO41442 4.6 9.3 1.0
CD B:GLN1165 4.8 9.8 1.0
CB B:ALA1246 4.8 9.9 1.0
OG B:SER1039 4.9 8.7 1.0
CE B:LYS1342 4.9 12.3 1.0
CE B:LYS1393 4.9 14.0 1.0

Magnesium binding site 4 out of 4 in 2akz

Go back to Magnesium Binding Sites List in 2akz
Magnesium binding site 4 out of 4 in the Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1441

b:9.2
occ:1.00
 F B:F1444 1.9 9.7 1.0
O B:SER1039 2.0 9.2 1.0
O1 B:PO41442 2.0 9.3 1.0
O B:HOH1448 2.1 8.7 1.0
O B:HOH1447 2.1 10.2 1.0
OG B:SER1039 2.1 8.7 1.0
CB B:SER1039 3.0 9.1 1.0
C B:SER1039 3.0 9.2 1.0
P B:PO41442 3.3 8.8 1.0
CA B:SER1039 3.5 9.4 1.0
O4 B:PO41442 3.6 10.9 1.0
MG B:MG1440 3.6 9.7 1.0
OD1 B:ASP1317 3.7 11.6 1.0
O3 B:PO41442 3.8 10.4 1.0
N B:SER1039 4.0 10.2 1.0
O B:HOH1446 4.0 10.3 1.0
NZ B:LYS1342 4.1 13.0 1.0
OD1 B:ASP1318 4.1 12.1 1.0
F B:F1445 4.1 13.9 1.0
OD2 B:ASP1318 4.1 12.0 1.0
NH2 B:ARG1371 4.1 10.0 1.0
OE1 B:GLN1165 4.1 11.0 1.0
NE2 B:GLN1165 4.1 10.8 1.0
N B:THR1040 4.2 8.8 1.0
O2 B:PO41442 4.4 9.1 1.0
CG B:ASP1318 4.5 10.8 1.0
CD B:GLN1165 4.6 9.8 1.0
CG B:ASP1317 4.7 9.7 1.0
CA B:THR1040 4.7 8.9 1.0
CB B:ALA1246 5.0 9.9 1.0
OD1 B:ASP1244 5.0 13.8 1.0

Reference:

J.Qin, G.Chai, J.M.Brewer, L.L.Lovelace, L.Lebioda. Fluoride Inhibition of Enolase: Crystal Structure and Thermodynamics Biochemistry V. 45 793 2006.
ISSN: ISSN 0006-2960
PubMed: 16411755
DOI: 10.1021/BI051558S
Page generated: Mon Dec 14 07:15:19 2020

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