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Magnesium in PDB 6bfz: Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form

Enzymatic activity of Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form

All present enzymatic activity of Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form:
4.2.1.11;

Protein crystallography data

The structure of Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form, PDB code: 6bfz was solved by H.Erlandsen, D.Wright, J.Krucinska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.69 / 2.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 111.262, 143.293, 207.040, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form (pdb code 6bfz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form, PDB code: 6bfz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6bfz

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Magnesium binding site 1 out of 6 in the Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form


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 Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:54.6
occ:1.00
 OD2 A:ASP316 2.7 39.9 1.0
OD1 A:ASP245 2.9 41.0 1.0
OD2 A:ASP290 2.9 37.1 1.0
OE2 A:GLU289 3.1 35.7 1.0
OD2 A:ASP245 3.1 50.3 1.0
CG A:ASP245 3.3 42.9 1.0
CG A:ASP316 3.6 43.1 1.0
CB A:ASP316 3.8 36.5 1.0
CG A:ASP290 3.8 35.3 1.0
CB A:ASP290 3.9 33.6 1.0
CD A:GLU289 4.1 40.0 1.0
CA A:ALA247 4.3 36.0 1.0
CG A:GLU289 4.3 37.4 1.0
CB A:ALA247 4.4 35.8 1.0
NE2 A:GLN166 4.5 40.9 1.0
N A:ALA247 4.6 39.6 1.0
N A:ASP317 4.8 34.6 1.0
OD1 A:ASP316 4.8 40.7 1.0
CB A:ASP245 4.8 37.0 1.0
OD1 A:ASP290 4.9 29.0 1.0

Magnesium binding site 2 out of 6 in 6bfz

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Magnesium binding site 2 out of 6 in the Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form


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 Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:53.7
occ:1.00
 OD2 B:ASP245 2.8 40.0 1.0
OD1 B:ASP245 2.9 40.2 1.0
OE2 B:GLU289 2.9 41.2 1.0
OD2 B:ASP316 2.9 36.8 1.0
OD2 B:ASP290 3.0 36.1 1.0
CG B:ASP245 3.2 43.5 1.0
O B:HOH805 3.6 47.9 1.0
CG B:ASP316 3.8 35.9 1.0
CB B:ASP316 3.8 37.1 1.0
CG B:ASP290 3.9 33.6 1.0
CD B:GLU289 3.9 42.2 1.0
CB B:ASP290 4.1 36.2 1.0
CB B:ALA247 4.1 41.0 1.0
CG B:GLU289 4.1 38.8 1.0
CA B:ALA247 4.2 39.8 1.0
NE2 B:GLN166 4.4 41.9 1.0
N B:ALA247 4.6 41.2 1.0
CB B:ASP245 4.7 41.2 1.0
O B:HOH782 4.8 53.6 1.0
N B:ASP317 4.9 37.7 1.0
OD1 B:ASP290 4.9 35.7 1.0
OD1 B:ASP316 5.0 39.8 1.0

Magnesium binding site 3 out of 6 in 6bfz

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Magnesium binding site 3 out of 6 in the Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form


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 Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:35.7
occ:1.00
 O1 E:PEP602 1.8 44.2 0.5
OE2 E:GLU289 1.9 29.3 1.0
O E:HOH718 2.0 32.2 1.0
OD2 E:ASP316 2.1 31.4 1.0
O1 E:2PG603 2.2 17.8 0.5
OD2 E:ASP245 2.3 31.2 1.0
O2 E:2PG603 2.6 20.0 0.5
C1 E:2PG603 2.7 22.9 0.5
CG E:ASP245 3.0 33.4 1.0
C1 E:PEP602 3.1 52.2 0.5
CD E:GLU289 3.1 34.3 1.0
CG E:ASP316 3.1 33.1 1.0
OD1 E:ASP245 3.2 30.6 1.0
CB E:ASP316 3.5 30.6 1.0
O2' E:PEP602 3.8 52.5 0.5
OD2 E:ASP290 3.9 30.1 1.0
CG E:GLU289 3.9 32.8 1.0
OE1 E:GLU289 4.0 31.8 1.0
NZ E:LYS392 4.0 32.9 1.0
C2 E:PEP602 4.1 53.7 0.5
NZ E:LYS341 4.2 32.2 1.0
OD1 E:ASP316 4.2 30.7 1.0
C3 E:PEP602 4.2 63.6 0.5
C2 E:2PG603 4.2 25.6 0.5
CD2 E:LEU339 4.4 26.0 1.0
NE2 E:GLN166 4.4 36.6 1.0
CB E:ASP245 4.4 33.9 1.0
CG E:ASP290 4.6 32.4 1.0
OE1 E:GLU167 4.8 36.1 1.0
CB E:ASP290 4.9 28.8 1.0
O1P E:PEP602 5.0 36.0 0.5

Magnesium binding site 4 out of 6 in 6bfz

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Magnesium binding site 4 out of 6 in the Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form


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 Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:39.2
occ:1.00
 OE2 F:GLU289 1.9 32.3 1.0
O F:HOH619 2.0 36.3 1.0
OD2 F:ASP245 2.2 43.0 1.0
OD2 F:ASP316 2.2 34.0 1.0
O2 F:2PG501 2.4 39.3 1.0
O1 F:2PG501 2.4 33.2 1.0
C1 F:2PG501 2.8 40.0 1.0
CG F:ASP245 3.0 40.5 1.0
OD1 F:ASP245 3.1 42.2 1.0
CD F:GLU289 3.1 35.5 1.0
CG F:ASP316 3.2 33.0 1.0
CB F:ASP316 3.6 35.0 1.0
CG F:GLU289 3.9 35.1 1.0
NZ F:LYS392 4.0 33.2 1.0
OD2 F:ASP290 4.0 41.8 1.0
OE1 F:GLU289 4.0 31.3 1.0
NZ F:LYS341 4.2 36.4 1.0
C2 F:2PG501 4.3 43.8 1.0
OD1 F:ASP316 4.3 33.1 1.0
NE2 F:GLN166 4.3 32.7 1.0
CB F:ASP245 4.4 36.5 1.0
CD2 F:LEU339 4.4 30.7 1.0
CG F:ASP290 4.7 37.3 1.0
OE2 F:GLU167 4.7 39.4 1.0
CB F:ASP290 4.9 35.7 1.0
O1P F:2PG501 4.9 45.2 1.0

Magnesium binding site 5 out of 6 in 6bfz

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Magnesium binding site 5 out of 6 in the Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form


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 Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:41.7
occ:1.00
 OD2 D:ASP316 2.0 33.7 1.0
OE2 D:GLU289 2.1 36.1 1.0
O D:HOH611 2.2 33.4 1.0
O2 D:2PG501 2.2 43.6 1.0
OD2 D:ASP245 2.3 42.9 1.0
O1 D:2PG501 2.4 40.4 1.0
C1 D:2PG501 2.7 45.9 1.0
CG D:ASP316 3.0 36.0 1.0
CG D:ASP245 3.2 45.5 1.0
CD D:GLU289 3.2 40.3 1.0
OD1 D:ASP245 3.3 38.6 1.0
CB D:ASP316 3.4 38.3 1.0
OD2 D:ASP290 3.9 38.2 1.0
NZ D:LYS392 4.0 36.2 1.0
OE1 D:GLU289 4.0 42.3 1.0
CG D:GLU289 4.1 37.5 1.0
OD1 D:ASP316 4.2 32.4 1.0
CD2 D:LEU339 4.2 30.3 1.0
NZ D:LYS341 4.2 43.8 1.0
C2 D:2PG501 4.2 40.2 1.0
NE2 D:GLN166 4.4 40.9 1.0
CB D:ASP245 4.6 42.9 1.0
CG D:ASP290 4.7 39.9 1.0
O2P D:2PG501 4.9 39.1 1.0
CA D:ASP316 5.0 35.1 1.0
CB D:ASP290 5.0 37.2 1.0
O1P D:2PG501 5.0 46.3 1.0
OE2 D:GLU167 5.0 46.8 1.0

Magnesium binding site 6 out of 6 in 6bfz

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Magnesium binding site 6 out of 6 in the Crystal Structure of Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form


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 Enolase From E. Coli with A Mixture of Apo Form, Substrate, and Product Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:50.6
occ:1.00
 OE2 C:GLU289 2.0 44.0 1.0
OD2 C:ASP316 2.1 43.2 1.0
O2 C:2PG501 2.3 50.7 1.0
O C:HOH636 2.3 44.6 1.0
OD2 C:ASP245 2.3 60.0 1.0
O1 C:2PG501 2.7 52.2 1.0
C1 C:2PG501 2.9 57.2 1.0
CG C:ASP316 3.0 40.1 1.0
CD C:GLU289 3.2 45.9 1.0
CG C:ASP245 3.2 57.2 1.0
CB C:ASP316 3.4 47.3 1.0
OD1 C:ASP245 3.5 60.1 1.0
NZ C:LYS392 3.9 44.1 1.0
OE1 C:GLU289 4.0 39.2 1.0
CG C:GLU289 4.0 37.8 1.0
OD2 C:ASP290 4.1 48.6 1.0
NZ C:LYS341 4.1 36.3 1.0
OD1 C:ASP316 4.1 39.6 1.0
CD2 C:LEU339 4.1 40.2 1.0
C2 C:2PG501 4.4 55.3 1.0
NE2 C:GLN166 4.5 59.4 1.0
CB C:ASP245 4.6 45.6 1.0
CG C:ASP290 4.9 46.6 1.0
CA C:ASP316 4.9 46.0 1.0
OD2 C:ASP317 5.0 80.9 1.0

Reference:

J.Krucinska, E.Falcone, H.Erlandsen, A.Hazeen, M.N.Lombardo, A.Estrada, V.L.Robinson, A.C.Anderson, D.L.Wright. Structural and Functional Studies of Bacterial Enolase, A Potential Target Against Gram-Negative Pathogens. Biochemistry V. 58 1188 2019.
ISSN: ISSN 1520-4995
PubMed: 30714720
DOI: 10.1021/ACS.BIOCHEM.8B01298
Page generated: Wed Aug 13 02:37:57 2025

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