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Magnesium in PDB 6npf: Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite.

Enzymatic activity of Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite.

All present enzymatic activity of Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite.:
4.2.1.11;

Protein crystallography data

The structure of Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite., PDB code: 6npf was solved by H.Erlandsen, J.Krucinska, M.Lombardo, D.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 93.03 / 2.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.180, 143.110, 206.679, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 25.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite. (pdb code 6npf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite., PDB code: 6npf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6npf

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Magnesium binding site 1 out of 6 in the Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:21.8
occ:1.00
 OD2 A:ASP245 1.9 41.9 1.0
OE2 A:GLU289 1.9 37.9 1.0
O A:HOH712 2.1 36.9 1.0
O41 A:TLA601 2.2 32.8 1.0
OD2 A:ASP316 2.2 37.9 1.0
O4 A:TLA601 2.2 34.1 1.0
C4 A:TLA601 2.5 39.5 1.0
CG A:ASP245 2.8 43.3 1.0
CD A:GLU289 3.1 36.7 1.0
CG A:ASP316 3.1 36.9 1.0
OD1 A:ASP245 3.1 47.2 1.0
CB A:ASP316 3.5 36.4 1.0
OD2 A:ASP290 3.9 33.9 1.0
CG A:GLU289 3.9 37.3 1.0
OE1 A:GLU289 4.0 31.5 1.0
C3 A:TLA601 4.0 39.0 1.0
NZ A:LYS392 4.1 37.3 1.0
CB A:ASP245 4.1 40.5 1.0
CD2 A:LEU339 4.2 37.0 1.0
NZ A:LYS341 4.2 41.0 1.0
OD1 A:ASP316 4.2 33.7 1.0
CG A:ASP290 4.6 34.8 1.0
NE2 A:GLN166 4.6 30.6 1.0
C2 A:TLA601 4.7 37.6 1.0
O3 A:TLA601 4.7 35.7 1.0
OE2 A:GLU167 4.8 44.5 1.0
O2 A:TLA601 4.9 36.4 1.0
CB A:ASP290 5.0 35.4 1.0
O A:HOH701 5.0 59.7 1.0

Magnesium binding site 2 out of 6 in 6npf

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Magnesium binding site 2 out of 6 in the Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:30.0
occ:1.00
 O B:HOH605 1.9 38.2 1.0
OD2 B:ASP316 1.9 44.6 1.0
OD2 B:ASP245 2.0 46.0 1.0
OE2 B:GLU289 2.1 40.7 1.0
O4 B:TLA501 2.2 37.1 1.0
O41 B:TLA501 2.4 34.6 1.0
C4 B:TLA501 2.6 41.3 1.0
CG B:ASP245 2.9 46.6 1.0
CG B:ASP316 2.9 45.8 1.0
OD1 B:ASP245 3.2 46.6 1.0
CD B:GLU289 3.3 45.3 1.0
CB B:ASP316 3.3 44.6 1.0
CG B:GLU289 3.9 46.6 1.0
OD2 B:ASP290 3.9 46.8 1.0
OD1 B:ASP316 4.0 48.5 1.0
C3 B:TLA501 4.1 43.0 1.0
NZ B:LYS392 4.1 37.5 1.0
NZ B:LYS341 4.2 48.0 1.0
CB B:ASP245 4.3 46.4 1.0
OE1 B:GLU289 4.3 43.7 1.0
CD2 B:LEU339 4.3 42.8 1.0
CG B:ASP290 4.6 45.7 1.0
NE2 B:GLN166 4.7 40.3 1.0
C2 B:TLA501 4.7 41.4 1.0
O3 B:TLA501 4.8 45.0 1.0
CA B:ASP316 4.8 44.0 1.0
OE2 B:GLU167 4.9 44.6 1.0
CB B:ASP290 5.0 45.1 1.0

Magnesium binding site 3 out of 6 in 6npf

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Magnesium binding site 3 out of 6 in the Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:26.0
occ:1.00
 OE2 C:GLU289 2.0 43.0 1.0
OD2 C:ASP316 2.0 31.8 1.0
O C:HOH807 2.2 17.9 1.0
OD2 C:ASP245 2.2 34.5 1.0
O1 C:TLA703 2.3 37.2 1.0
C1 C:TLA703 2.9 41.1 1.0
O11 C:TLA703 2.9 38.9 1.0
CG C:ASP245 2.9 37.8 1.0
CG C:ASP316 3.0 33.4 1.0
OD1 C:ASP245 3.2 37.8 1.0
CD C:GLU289 3.2 44.5 1.0
CB C:ASP316 3.3 32.6 1.0
OD2 C:ASP290 3.7 46.1 1.0
CG C:GLU289 3.9 40.0 1.0
NZ C:LYS341 3.9 42.7 1.0
CD2 C:LEU339 4.0 30.6 1.0
NZ C:LYS392 4.0 32.8 1.0
OD1 C:ASP316 4.1 33.0 1.0
OE1 C:GLU289 4.2 48.2 1.0
O C:HOH815 4.2 35.8 1.0
CB C:ASP245 4.2 39.5 1.0
C2 C:TLA703 4.2 41.6 1.0
CG C:ASP290 4.5 44.2 1.0
O2 C:TLA703 4.6 39.3 1.0
NE2 C:GLN166 4.6 45.5 1.0
CA C:ASP316 4.8 35.0 1.0
CB C:ASP290 4.9 42.2 1.0

Magnesium binding site 4 out of 6 in 6npf

Go back to Magnesium Binding Sites List in 6npf
Magnesium binding site 4 out of 6 in the Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:39.7
occ:1.00
 OD2 D:ASP316 1.7 42.1 1.0
OAD D:KVM601 1.9 70.1 1.0
O D:HOH711 2.1 32.7 1.0
OD2 D:ASP245 2.1 45.2 1.0
OE2 D:GLU289 2.1 37.5 1.0
OAL D:KVM601 2.2 53.6 1.0
CG D:ASP316 2.8 44.3 1.0
NAC D:KVM601 2.9 70.2 1.0
CAK D:KVM601 2.9 64.4 1.0
CG D:ASP245 3.0 43.4 1.0
CD D:GLU289 3.4 45.4 1.0
OD1 D:ASP245 3.4 44.8 1.0
CB D:ASP316 3.5 45.7 1.0
NZ D:LYS392 3.8 37.0 1.0
OD1 D:ASP316 3.9 41.5 1.0
NZ D:LYS341 4.0 42.0 1.0
OD2 D:ASP290 4.0 52.5 1.0
OE1 D:GLU289 4.2 44.3 1.0
CAB D:KVM601 4.2 68.2 1.0
CD2 D:LEU339 4.2 34.5 1.0
CG D:GLU289 4.3 46.3 1.0
CAF D:KVM601 4.3 64.3 1.0
CB D:ASP245 4.3 46.0 1.0
NE2 D:GLN166 4.6 51.1 1.0
OE2 D:GLU167 4.9 48.5 1.0
OAH D:KVM601 4.9 59.5 1.0
CAE D:KVM601 5.0 68.9 1.0
CE D:LYS392 5.0 39.9 1.0
CA D:ASP316 5.0 48.8 1.0
OAA D:KVM601 5.0 61.1 1.0

Magnesium binding site 5 out of 6 in 6npf

Go back to Magnesium Binding Sites List in 6npf
Magnesium binding site 5 out of 6 in the Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg702

b:40.8
occ:1.00
 OAD F:KVM703 1.7 67.0 1.0
O F:HOH811 2.0 35.0 1.0
OD2 F:ASP245 2.0 49.2 1.0
OD2 F:ASP316 2.1 42.2 1.0
OE2 F:GLU289 2.2 51.6 1.0
OAL F:KVM703 2.3 62.4 1.0
NAC F:KVM703 2.6 75.9 1.0
CAK F:KVM703 2.8 71.1 1.0
CG F:ASP245 3.0 47.0 1.0
CG F:ASP316 3.0 41.3 1.0
CD F:GLU289 3.4 55.2 1.0
OD1 F:ASP245 3.4 48.2 1.0
CB F:ASP316 3.6 40.0 1.0
OD2 F:ASP290 3.8 46.5 1.0
CAB F:KVM703 3.9 78.7 1.0
NZ F:LYS392 4.0 53.8 1.0
OD1 F:ASP316 4.1 45.8 1.0
NZ F:LYS341 4.1 46.7 1.0
OE1 F:GLU289 4.2 53.6 1.0
CG F:GLU289 4.2 52.0 1.0
CAF F:KVM703 4.2 73.3 1.0
CB F:ASP245 4.3 45.9 1.0
CD2 F:LEU339 4.4 41.1 1.0
NE2 F:GLN166 4.6 66.5 1.0
OE2 F:GLU167 4.7 55.7 1.0
OAA F:KVM703 4.7 81.6 1.0
CAE F:KVM703 4.8 80.0 1.0
CG F:ASP290 4.8 49.5 1.0
OAH F:KVM703 4.8 64.4 1.0

Magnesium binding site 6 out of 6 in 6npf

Go back to Magnesium Binding Sites List in 6npf
Magnesium binding site 6 out of 6 in the Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of E.Coli Enolase in Complex with An Analog of the Natural Product Sf-2312 Metabolite. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:42.5
occ:1.00
 OAA E:KVM602 1.9 85.6 1.0
OD2 E:ASP245 2.0 58.8 1.0
OD2 E:ASP316 2.1 55.5 1.0
OE2 E:GLU289 2.2 60.5 1.0
CAB E:KVM602 2.3 84.5 1.0
OAD E:KVM602 2.4 97.8 1.0
O E:HOH701 2.5 37.3 1.0
NAC E:KVM602 2.5 83.1 1.0
CG E:ASP316 3.0 58.6 1.0
CG E:ASP245 3.1 55.4 1.0
CD E:GLU289 3.3 62.4 1.0
NZ E:LYS392 3.4 65.1 1.0
CAE E:KVM602 3.5 81.6 1.0
CB E:ASP316 3.7 62.1 1.0
CAK E:KVM602 3.7 80.8 1.0
NZ E:LYS341 3.8 58.0 1.0
OD1 E:ASP245 3.9 55.0 1.0
CD2 E:LEU339 3.9 67.4 1.0
OD1 E:ASP316 3.9 64.3 1.0
OD2 E:ASP290 4.0 64.0 1.0
CB E:ASP245 4.1 52.7 1.0
O E:HOH708 4.1 59.1 1.0
OE1 E:GLU289 4.2 70.0 1.0
CG E:GLU289 4.2 60.6 1.0
CAF E:KVM602 4.2 83.2 1.0
NE2 E:GLN166 4.4 46.0 1.0
OE2 E:GLU167 4.5 73.5 1.0
OAL E:KVM602 4.6 64.2 1.0
CE E:LYS392 4.6 58.4 1.0

Reference:

J.Krucinska, M.N.Lombardo, H.Erlandsen, A.Hazeen, S.S.Duay, J.G.Pattis, V.L.Robinson, E.R.May, D.L.Wright. Functional and Structural Basis of E. Coli Enolase Inhibition By SF2312: A Mimic of the Carbanion Intermediate. Sci Rep V. 9 17106 2019.
ISSN: ESSN 2045-2322
PubMed: 31745118
DOI: 10.1038/S41598-019-53301-3
Page generated: Tue Oct 1 12:52:53 2024

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