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Magnesium in PDB 2fym: Crystal Structure of E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E.

Enzymatic activity of Crystal Structure of E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E.

All present enzymatic activity of Crystal Structure of E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E.:
4.2.1.11;

Protein crystallography data

The structure of Crystal Structure of E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E., PDB code: 2fym was solved by V.Chandran, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.054, 124.201, 96.076, 90.00, 90.58, 90.00
R / Rfree (%) 16.5 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E. (pdb code 2fym). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E., PDB code: 2fym:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2fym

Go back to Magnesium Binding Sites List in 2fym
Magnesium binding site 1 out of 4 in the Crystal Structure of E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E.


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 E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1431

b:16.1
occ:1.00
 OD2 A:ASP316 2.3 16.6 1.0
OE2 A:GLU289 2.3 13.2 1.0
OD2 A:ASP245 2.4 18.4 1.0
O A:HOH1863 2.4 40.0 1.0
O A:HOH1442 2.4 15.8 1.0
O A:HOH1729 2.7 34.1 1.0
CG A:ASP245 3.2 16.7 1.0
CG A:ASP316 3.3 15.8 1.0
CD A:GLU289 3.5 13.2 1.0
OD1 A:ASP245 3.5 18.6 1.0
O A:HOH1529 3.7 29.8 1.0
CB A:ASP316 3.8 15.8 1.0
NZ A:LYS392 4.0 13.5 1.0
OD2 A:ASP290 4.2 15.1 1.0
O A:HOH1824 4.2 32.6 1.0
NE2 A:GLN166 4.3 17.2 1.0
CG A:GLU289 4.3 12.9 1.0
OE1 A:GLU289 4.3 13.0 1.0
O A:HOH1687 4.4 22.9 1.0
OD1 A:ASP316 4.4 16.9 1.0
NZ A:LYS341 4.5 17.3 1.0
CB A:ASP245 4.5 14.5 1.0
CD2 A:LEU339 4.7 15.8 1.0
O A:HOH1554 4.8 23.9 1.0

Magnesium binding site 2 out of 4 in 2fym

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Magnesium binding site 2 out of 4 in the Crystal Structure of E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E.


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 E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1431

b:21.1
occ:1.00
 O C:HOH1835 2.2 32.4 1.0
OE2 C:GLU289 2.3 21.6 1.0
OD2 C:ASP316 2.3 21.1 1.0
O C:HOH1445 2.4 19.3 1.0
OD2 C:ASP245 2.5 24.0 1.0
CG C:ASP245 3.3 24.1 1.0
CG C:ASP316 3.3 21.4 1.0
CD C:GLU289 3.4 20.0 1.0
OD1 C:ASP245 3.6 25.3 1.0
CB C:ASP316 3.8 21.1 1.0
O C:HOH1604 3.8 32.0 1.0
NZ C:LYS392 4.1 22.1 1.0
OD2 C:ASP290 4.2 21.5 1.0
CG C:GLU289 4.2 19.1 1.0
NE2 C:GLN166 4.3 23.8 1.0
OE1 C:GLU289 4.3 21.4 1.0
OD1 C:ASP316 4.4 22.3 1.0
O C:HOH1494 4.5 27.9 1.0
CB C:ASP245 4.5 23.0 1.0
NZ C:LYS341 4.6 18.6 1.0
O C:HOH1666 4.6 30.0 1.0
O C:HOH1841 4.7 44.3 1.0
CD2 C:LEU339 4.8 19.8 1.0
O C:HOH1845 4.8 55.8 1.0

Magnesium binding site 3 out of 4 in 2fym

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Magnesium binding site 3 out of 4 in the Crystal Structure of E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E.


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 E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1431

b:20.1
occ:1.00
 OE2 D:GLU289 2.2 19.1 1.0
OD2 D:ASP316 2.3 20.5 1.0
O D:HOH1868 2.3 38.9 1.0
OD2 D:ASP245 2.3 21.7 1.0
O D:HOH1475 2.4 18.7 1.0
CG D:ASP245 3.2 21.3 1.0
CG D:ASP316 3.4 20.3 1.0
CD D:GLU289 3.4 18.8 1.0
OD1 D:ASP245 3.5 21.0 1.0
CB D:ASP316 3.8 20.3 1.0
O D:HOH1546 3.9 26.2 1.0
O D:HOH1865 3.9 36.8 1.0
NZ D:LYS392 3.9 18.0 1.0
OD2 D:ASP290 4.2 19.6 1.0
CG D:GLU289 4.2 18.0 1.0
OE1 D:GLU289 4.3 19.3 1.0
NE2 D:GLN166 4.4 23.8 1.0
OD1 D:ASP316 4.4 20.7 1.0
CB D:ASP245 4.5 20.6 1.0
NZ D:LYS341 4.5 18.2 1.0
O D:HOH1541 4.6 31.0 1.0
O D:HOH1648 4.6 26.6 1.0
CD2 D:LEU339 4.7 17.5 1.0

Magnesium binding site 4 out of 4 in 2fym

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Magnesium binding site 4 out of 4 in the Crystal Structure of E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E.


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 E. Coli Enolase Complexed with the Minimal Binding Segment of Rnase E. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1431

b:15.0
occ:1.00
 OE2 F:GLU289 2.3 12.5 1.0
OD2 F:ASP316 2.3 16.5 1.0
O F:HOH1478 2.3 15.2 1.0
O F:HOH1569 2.4 26.6 1.0
OD2 F:ASP245 2.4 13.6 1.0
O F:HOH1573 2.6 25.7 1.0
CG F:ASP245 3.3 14.0 1.0
CG F:ASP316 3.4 14.5 1.0
CD F:GLU289 3.4 12.5 1.0
OD1 F:ASP245 3.5 14.4 1.0
NZ F:LYS392 3.8 14.0 1.0
CB F:ASP316 3.8 14.2 1.0
O F:HOH1763 3.8 30.5 1.0
O F:HOH1717 3.9 26.9 1.0
NZ F:LYS341 4.1 15.9 1.0
OD2 F:ASP290 4.2 13.6 1.0
OE1 F:GLU289 4.2 14.2 1.0
CG F:GLU289 4.3 11.8 1.0
O F:HOH1951 4.4 27.2 1.0
CD2 F:LEU339 4.4 13.8 1.0
OD1 F:ASP316 4.5 14.6 1.0
O F:HOH1748 4.5 26.6 1.0
CB F:ASP245 4.6 13.5 1.0
O F:HOH1729 4.6 32.0 1.0
NE2 F:GLN166 4.8 21.9 1.0
O F:HOH1828 4.9 23.6 1.0

Reference:

V.Chandran, B.F.Luisi. Recognition of Enolase in the Escherichia Coli Rna Degradosome J.Mol.Biol. V. 358 8 2006.
ISSN: ISSN 0022-2836
PubMed: 16516921
DOI: 10.1016/J.JMB.2006.02.012
Page generated: Tue Aug 13 23:20:13 2024

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