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Magnesium in PDB 4gme: Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 Complexed with Magnesium and D-Mannonate

Protein crystallography data

The structure of Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 Complexed with Magnesium and D-Mannonate, PDB code: 4gme was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.62 / 2.00
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 115.801, 115.801, 118.131, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.6

Other elements in 4gme:

The structure of Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 Complexed with Magnesium and D-Mannonate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 Complexed with Magnesium and D-Mannonate (pdb code 4gme). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 Complexed with Magnesium and D-Mannonate, PDB code: 4gme:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4gme

Go back to Magnesium Binding Sites List in 4gme
Magnesium binding site 1 out of 2 in the Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 Complexed with Magnesium and D-Mannonate


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 Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 Complexed with Magnesium and D-Mannonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:25.3
occ:1.00
OE2 A:GLU260 2.0 30.8 1.0
O2 A:CO3504 2.1 31.7 1.0
O3 A:CO3504 2.1 54.0 1.0
OD2 A:ASP234 2.1 25.3 1.0
O A:HOH601 2.2 25.8 1.0
OE1 A:GLU286 2.3 27.0 1.0
C A:CO3504 2.4 54.5 1.0
CG A:ASP234 3.1 31.5 1.0
CD A:GLU286 3.1 26.3 1.0
CD A:GLU260 3.1 19.6 1.0
OE2 A:GLU286 3.2 25.7 1.0
O1 A:CO3504 3.6 26.0 1.0
OD1 A:ASP234 3.6 24.7 1.0
NH2 A:ARG307 3.6 28.8 1.0
O A:HOH602 3.7 25.6 1.0
OE1 A:GLU260 3.7 17.1 1.0
CD2 A:HIS236 4.0 22.9 1.0
CG A:GLU260 4.2 19.6 1.0
CB A:ASP234 4.2 25.4 1.0
O A:HOH804 4.3 39.2 1.0
NH1 A:ARG171 4.3 24.6 1.0
OD2 A:ASP261 4.4 24.5 1.0
NE2 A:HIS236 4.5 27.9 1.0
CG A:GLU286 4.5 25.3 1.0
OH A:TYR183 4.5 25.8 1.0
CZ A:ARG307 4.6 28.9 1.0
NE A:ARG307 4.6 22.6 1.0
OH C:TYR99 4.7 29.1 1.0
CG A:ASP261 4.9 31.8 1.0
CD2 A:HIS336 4.9 20.9 1.0

Magnesium binding site 2 out of 2 in 4gme

Go back to Magnesium Binding Sites List in 4gme
Magnesium binding site 2 out of 2 in the Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 Complexed with Magnesium and D-Mannonate


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 Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 Complexed with Magnesium and D-Mannonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:27.3
occ:1.00
OE2 C:GLU260 1.8 19.2 1.0
O1B C:CS2503 1.9 32.6 1.0
OD2 C:ASP234 1.9 24.1 1.0
OE1 C:GLU286 2.1 22.8 1.0
O C:HOH601 2.1 20.9 1.0
O2 C:CS2503 2.3 25.3 1.0
C1 C:CS2503 2.8 31.7 1.0
CG C:ASP234 2.9 34.8 1.0
CD C:GLU260 2.9 18.9 1.0
C2 C:CS2503 3.0 33.3 1.0
CD C:GLU286 3.0 35.2 1.0
OD1 C:ASP234 3.4 18.9 1.0
OE2 C:GLU286 3.4 22.2 1.0
NH2 C:ARG307 3.7 23.5 1.0
OE1 C:GLU260 3.7 21.8 1.0
OD2 C:ASP261 3.8 26.6 1.0
O C:HOH602 3.8 18.3 1.0
CG C:GLU260 4.0 21.3 1.0
O1A C:CS2503 4.0 36.0 1.0
CD2 C:HIS236 4.1 24.9 1.0
CB C:ASP234 4.2 18.4 1.0
O C:HOH675 4.2 22.8 1.0
CG C:GLU286 4.3 21.9 1.0
C3 C:CS2503 4.3 35.9 1.0
CG C:ASP261 4.5 32.1 1.0
NH1 C:ARG171 4.6 22.8 1.0
CZ C:ARG307 4.7 24.7 1.0
OH A:TYR99 4.7 31.2 1.0
NE2 C:HIS236 4.7 31.8 1.0
NE C:ARG307 4.7 23.3 1.0
OH C:TYR183 4.8 34.9 1.0
CD2 C:HIS336 4.9 26.8 1.0
C4 C:CS2503 4.9 26.8 1.0

Reference:

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo. Crystal Structure of Mannonate Dehydratase From Caulobacter Crescentus CB15 To Be Published.
Page generated: Mon Dec 14 16:28:42 2020

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