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Magnesium in PDB 4ihc: Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703

Protein crystallography data

The structure of Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703, PDB code: 4ihc 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, N.F.Al Obaidi, M.Stead, J.Love, J.A.Gerlt, S.C.Almo, Enzyme Functioninitiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.331, 224.347, 87.076, 90.00, 97.96, 90.00
R / Rfree (%) 17.3 / 22.8

Other elements in 4ihc:

The structure of Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 also contains other interesting chemical elements:

Iodine (I) 19 atoms
Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 (pdb code 4ihc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703, PDB code: 4ihc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4ihc

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Magnesium binding site 1 out of 8 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:11.3
occ:1.00
 O A:HOH730 1.9 16.2 1.0
OE2 A:GLU249 1.9 27.6 1.0
O A:HOH698 2.0 14.9 1.0
OD2 A:ASP223 2.0 10.2 1.0
OE1 A:GLU275 2.3 10.0 1.0
O1 A:FMT503 2.6 32.4 1.0
C A:FMT503 3.0 42.9 1.0
CD A:GLU249 3.0 29.2 1.0
CG A:ASP223 3.0 16.9 1.0
CD A:GLU275 3.0 19.3 1.0
OE2 A:GLU275 3.3 26.1 1.0
OD1 A:ASP223 3.3 12.3 1.0
O2 A:FMT503 3.7 30.2 1.0
OE1 A:GLU249 3.7 22.7 1.0
CG A:GLU249 3.9 17.9 1.0
NH2 A:ARG296 4.0 4.9 1.0
O A:HOH660 4.2 21.5 1.0
NH1 A:ARG152 4.3 21.4 1.0
OD2 A:ASP250 4.3 37.3 1.0
O A:HOH622 4.3 15.5 1.0
CG A:GLU275 4.4 12.7 1.0
CD2 A:HIS225 4.4 40.4 1.0
CB A:ASP223 4.4 10.5 1.0
NE2 A:HIS325 4.8 7.3 1.0
NE2 A:HIS225 4.9 51.0 1.0
CG A:ASP250 4.9 38.5 1.0
OH B:TYR80 4.9 11.5 1.0
NE A:ARG152 5.0 26.7 1.0
CD2 A:HIS325 5.0 7.3 1.0

Magnesium binding site 2 out of 8 in 4ihc

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Magnesium binding site 2 out of 8 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:14.1
occ:1.00
 O B:HOH696 2.0 15.9 1.0
O1 B:FMT505 2.0 28.7 1.0
OD2 B:ASP223 2.1 19.6 1.0
OE2 B:GLU249 2.1 23.0 1.0
O B:HOH744 2.2 18.0 1.0
OE1 B:GLU275 2.3 12.9 1.0
C B:FMT505 2.7 49.2 1.0
CD B:GLU275 3.0 14.0 1.0
OE2 B:GLU275 3.0 13.5 1.0
CD B:GLU249 3.1 33.7 1.0
CG B:ASP223 3.1 20.9 1.0
OD1 B:ASP223 3.5 8.8 1.0
O2 B:FMT505 3.7 29.7 1.0
OE1 B:GLU249 3.8 25.1 1.0
NH2 B:ARG296 3.8 12.4 1.0
CG B:GLU249 4.0 19.5 1.0
CD2 B:HIS225 4.1 24.1 1.0
OD2 B:ASP250 4.3 29.6 1.0
O B:HOH628 4.3 19.8 1.0
CG B:GLU275 4.4 14.6 1.0
CB B:ASP223 4.4 10.2 1.0
O B:HOH710 4.4 16.0 1.0
NE2 B:HIS325 4.5 9.6 1.0
NE2 B:HIS225 4.7 26.7 1.0
CD2 B:HIS325 4.9 10.9 1.0
NH1 B:ARG152 4.9 33.8 1.0
CZ B:ARG296 4.9 15.7 1.0
CG B:ASP250 5.0 32.2 1.0
NE B:ARG296 5.0 16.7 1.0

Magnesium binding site 3 out of 8 in 4ihc

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Magnesium binding site 3 out of 8 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:16.4
occ:1.00
 O C:HOH783 1.8 13.8 1.0
O1 C:FMT503 1.9 35.3 1.0
OE2 C:GLU249 2.1 24.0 1.0
OE1 C:GLU275 2.1 17.0 1.0
OD2 C:ASP223 2.2 12.5 1.0
O C:HOH724 2.2 22.6 1.0
CD C:GLU275 2.8 20.5 1.0
CD C:GLU249 3.0 39.2 1.0
OE2 C:GLU275 3.0 12.7 1.0
C C:FMT503 3.1 26.5 1.0
CG C:ASP223 3.1 16.2 1.0
OD1 C:ASP223 3.3 13.7 1.0
OD2 C:ASP250 3.7 31.2 1.0
OE1 C:GLU249 3.7 19.7 1.0
O2 C:FMT503 3.7 27.5 1.0
CG C:GLU249 4.0 23.6 1.0
CD2 C:HIS225 4.0 15.1 1.0
NH2 C:ARG296 4.0 10.7 1.0
CG C:GLU275 4.1 13.1 1.0
O C:HOH651 4.2 25.3 1.0
NH1 C:ARG152 4.4 26.9 1.0
CB C:ASP223 4.5 10.7 1.0
O C:HOH619 4.5 17.6 1.0
CG C:ASP250 4.6 52.0 1.0
NE2 C:HIS225 4.6 15.9 1.0
NE2 C:HIS325 4.7 11.8 1.0
CD2 C:HIS325 4.9 10.7 1.0
CB C:GLU275 4.9 15.7 1.0
OH G:TYR80 4.9 23.3 1.0

Magnesium binding site 4 out of 8 in 4ihc

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Magnesium binding site 4 out of 8 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:14.7
occ:1.00
 O D:HOH724 1.9 14.7 1.0
O D:HOH803 2.1 25.6 1.0
OD2 D:ASP223 2.1 28.8 1.0
OE2 D:GLU249 2.2 22.6 1.0
OE1 D:GLU275 2.2 13.1 1.0
O1 D:FMT506 2.3 28.9 1.0
C D:FMT506 3.0 53.6 1.0
CD D:GLU275 3.0 20.5 1.0
CD D:GLU249 3.1 30.3 1.0
CG D:ASP223 3.2 20.9 1.0
OE2 D:GLU275 3.2 18.1 1.0
OD1 D:ASP223 3.5 17.9 1.0
OE1 D:GLU249 3.7 22.3 1.0
O2 D:FMT506 3.8 43.8 1.0
NH2 D:ARG296 3.9 12.7 1.0
O D:HOH620 3.9 16.9 1.0
CG D:GLU249 4.0 18.7 1.0
OD2 D:ASP250 4.0 34.6 1.0
O D:HOH662 4.0 30.4 1.0
NH1 D:ARG152 4.2 36.0 1.0
CD2 D:HIS225 4.2 48.6 1.0
CG D:GLU275 4.3 17.6 1.0
CB D:ASP223 4.5 15.1 1.0
NE2 D:HIS325 4.7 16.3 1.0
NE2 D:HIS225 4.7 50.3 1.0
CG D:ASP250 4.8 25.7 1.0
CZ D:ARG296 4.9 12.7 1.0
CD2 D:HIS325 4.9 16.0 1.0
CB D:GLU275 5.0 12.8 1.0

Magnesium binding site 5 out of 8 in 4ihc

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Magnesium binding site 5 out of 8 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:17.9
occ:1.00
 O E:HOH723 2.1 22.8 1.0
OE2 E:GLU249 2.1 22.1 1.0
O E:HOH724 2.1 14.9 1.0
OE1 E:GLU275 2.1 20.1 1.0
OD2 E:ASP223 2.2 18.7 1.0
O2 E:FMT505 2.2 23.1 1.0
CD E:GLU275 2.9 13.2 1.0
OE2 E:GLU275 2.9 17.9 1.0
C E:FMT505 3.0 29.9 1.0
CD E:GLU249 3.1 18.1 1.0
CG E:ASP223 3.2 11.7 1.0
OD1 E:ASP223 3.5 15.7 1.0
O1 E:FMT505 3.6 36.2 1.0
OE1 E:GLU249 3.9 22.7 1.0
NH2 E:ARG296 3.9 7.1 1.0
CG E:GLU249 4.0 12.2 1.0
NH1 E:ARG152 4.1 30.1 1.0
OD2 E:ASP250 4.1 27.6 1.0
CD2 E:HIS225 4.2 37.2 1.0
O E:HOH653 4.2 17.7 1.0
O E:HOH829 4.2 24.5 1.0
CG E:GLU275 4.3 17.7 1.0
CB E:ASP223 4.5 15.2 1.0
NE2 E:HIS325 4.6 12.4 1.0
NE2 E:HIS225 4.8 24.2 1.0
CD2 E:HIS325 4.9 9.9 1.0
CG E:ASP250 4.9 32.9 1.0
CZ E:ARG296 5.0 7.4 1.0

Magnesium binding site 6 out of 8 in 4ihc

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Magnesium binding site 6 out of 8 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


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 Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:20.6
occ:1.00
 O F:HOH682 2.0 14.4 1.0
O F:HOH794 2.0 16.7 1.0
OE1 F:GLU275 2.0 17.4 1.0
OE2 F:GLU249 2.1 37.2 1.0
O2 F:FMT503 2.1 31.4 1.0
OD2 F:ASP223 2.3 20.5 1.0
CD F:GLU275 2.7 26.8 1.0
OE2 F:GLU275 3.0 22.1 1.0
CD F:GLU249 3.0 33.6 1.0
CG F:ASP223 3.2 18.9 1.0
C F:FMT503 3.2 26.8 1.0
OD1 F:ASP223 3.5 13.6 1.0
OE1 F:GLU249 3.8 23.2 1.0
O1 F:FMT503 3.9 31.9 1.0
CG F:GLU249 3.9 14.4 1.0
CG F:GLU275 4.0 21.2 1.0
NH2 F:ARG296 4.1 10.4 1.0
O F:HOH621 4.2 18.8 1.0
OD2 F:ASP250 4.2 25.4 1.0
CD2 F:HIS225 4.4 47.1 1.0
O F:HOH635 4.4 23.1 1.0
NH1 F:ARG152 4.5 32.4 1.0
CB F:ASP223 4.6 13.1 1.0
NE2 F:HIS325 4.7 12.9 1.0
NE2 F:HIS225 4.7 44.7 1.0
CB F:GLU275 4.8 15.2 1.0
CD2 F:HIS325 4.8 10.2 1.0
OH E:TYR80 4.9 25.4 1.0
O F:HOH652 5.0 19.8 1.0
CG F:ASP250 5.0 21.3 1.0

Magnesium binding site 7 out of 8 in 4ihc

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Magnesium binding site 7 out of 8 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg501

b:15.6
occ:1.00
 O G:HOH813 1.8 19.2 1.0
OE2 G:GLU249 2.0 27.8 1.0
OD2 G:ASP223 2.0 16.0 1.0
O G:HOH661 2.1 16.2 1.0
O2 G:FMT505 2.2 19.6 1.0
OE1 G:GLU275 2.2 15.8 1.0
CD G:GLU275 3.0 18.6 1.0
CD G:GLU249 3.0 32.1 1.0
CG G:ASP223 3.1 9.5 1.0
OE2 G:GLU275 3.2 16.7 1.0
C G:FMT505 3.3 37.9 1.0
OD1 G:ASP223 3.5 11.4 1.0
OE1 G:GLU249 3.7 24.7 1.0
O1 G:FMT505 3.9 28.5 1.0
CG G:GLU249 4.0 15.8 1.0
NH2 G:ARG296 4.0 11.1 1.0
CD2 G:HIS225 4.1 41.8 1.0
O G:HOH639 4.1 22.1 1.0
NH1 G:ARG152 4.1 29.7 1.0
O G:HOH619 4.3 17.5 1.0
CG G:GLU275 4.3 17.6 1.0
CB G:ASP223 4.4 14.9 1.0
OD2 G:ASP250 4.6 32.8 1.0
NE2 G:HIS225 4.6 29.8 1.0
NE2 G:HIS325 4.7 8.1 1.0
CD2 G:HIS325 4.9 7.6 1.0
OH C:TYR80 5.0 19.7 1.0
CZ G:ARG152 5.0 31.9 1.0

Magnesium binding site 8 out of 8 in 4ihc

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Magnesium binding site 8 out of 8 in the Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Probable Mannonate Dehydratase DD703_0947 (Target Efi-502222) From Dickeya Dadantii ECH703 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg501

b:14.2
occ:1.00
 O H:HOH711 2.0 13.2 1.0
OD2 H:ASP223 2.1 15.9 1.0
O H:HOH625 2.1 12.5 1.0
OE2 H:GLU249 2.1 22.0 1.0
OE1 H:GLU275 2.3 17.0 1.0
O1 H:FMT505 2.3 25.0 1.0
C H:FMT505 2.7 29.8 1.0
CD H:GLU275 3.0 18.1 1.0
CD H:GLU249 3.1 23.0 1.0
OE2 H:GLU275 3.1 16.0 1.0
CG H:ASP223 3.1 13.1 1.0
OD1 H:ASP223 3.5 11.7 1.0
O2 H:FMT505 3.6 17.2 1.0
OE1 H:GLU249 3.7 16.2 1.0
NH2 H:ARG296 4.0 12.6 1.0
O H:HOH800 4.0 15.1 1.0
CG H:GLU249 4.0 12.7 1.0
CD2 H:HIS225 4.2 23.5 1.0
OD2 H:ASP250 4.2 24.1 1.0
NH1 H:ARG152 4.3 40.5 1.0
O H:HOH642 4.4 14.9 1.0
CB H:ASP223 4.4 8.8 1.0
CG H:GLU275 4.4 11.3 1.0
NE2 H:HIS225 4.7 30.1 1.0
NE2 H:HIS325 4.7 10.9 1.0
CG H:ASP250 5.0 29.2 1.0
CD2 H:HIS325 5.0 10.8 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, N.F.Al Obaidi, M.Stead, J.Love, J.A.Gerlt, S.C.Almo. Crystal Structure of Mannonate Dehydratase DD703_0947 From Dickeya Dadantii ECH703 To Be Published.
Page generated: Fri Aug 16 16:43:14 2024

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