Magnesium in PDB 3vcn: Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15

The structure of Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15, PDB code: 3vcn 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)	50.00 / 1.45
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	116.302, 116.302, 118.078, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 18.8

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

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 (pdb code 3vcn). 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 Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15, PDB code: 3vcn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:16.2 occ:1.00 OD2 A:ASP211 2.0 17.6 1.0 O A:HOH635 2.0 18.8 1.0 OE2 A:GLU237 2.1 18.8 1.0 OE1 A:GLU263 2.1 18.4 1.0 O A:HOH791 2.2 19.7 1.0 O2 A:CO3503 2.2 19.4 1.0 CG A:ASP211 3.0 15.6 1.0 CD A:GLU263 3.0 18.1 1.0 CD A:GLU237 3.2 16.9 1.0 C A:CO3503 3.2 22.3 1.0 OE2 A:GLU263 3.3 18.1 1.0 OD1 A:ASP211 3.4 16.5 1.0 O1 A:CO3503 3.4 24.8 1.0 NH2 A:ARG284 3.8 19.4 1.0 OE1 A:GLU237 3.9 18.2 1.0 O A:HOH608 3.9 17.9 1.0 CD2 A:HIS213 4.0 18.9 1.0 CG A:GLU237 4.0 15.8 1.0 OD2 A:ASP238 4.1 18.9 1.0 O A:HOH684 4.1 18.1 1.0 CB A:ASP211 4.3 15.8 1.0 O3 A:CO3503 4.3 22.6 1.0 CG A:GLU263 4.4 18.7 1.0 NE2 A:HIS213 4.4 17.8 1.0 NH1 A:ARG148 4.6 16.3 1.0 CG A:ASP238 4.7 16.6 1.0 OH A:TYR160 4.7 20.9 1.0 OH C:TYR76 4.7 17.2 1.0 CZ A:ARG284 4.7 17.4 1.0 CD2 A:HIS313 4.8 18.5 1.0 NE A:ARG284 4.8 16.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:36.3 occ:1.00 O A:HOH974 2.0 34.3 1.0 O A:HOH980 2.1 37.4 1.0 O A:HOH979 2.1 39.7 1.0 O A:HOH860 2.1 27.9 1.0 O A:HOH975 2.1 36.7 1.0 O A:HOH976 2.1 36.5 1.0 O A:HOH780 4.2 24.6 1.0 OD1 A:ASP165 4.2 22.0 1.0 O A:HOH680 4.2 26.1 1.0 OD2 A:ASP165 4.3 21.6 1.0 O A:HOH770 4.5 27.3 1.0 CG A:ASP165 4.6 22.1 1.0 CZ A:PHE168 4.8 24.4 1.0 CE2 A:PHE168 4.9 19.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15


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 Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:19.1 occ:1.00 OE2 C:GLU237 2.0 18.2 1.0 OD2 C:ASP211 2.1 18.7 1.0 O C:HOH660 2.1 18.2 1.0 OE1 C:GLU263 2.1 17.8 1.0 O C:HOH641 2.2 21.1 1.0 O2 C:CO3503 2.2 19.9 1.0 CG C:ASP211 3.0 16.9 1.0 CD C:GLU263 3.1 20.0 1.0 CD C:GLU237 3.1 17.1 1.0 C C:CO3503 3.2 22.1 1.0 OE2 C:GLU263 3.3 19.3 1.0 OD1 C:ASP211 3.5 18.1 1.0 O3 C:CO3503 3.5 25.7 1.0 NH2 C:ARG284 3.8 16.3 1.0 OE1 C:GLU237 3.9 17.3 1.0 O C:HOH606 3.9 18.0 1.0 CD2 C:HIS213 4.0 20.0 1.0 CG C:GLU237 4.0 15.8 1.0 O C:HOH645 4.1 17.7 1.0 OD2 C:ASP238 4.2 17.7 1.0 CB C:ASP211 4.3 15.8 1.0 O1 C:CO3503 4.3 25.6 1.0 CG C:GLU263 4.4 19.1 1.0 NH1 C:ARG148 4.5 18.9 1.0 NE2 C:HIS213 4.5 18.9 1.0 OH C:TYR160 4.7 21.3 1.0 OH A:TYR76 4.7 17.6 1.0 CG C:ASP238 4.7 16.3 1.0 CD2 C:HIS313 4.7 15.6 1.0 CZ C:ARG284 4.8 16.0 1.0 NE C:ARG284 4.8 16.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15


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 Mannonate Dehydratase (Target Efi-502209) From Caulobacter Crescentus CB15 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg505 b:35.5 occ:1.00 O C:HOH968 2.0 34.3 1.0 O C:HOH933 2.0 32.5 1.0 O C:HOH969 2.1 39.9 1.0 O C:HOH824 2.2 31.7 1.0 O C:HOH797 2.2 31.1 1.0 O C:HOH967 2.3 37.7 1.0 O C:HOH983 4.1 42.9 1.0 O C:HOH985 4.1 39.5 1.0 O C:HOH764 4.2 24.7 1.0 OD1 C:ASP165 4.2 25.7 1.0 OD2 C:ASP165 4.3 24.5 1.0 O C:HOH727 4.3 25.8 1.0 O C:HOH761 4.4 27.4 1.0 CG C:ASP165 4.7 23.7 1.0 CZ C:PHE168 4.9 22.6 1.0

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.