Magnesium in PDB 4ggh: Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221)

The structure of Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221), PDB code: 4ggh was solved by M.W.Vetting, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzymefunction Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.62 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	92.948, 209.550, 208.468, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.3

The structure of Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221) also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Magnesium atom in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221) (pdb code 4ggh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221), PDB code: 4ggh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:8.8 occ:1.00 O D:ASN247 2.1 8.0 1.0 O D:HOH502 2.2 25.3 1.0 O D:HOH501 2.3 6.8 1.0 O A:ASN247 2.4 11.1 1.0 C D:ASN247 3.3 11.3 1.0 C A:ASN247 3.5 10.7 1.0 CA D:GLN248 4.0 10.8 1.0 N D:GLN248 4.1 7.2 1.0 CA A:GLN248 4.2 10.5 1.0 CB D:ASN247 4.2 18.6 1.0 CA D:ASN247 4.2 13.1 1.0 CB D:GLN248 4.3 13.3 1.0 N A:GLN248 4.3 10.2 1.0 CB A:GLN248 4.3 12.1 1.0 CB A:ASN247 4.4 17.7 1.0 CA A:ASN247 4.5 13.7 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:13.7 occ:1.00 O A:HOH925 2.1 14.7 0.5 OE1 A:GLU257 2.1 11.9 1.0 O A:HOH501 2.1 11.8 1.0 O A:HOH502 2.1 12.2 1.0 OE2 A:GLU231 2.1 13.8 1.0 OD2 A:ASP205 2.1 14.5 1.0 CD A:GLU257 3.0 15.0 1.0 CD A:GLU231 3.1 14.4 1.0 CG A:ASP205 3.2 12.2 1.0 OE2 A:GLU257 3.2 15.6 1.0 OD1 A:ASP205 3.6 9.1 1.0 OE1 A:GLU231 3.7 11.0 1.0 O A:HOH925 3.9 15.3 0.5 O A:HOH643 4.0 21.6 1.0 NH2 A:ARG278 4.0 8.9 1.0 CG A:GLU231 4.0 14.8 1.0 O A:HOH547 4.1 13.8 1.0 O A:HOH506 4.2 9.6 1.0 CD2 A:HIS207 4.3 22.8 1.0 CG A:GLU257 4.3 11.2 1.0 NE2 A:HIS307 4.4 15.9 1.0 OD2 A:ASP232 4.5 17.1 1.0 CB A:ASP205 4.5 15.4 1.0 CD2 A:HIS307 4.5 18.1 1.0 O A:HOH908 4.7 50.6 1.0 CG A:ASP232 5.0 16.3 1.0 NE2 A:HIS207 5.0 16.5 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:12.2 occ:1.00 O B:HOH501 2.1 14.0 1.0 O B:HOH502 2.1 16.1 1.0 OE1 B:GLU257 2.1 10.5 1.0 OD2 B:ASP205 2.1 10.5 1.0 O B:HOH906 2.1 0.0 0.5 OE2 B:GLU231 2.2 14.5 1.0 CD B:GLU257 3.0 14.7 1.0 CD B:GLU231 3.1 18.0 1.0 CG B:ASP205 3.1 15.1 1.0 OE2 B:GLU257 3.3 15.9 1.0 OD1 B:ASP205 3.5 13.9 1.0 OE1 B:GLU231 3.7 15.3 1.0 O B:HOH906 3.8 8.2 0.5 NH2 B:ARG278 3.9 14.0 1.0 CG B:GLU231 4.0 13.2 1.0 O B:HOH528 4.1 12.3 1.0 CD2 B:HIS207 4.2 19.2 1.0 O B:HOH553 4.2 10.3 1.0 CG B:GLU257 4.4 9.2 1.0 NE2 B:HIS307 4.4 10.5 1.0 CB B:ASP205 4.4 14.4 1.0 OD2 B:ASP232 4.5 19.0 1.0 CD2 B:HIS307 4.6 10.5 1.0 NE2 B:HIS207 4.8 18.7 1.0 CG B:ASP232 4.9 17.1 1.0 CZ B:ARG278 5.0 17.6 1.0 CB B:GLU257 5.0 9.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:11.1 occ:1.00 O C:HOH501 2.1 10.7 1.0 O C:HOH925 2.1 0.2 0.5 O C:HOH502 2.1 16.8 1.0 OE2 C:GLU231 2.1 16.2 1.0 OE1 C:GLU257 2.1 12.9 1.0 OD2 C:ASP205 2.1 15.1 1.0 CD C:GLU257 3.0 12.7 1.0 CD C:GLU231 3.1 17.5 1.0 CG C:ASP205 3.2 16.3 1.0 OE2 C:GLU257 3.3 12.7 1.0 OD1 C:ASP205 3.6 13.7 1.0 OE1 C:GLU231 3.8 11.3 1.0 O C:HOH925 3.8 11.1 0.5 O C:HOH546 4.0 15.3 1.0 CG C:GLU231 4.1 7.2 1.0 NH2 C:ARG278 4.1 9.7 1.0 CD2 C:HIS207 4.2 22.8 1.0 O C:HOH551 4.3 12.3 1.0 CG C:GLU257 4.4 9.0 1.0 OD2 C:ASP232 4.4 15.6 1.0 NE2 C:HIS307 4.4 9.9 1.0 O C:HOH853 4.4 37.3 1.0 CB C:ASP205 4.5 8.0 1.0 CD2 C:HIS307 4.6 11.2 1.0 NE2 C:HIS207 4.7 25.1 1.0 NH2 C:ARG151 4.8 12.4 0.5 O C:HOH850 4.9 42.0 1.0 CG C:ASP232 4.9 14.3 1.0 CB C:GLU257 5.0 12.7 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:13.1 occ:1.00 O D:HOH504 2.1 12.6 1.0 OE2 D:GLU231 2.1 14.9 1.0 OD2 D:ASP205 2.1 10.3 1.0 O D:HOH503 2.1 10.1 1.0 OE1 D:GLU257 2.1 12.9 1.0 O D:HOH928 2.1 0.5 0.5 CD D:GLU257 3.0 13.9 1.0 CD D:GLU231 3.1 17.1 1.0 CG D:ASP205 3.1 8.5 1.0 OE2 D:GLU257 3.3 10.1 1.0 OD1 D:ASP205 3.5 9.8 1.0 OE1 D:GLU231 3.7 11.2 1.0 O D:HOH928 3.8 9.7 0.5 O D:HOH564 3.9 24.6 1.0 O D:HOH517 4.1 12.5 1.0 NH2 D:ARG278 4.1 12.4 1.0 CG D:GLU231 4.2 10.4 1.0 CD2 D:HIS207 4.2 18.1 1.0 O D:HOH536 4.2 12.2 1.0 CG D:GLU257 4.4 13.4 1.0 CB D:ASP205 4.4 8.6 1.0 NE2 D:HIS307 4.5 11.1 1.0 CD2 D:HIS307 4.6 10.1 1.0 OD2 D:ASP232 4.7 19.4 1.0 NE2 D:HIS207 4.8 20.9 1.0

M.W.Vetting, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Hepes, and Ethylene Glycol Bound (Ordered Loops, Space Group C2221) To Be Published.