Magnesium in PDB 4j1o: Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate)

The structure of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate), PDB code: 4j1o was solved by M.W.Vetting, R.Toro, R.Bhosle, S.R.Wasserman, L.L.Morisco, S.Sojitra, S.Chamala, A.Kar, J.Lafleur, G.Villigas, B.Evans, J.Hammonds, A.Gizzi, M.Stead, B.Hillerich, J.Love, R.D.Seidel, J.B.Bonanno, J.A.Gerlt, S.C.Almo, New York Structural Genomics Research Consortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.09 / 1.60
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.297, 117.297, 110.528, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.1

The structure of Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate) also contains other interesting chemical elements:

Iodine

(I)

11 atoms

The binding sites of Magnesium atom in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate) (pdb code 4j1o). 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 (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate), PDB code: 4j1o:
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 (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate)


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 (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:9.8 occ:1.00 OD2 A:ASP242 2.0 10.9 1.0 O A:HOH503 2.0 9.1 1.0 OE2 A:GLU219 2.1 12.9 1.0 OD2 A:ASP194 2.1 10.5 1.0 O A:PBE412 2.2 22.9 1.0 OXT A:PBE412 2.2 13.4 1.0 C A:PBE412 2.6 18.1 1.0 CG A:ASP242 3.1 10.8 1.0 CD A:GLU219 3.1 17.9 1.0 CG A:ASP194 3.1 9.8 1.0 OD1 A:ASP194 3.5 9.8 1.0 CB A:ASP242 3.5 7.4 1.0 ND2 A:ASN196 3.8 17.6 1.0 CG A:GLU219 3.8 7.8 1.0 NE2 A:GLN162 3.8 12.9 1.0 OH A:TYR56 3.9 16.9 1.0 O A:HOH676 3.9 22.6 1.0 OE1 A:GLU219 4.0 19.7 1.0 CA A:PBE412 4.0 18.0 1.0 NZ A:LYS164 4.1 27.4 1.0 OE1 A:GLU243 4.2 7.8 1.0 OD1 A:ASP242 4.2 12.1 1.0 NZ A:LYS266 4.3 14.8 1.0 CB A:ASP194 4.4 8.1 1.0 O A:HOH567 4.6 15.0 1.0 CD A:GLN162 4.6 11.9 1.0 CG A:ASN196 4.6 19.4 1.0 CB A:PBE412 4.8 21.5 1.0 CD A:GLU243 4.8 10.3 1.0 OE2 A:GLU243 4.8 14.4 1.0 OE1 A:GLN162 4.8 15.0 1.0 OD1 A:ASN196 4.9 17.1 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate)


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 (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:13.7 occ:1.00 O A:HOH600 2.0 20.7 1.0 O A:HOH638 2.1 21.2 1.0 O A:HOH603 2.1 20.9 1.0 O A:HOH537 2.1 13.1 1.0 O A:HOH595 2.1 17.1 1.0 O A:HOH549 2.1 14.9 1.0 O A:PHE158 4.1 10.1 1.0 O A:THR187 4.1 17.3 1.0 O A:HOH693 4.2 32.4 1.0 O A:HOH701 4.3 26.6 1.0 O A:HOH723 4.3 36.0 1.0 O A:HOH617 4.3 20.4 1.0 OG1 A:THR189 4.4 10.2 1.0 O A:VAL154 4.5 11.7 1.0 O A:GLY157 4.5 10.3 1.0 CA A:PRO159 4.5 10.6 1.0 O A:HOH564 4.7 18.0 1.0 C A:PHE158 4.7 10.5 1.0 CG1 A:VAL154 4.7 14.2 1.0 C A:GLY157 4.8 9.7 1.0 N A:PRO159 5.0 8.2 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate)


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 (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:23.4 occ:1.00 OG A:SER369 2.0 24.5 1.0 O A:HOH851 2.1 25.6 1.0 O A:SER369 2.1 18.4 1.0 O A:HOH784 2.1 29.7 1.0 O A:HOH551 2.1 19.6 1.0 CB A:SER369 2.9 21.5 1.0 C A:SER369 3.0 17.5 1.0 CA A:SER369 3.4 14.9 1.0 O A:ALA4 3.9 14.6 1.0 OXT A:SER369 4.1 18.7 1.0 O A:HOH798 4.4 39.0 1.0 N A:SER369 4.8 13.0 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate)


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 (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:9.3 occ:1.00 OD2 B:ASP242 2.0 10.5 1.0 O B:HOH509 2.0 10.0 1.0 OE2 B:GLU219 2.1 10.8 1.0 OD2 B:ASP194 2.1 10.6 1.0 OXT B:PBE407 2.1 28.1 1.0 O B:PBE407 2.2 14.5 1.0 C B:PBE407 2.5 25.4 1.0 CG B:ASP242 3.1 12.0 1.0 CD B:GLU219 3.1 18.3 1.0 CG B:ASP194 3.1 10.4 1.0 OD1 B:ASP194 3.5 10.1 1.0 CB B:ASP242 3.5 8.4 1.0 O B:HOH680 3.7 21.4 1.0 ND2 B:ASN196 3.8 17.6 1.0 NE2 B:GLN162 3.8 13.6 1.0 CG B:GLU219 3.8 12.5 1.0 OH B:TYR56 3.9 19.2 1.0 CA B:PBE407 4.0 26.1 1.0 OE1 B:GLU219 4.0 21.9 1.0 OE1 B:GLU243 4.2 9.0 1.0 NZ B:LYS164 4.2 25.7 1.0 OD1 B:ASP242 4.2 9.4 1.0 NZ B:LYS266 4.3 14.7 1.0 CB B:ASP194 4.4 7.9 1.0 O B:HOH534 4.5 14.4 1.0 CD B:GLN162 4.6 16.4 1.0 CG B:ASN196 4.7 17.6 1.0 OE1 B:GLN162 4.8 21.7 1.0 CD B:GLU243 4.8 12.4 1.0 CB B:PBE407 4.8 32.5 1.0 OE2 B:GLU243 4.8 19.1 1.0 OD1 B:ASN196 5.0 19.0 1.0 N B:PBE407 5.0 40.5 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of An Enolase (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate)


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 (Mandelate Racemase Subgroup) From Paracococus Denitrificans PD1222 (Target Nysgrc-012907) with Bound L- Proline Betaine (Substrate) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:22.1 occ:1.00 O B:HOH588 2.0 20.5 1.0 O B:HOH782 2.1 32.4 1.0 O B:HOH772 2.1 29.7 1.0 O B:HOH709 2.1 33.0 1.0 O B:HOH744 2.1 30.4 1.0 O B:HOH645 2.1 22.4 1.0 O B:PHE158 4.0 11.6 1.0 O B:HOH673 4.2 32.8 1.0 O B:THR187 4.2 25.2 1.0 OG1 B:THR189 4.4 13.8 1.0 O B:GLY157 4.5 10.9 1.0 O B:HOH827 4.5 40.0 1.0 CA B:PRO159 4.5 11.8 1.0 O B:VAL154 4.6 13.8 1.0 C B:PHE158 4.7 10.0 1.0 C B:GLY157 4.7 9.2 1.0 CG1 B:VAL154 4.8 15.7 1.0 O B:HOH731 4.9 29.8 1.0 N B:PRO159 4.9 10.2 1.0 CA B:GLY157 4.9 12.3 1.0

R.Kumar, S.Zhao, M.W.Vetting, B.M.Wood, A.Sakai, K.Cho, J.Solbiati, S.C.Almo, J.V.Sweedler, M.P.Jacobson, J.A.Gerlt, J.E.Cronan. Prediction and Biochemical Demonstration of A Catabolic Pathway For the Osmoprotectant Proline Betaine. Mbio V. 5 00933 2014.
ISSN: ESSN 2150-7511
PubMed: 24520058
DOI: 10.1128/MBIO.00933-13