Iodine 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:

Magnesium

(Mg)

5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Iodine 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 Iodine atom.
In total 11 binding sites of Iodine 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 Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 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 Iodine with other atoms in the I 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:I404 b:26.5 occ:0.35 N A:ARG315 3.4 7.7 1.0 CB A:ARG315 3.7 15.9 1.0 CD A:PRO314 3.8 10.5 1.0 CG A:GLN313 3.8 15.3 1.0 CB A:PRO314 3.9 12.6 1.0 CG A:ARG315 3.9 20.3 1.0 N A:PRO314 4.0 8.0 1.0 O A:HOH624 4.1 30.2 1.0 CA A:ARG315 4.1 10.6 1.0 CG A:PRO314 4.2 12.2 1.0 C A:PRO314 4.2 9.4 1.0 CA A:PRO314 4.3 7.3 1.0 NE2 A:GLN313 4.4 22.6 1.0 CD A:GLN313 4.4 20.1 1.0 CD A:ARG315 4.5 30.4 1.0 C A:GLN313 4.7 8.5 1.0

Iodine binding site 2 out of 11 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 Iodine with other atoms in the I 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:I405 b:34.1 occ:0.31 O A:HOH659 3.3 22.4 1.0 O A:HOH741 3.5 37.7 1.0 CG2 A:VAL365 4.0 14.3 1.0 CB A:ARG65 4.2 11.2 1.0 CB A:ALA366 4.2 15.8 1.0 O A:VAL365 4.3 17.3 1.0 I A:IOD410 4.5 34.3 0.3 CB A:VAL365 4.5 15.2 1.0 CD A:ARG65 4.5 28.0 1.0 C A:VAL365 4.7 18.1 1.0 O A:ARG65 4.8 9.5 1.0 O A:HOH585 4.9 16.6 1.0 CG A:ARG65 5.0 14.3 1.0 NE A:ARG65 5.0 34.1 1.0

Iodine binding site 3 out of 11 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 Iodine with other atoms in the I 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:I406 b:35.1 occ:0.25 N A:ALA44 3.2 11.3 1.0 NZ A:LYS114 3.7 22.2 1.0 CD1 A:LEU43 3.8 21.6 1.0 O A:ALA44 3.9 14.3 1.0 CB A:ALA44 3.9 14.8 1.0 CA A:ALA44 4.0 11.8 1.0 I A:IOD408 4.0 37.5 0.3 CA A:LEU43 4.1 14.1 1.0 C A:LEU43 4.1 13.9 1.0 C A:ALA44 4.4 11.2 1.0 CG A:LEU43 4.5 19.7 1.0 O A:GLY42 4.5 18.1 1.0 CD A:LYS114 4.5 19.4 1.0 CE A:LYS114 4.8 23.7 1.0 CB A:LEU43 4.8 15.8 1.0

Iodine binding site 4 out of 11 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 Iodine with other atoms in the I 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 A:I407 b:23.3 occ:0.36 O A:HOH590 2.8 17.9 1.0 O A:HOH698 2.8 27.5 1.0 O A:HOH570 3.1 17.4 1.0 O A:HOH569 3.8 14.5 1.0 O A:HOH589 3.9 23.1 1.0 CB A:ALA57 4.0 10.9 1.0 OG A:SER59 4.0 20.3 1.0 CA A:ARG269 4.0 5.7 1.0 CB A:ARG269 4.0 7.9 1.0 CG A:ARG269 4.1 7.5 1.0 O A:HOH593 4.1 17.4 1.0 O A:HOH660 4.2 29.2 1.0 O A:HOH658 4.2 22.6 1.0 CB A:SER59 4.2 14.7 1.0 CB A:TYR99 4.3 8.4 1.0 O A:HOH539 4.5 13.7 1.0 N A:ARG269 4.6 6.3 1.0 CD A:ARG269 4.7 8.5 1.0 CD1 A:TYR99 4.8 10.2 1.0 CG A:TYR99 4.8 11.1 1.0 O A:HOH561 4.8 16.7 1.0 CD A:PRO58 4.9 16.8 1.0 N A:PRO58 5.0 14.6 1.0 O A:PRO58 5.0 13.8 1.0

Iodine binding site 5 out of 11 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 Iodine with other atoms in the I 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 A:I408 b:37.5 occ:0.26 NE1 A:TRP46 3.4 11.8 1.0 NZ A:LYS114 3.9 22.2 1.0 I A:IOD406 4.0 35.1 0.2 CD1 A:TRP46 4.0 11.6 1.0 CB A:ALA44 4.2 14.8 1.0 OE2 A:GLU358 4.3 26.2 0.5 CE2 A:TRP46 4.5 11.4 1.0 O A:HOH631 4.5 18.6 1.0 CG2 A:THR355 4.6 24.4 1.0 CE A:LYS36 4.7 22.5 1.0 CD A:PRO356 4.7 17.0 1.0 O A:ALA44 4.9 14.3 1.0

Iodine binding site 6 out of 11 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 Iodine with other atoms in the I binding site number 6 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:I409 b:23.2 occ:0.29 N A:ALA61 3.3 11.0 1.0 O A:HOH642 3.4 23.5 1.0 OE1 A:GLN31 3.6 30.3 0.6 CA A:HIS60 3.8 10.4 1.0 N A:PRO54 3.8 12.8 1.0 CB A:HIS60 3.9 10.6 1.0 CD A:PRO54 3.9 13.3 1.0 C A:GLY53 4.0 16.7 1.0 CB A:ALA61 4.0 12.2 1.0 C A:HIS60 4.1 9.7 1.0 CB A:PRO54 4.1 12.6 1.0 CA A:PRO54 4.2 12.7 1.0 CA A:ALA61 4.3 12.5 1.0 CA A:GLY53 4.3 17.0 1.0 O A:GLY53 4.4 16.2 1.0 CD A:GLN31 4.5 31.2 0.6 CG A:PRO54 4.5 13.9 1.0 O A:HOH840 4.5 32.8 1.0 CB A:PRO51 4.6 14.8 1.0 N A:GLY53 4.6 17.1 1.0 O A:PRO51 4.7 14.6 1.0

Iodine binding site 7 out of 11 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 Iodine with other atoms in the I binding site number 7 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:I410 b:34.3 occ:0.27 O A:HOH585 3.4 16.6 1.0 CA A:ALA66 3.7 9.4 1.0 CB A:ALA66 3.9 10.2 1.0 N A:ALA66 4.2 8.5 1.0 I A:IOD405 4.5 34.1 0.3 O A:ARG65 4.5 9.5 1.0 CB A:ALA69 4.6 9.6 1.0 C A:ARG65 4.6 10.4 1.0 O A:HOH741 4.8 37.7 1.0 C A:ALA66 5.0 8.2 1.0

Iodine binding site 8 out of 11 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 Iodine with other atoms in the I binding site number 8 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:I403 b:24.2 occ:0.34 N B:ARG315 3.4 8.6 1.0 CB B:ARG315 3.7 10.1 1.0 CG B:ARG315 3.8 16.6 1.0 CG B:GLN313 3.9 14.3 1.0 CD B:PRO314 3.9 10.1 1.0 CB B:PRO314 4.0 10.6 1.0 N B:PRO314 4.0 7.0 1.0 CA B:ARG315 4.2 7.6 1.0 C B:PRO314 4.3 8.2 1.0 CA B:PRO314 4.3 8.2 1.0 CG B:PRO314 4.3 11.7 1.0 CD B:ARG315 4.4 26.0 1.0 CD B:GLN313 4.4 19.6 1.0 NE2 B:GLN313 4.5 24.9 1.0 C B:GLN313 4.7 8.8 1.0

Iodine binding site 9 out of 11 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 Iodine with other atoms in the I binding site number 9 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:I404 b:27.6 occ:0.26 N B:ALA61 3.3 12.2 1.0 O B:HOH602 3.3 19.6 1.0 N B:PRO54 3.9 16.7 1.0 CA B:HIS60 3.9 11.7 1.0 CB B:HIS60 3.9 12.5 1.0 C B:GLY53 3.9 22.1 1.0 CB B:ALA61 3.9 14.1 1.0 CD B:PRO54 4.0 18.1 1.0 C B:HIS60 4.1 11.4 1.0 NE2 B:GLN31 4.1 38.3 1.0 CA B:PRO54 4.2 15.6 1.0 CB B:PRO54 4.2 16.2 1.0 CA B:ALA61 4.2 12.1 1.0 O B:GLY53 4.3 23.1 1.0 CA B:GLY53 4.3 18.4 1.0 O B:HOH707 4.5 33.1 1.0 CB B:PRO51 4.5 12.1 1.0 CG B:PRO54 4.6 17.9 1.0 N B:GLY53 4.6 17.1 1.0 O B:PRO51 4.7 15.1 1.0

Iodine binding site 10 out of 11 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 Iodine with other atoms in the I binding site number 10 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:I405 b:34.1 occ:0.32 O B:HOH560 3.3 15.1 1.0 CA B:ALA66 3.7 9.6 1.0 O B:HOH632 3.9 25.9 1.0 CB B:ALA66 4.0 10.3 1.0 N B:ALA66 4.1 9.7 1.0 O B:ARG65 4.5 12.7 1.0 C B:ARG65 4.5 10.2 1.0 CB B:ALA69 4.6 15.0 1.0 O B:HOH800 4.8 39.0 1.0 C B:ALA66 5.0 10.9 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