Iodine in PDB 4h2h: Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)

Protein crystallography data

The structure of Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine), PDB code: 4h2h was solved by M.W.Vetting, L.L.Morisco, S.R.Wasserman, S.Sojitra, 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) 25.68 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.035, 152.824, 113.027, 90.00, 105.20, 90.00
R / Rfree (%) 15.9 / 19.2

Other elements in 4h2h:

The structure of Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 8 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 61;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) (pdb code 4h2h). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 61 binding sites of Iodine where determined in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine), PDB code: 4h2h:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 61 in 4h2h

Go back to Iodine Binding Sites List in 4h2h
Iodine binding site 1 out of 61 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:44.8
occ:0.39
 O C:HOH549 2.9 26.9 1.0
N A:GLY185 3.1 26.4 1.0
N A:GLY187 3.4 26.2 1.0
CA A:GLY185 3.5 30.8 1.0
CA A:GLY187 3.6 26.2 1.0
C A:GLY185 3.9 30.8 1.0
CG C:GLU170 3.9 29.7 1.0
N A:THR186 4.0 25.8 1.0
CH2 A:TRP180 4.2 24.6 1.0
C A:ARG184 4.3 28.2 1.0
C A:THR186 4.5 27.9 1.0
CA A:ARG184 4.5 24.1 1.0
O A:GLY185 4.6 32.5 1.0
OE2 C:GLU170 4.6 35.8 1.0
C A:GLY187 4.7 25.7 1.0
CD C:GLU170 4.7 33.2 1.0
CZ3 A:TRP180 4.8 25.9 1.0
CB C:GLU170 4.9 21.2 1.0
CA A:THR186 4.9 26.3 1.0

Iodine binding site 2 out of 61 in 4h2h

Go back to Iodine Binding Sites List in 4h2h
Iodine binding site 2 out of 61 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:30.3
occ:0.24
 N A:ASN248 3.1 11.6 1.0
N A:LEU247 3.5 12.3 0.6
N A:LEU247 3.5 12.5 0.4
CB A:ASN248 3.6 12.7 1.0
O D:HOH746 3.7 27.9 1.0
CB A:SER246 3.7 14.9 1.0
O A:HOH747 3.7 49.0 1.0
CB A:LEU247 3.7 12.9 0.6
O A:HOH579 3.9 21.6 1.0
CB D:ALA284 3.9 9.7 1.0
CA A:ASN248 3.9 10.9 1.0
CA A:LEU247 3.9 12.8 0.6
CB A:LEU247 4.0 13.2 0.4
C A:LEU247 4.0 10.5 0.6
C A:LEU247 4.0 10.7 0.4
CA A:LEU247 4.0 12.6 0.4
OG A:SER246 4.0 16.2 1.0
O D:ALA284 4.2 14.2 1.0
CA D:ALA284 4.2 9.4 1.0
C A:SER246 4.3 14.5 1.0
CA A:SER246 4.4 12.2 1.0
C D:ALA284 4.7 11.9 1.0
CG A:LEU247 4.7 14.7 0.6
O B:HOH735 5.0 32.2 1.0
CG A:ASN248 5.0 16.6 1.0

Iodine binding site 3 out of 61 in 4h2h

Go back to Iodine Binding Sites List in 4h2h
Iodine binding site 3 out of 61 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:23.4
occ:0.54
 N A:ARG314 3.6 13.4 1.0
CD A:PRO313 3.8 17.8 1.0
CB A:ARG314 3.9 18.0 1.0
N A:PRO313 4.1 12.8 1.0
CG A:ARG314 4.1 26.9 1.0
CB A:PRO313 4.2 17.8 1.0
NH1 A:ARG314 4.2 47.7 1.0
CD A:ARG314 4.3 33.6 1.0
CG A:PRO313 4.3 19.1 1.0
CA A:ARG314 4.4 14.9 1.0
C A:PRO313 4.5 14.6 1.0
CA A:PRO313 4.5 13.3 1.0
CD2 A:LEU312 4.7 25.4 1.0
C A:LEU312 4.7 13.0 1.0
CB A:LEU312 4.9 16.6 1.0

Iodine binding site 4 out of 61 in 4h2h

Go back to Iodine Binding Sites List in 4h2h
Iodine binding site 4 out of 61 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:20.7
occ:0.38
 O A:HOH663 2.4 35.7 1.0
O A:HOH540 3.3 15.3 1.0
O A:HOH712 3.4 34.4 1.0
O A:HOH519 3.8 20.9 1.0
CA A:ARG268 3.9 8.2 1.0
CB A:ARG268 3.9 10.7 1.0
CG A:ARG268 4.0 11.2 1.0
O A:HOH638 4.1 28.9 1.0
CB A:ALA57 4.1 20.5 1.0
CB A:ALA59 4.1 13.7 1.0
CB A:TYR98 4.3 14.3 1.0
O A:HOH648 4.3 25.4 1.0
O A:HOH564 4.5 18.8 1.0
N A:ARG268 4.5 10.0 1.0
O A:HOH523 4.6 18.3 1.0
CD A:ARG268 4.6 14.1 1.0
O A:HOH536 4.6 17.8 1.0
CD1 A:TYR98 4.7 13.9 1.0
O A:GLU58 4.7 14.7 1.0
CG A:TYR98 4.8 13.4 1.0
O A:HOH585 4.8 24.1 1.0
N A:GLU58 5.0 17.2 1.0

Iodine binding site 5 out of 61 in 4h2h

Go back to Iodine Binding Sites List in 4h2h
Iodine binding site 5 out of 61 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I408

b:52.2
occ:0.31
 O A:HOH653 3.5 30.4 1.0
NE A:ARG88 3.8 40.4 1.0
CA A:ARG88 3.9 15.0 1.0
N A:ARG88 4.1 13.3 1.0
CD A:ARG88 4.1 33.1 1.0
CB A:ARG88 4.1 14.9 1.0
CG2 A:THR87 4.2 25.7 1.0
C A:THR87 4.4 15.3 1.0
O A:THR87 4.6 17.6 1.0
OG A:SER91 4.7 26.1 1.0
CG A:ARG88 4.8 24.8 1.0
CB A:THR87 4.8 21.5 1.0
CZ A:ARG88 4.9 39.8 1.0

Iodine binding site 6 out of 61 in 4h2h

Go back to Iodine Binding Sites List in 4h2h
Iodine binding site 6 out of 61 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I409

b:58.0
occ:0.34
 NZ A:LYS36 3.4 26.8 1.0
CB A:PRO357 3.8 30.3 1.0
O A:HOH758 3.8 50.0 1.0
CD1 A:ILE38 3.9 34.8 1.0
CD A:LYS36 4.0 18.8 1.0
CE A:LYS36 4.2 20.7 1.0
CG2 A:ILE44 4.5 29.4 1.0
CG A:PRO357 4.5 31.7 1.0
CG1 A:ILE38 4.6 27.0 1.0
CA A:PRO357 4.9 25.0 1.0

Iodine binding site 7 out of 61 in 4h2h

Go back to Iodine Binding Sites List in 4h2h
Iodine binding site 7 out of 61 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I410

b:69.2
occ:0.39
 N A:HIS329 3.4 25.0 1.0
CB A:HIS329 3.8 23.8 1.0
CD2 A:HIS329 3.8 26.6 1.0
CG A:HIS329 4.2 24.2 1.0
CB A:ALA332 4.2 37.1 1.0
CA A:HIS329 4.2 21.5 1.0
CA A:GLU328 4.3 33.8 1.0
C A:GLU328 4.3 32.5 1.0
O A:ALA327 4.5 43.0 1.0
O A:HIS329 4.5 28.3 1.0
CA A:ALA332 4.8 34.1 1.0
C A:HIS329 4.9 24.9 1.0

Iodine binding site 8 out of 61 in 4h2h

Go back to Iodine Binding Sites List in 4h2h
Iodine binding site 8 out of 61 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I411

b:31.1
occ:0.37
 O A:HOH641 3.3 39.6 1.0
CB A:GLU333 3.9 33.4 1.0
CG A:GLU333 4.0 39.6 1.0
CA A:GLU333 4.2 30.4 1.0
CD A:GLU333 4.6 48.0 1.0
OE1 A:GLU333 4.6 47.9 1.0
N A:GLU333 4.9 29.6 1.0

Iodine binding site 9 out of 61 in 4h2h

Go back to Iodine Binding Sites List in 4h2h
Iodine binding site 9 out of 61 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I404

b:46.8
occ:0.36
 O F:HOH566 2.9 26.9 1.0
N B:GLY185 3.2 30.2 1.0
N B:GLY187 3.4 27.7 1.0
CA B:GLY187 3.6 31.5 1.0
CA B:GLY185 3.6 35.6 1.0
C B:GLY185 3.9 36.8 1.0
CG F:GLU170 3.9 25.6 1.0
N B:THR186 4.1 30.3 1.0
CH2 B:TRP180 4.4 24.4 1.0
C B:ARG184 4.4 30.7 1.0
O B:GLY185 4.6 40.5 1.0
C B:THR186 4.6 29.9 1.0
OE2 F:GLU170 4.6 33.3 1.0
C B:GLY187 4.7 28.1 1.0
CA B:ARG184 4.7 24.3 1.0
CD F:GLU170 4.7 29.5 1.0
CZ3 B:TRP180 4.9 25.3 1.0
O B:HOH663 4.9 35.1 1.0
CB F:GLU170 4.9 21.6 1.0
CA B:THR186 5.0 28.7 1.0

Iodine binding site 10 out of 61 in 4h2h

Go back to Iodine Binding Sites List in 4h2h
Iodine binding site 10 out of 61 in the Crystal Structure of An Enolase (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine)


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 (Mandalate Racemase Subgroup, Target Efi-502101) From Pelagibaca Bermudensis HTCC2601, with Bound Mg and L-4-Hydroxyproline Betaine (Betonicine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I405

b:23.4
occ:0.55
 N B:ARG314 3.6 16.0 0.4
N B:ARG314 3.6 16.1 0.6
CB B:ARG314 3.9 19.7 0.4
CD B:PRO313 3.9 16.1 1.0
CB B:ARG314 3.9 17.6 0.6
CG B:ARG314 4.0 23.6 0.6
CG B:ARG314 4.0 25.5 0.4
N B:PRO313 4.1 13.1 1.0
CB B:PRO313 4.1 17.8 1.0
CA B:ARG314 4.3 17.1 0.4
CG B:PRO313 4.3 18.7 1.0
CA B:ARG314 4.4 16.7 0.6
CD B:ARG314 4.4 27.0 0.6
C B:PRO313 4.5 12.9 1.0
CA B:PRO313 4.5 13.1 1.0
CD2 B:LEU312 4.5 33.7 1.0
CD B:ARG314 4.6 27.6 0.4
NE B:ARG314 4.7 28.1 0.4
C B:LEU312 4.8 13.3 1.0
CB B:LEU312 5.0 14.5 1.0

Reference:

S.Zhao, R.Kumar, A.Sakai, M.W.Vetting, B.M.Wood, S.Brown, J.B.Bonanno, B.S.Hillerich, R.D.Seidel, P.C.Babbitt, S.C.Almo, J.V.Sweedler, J.A.Gerlt, J.E.Cronan, M.P.Jacobson. Discovery of New Enzymes and Metabolic Pathways By Using Structure and Genome Context. Nature V. 502 698 2013.
ISSN: ISSN 0028-0836
PubMed: 24056934
DOI: 10.1038/NATURE12576
Page generated: Sun Dec 13 19:33:02 2020

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