Iodine in PDB 7ccy: Crystal Structure of the 2-Iodoporphobilinogen-Bound Holo Form of Human Hydroxymethylbilane Synthase

Enzymatic activity of Crystal Structure of the 2-Iodoporphobilinogen-Bound Holo Form of Human Hydroxymethylbilane Synthase

All present enzymatic activity of Crystal Structure of the 2-Iodoporphobilinogen-Bound Holo Form of Human Hydroxymethylbilane Synthase:
2.5.1.61;

Protein crystallography data

The structure of Crystal Structure of the 2-Iodoporphobilinogen-Bound Holo Form of Human Hydroxymethylbilane Synthase, PDB code: 7ccy was solved by H.Sato, M.Sugishima, K.Wada, K.Hirabayashi, M.Tsukaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.91 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.011, 81.237, 109.097, 90, 90, 90
R / Rfree (%) 20.2 / 27.3

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the 2-Iodoporphobilinogen-Bound Holo Form of Human Hydroxymethylbilane Synthase (pdb code 7ccy). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total only one binding site of Iodine was determined in the Crystal Structure of the 2-Iodoporphobilinogen-Bound Holo Form of Human Hydroxymethylbilane Synthase, PDB code: 7ccy:

Iodine binding site 1 out of 1 in 7ccy

Go back to Iodine Binding Sites List in 7ccy
Iodine binding site 1 out of 1 in the Crystal Structure of the 2-Iodoporphobilinogen-Bound Holo Form of Human Hydroxymethylbilane Synthase


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 the 2-Iodoporphobilinogen-Bound Holo Form of Human Hydroxymethylbilane Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I401

b:49.5
occ:0.76
 I4A C:FWL401 0.0 49.5 0.8
C4A C:FWL401 2.2 43.3 0.8
NA C:FWL401 3.1 37.7 0.8
CD1 C:PHE77 3.2 72.1 1.0
C3A C:FWL401 3.2 37.6 0.8
CE1 C:PHE77 3.5 71.8 1.0
CG C:PHE77 3.7 73.5 1.0
C7A C:FWL401 3.7 37.9 0.8
C8A C:FWL401 3.9 40.3 0.8
OD2 C:ASP99 3.9 31.3 1.0
OD1 C:ASP99 4.1 34.1 1.0
CG C:ASP99 4.1 33.8 1.0
CZ C:PHE77 4.2 70.7 1.0
CB C:PHE77 4.2 72.0 1.0
C1A C:FWL401 4.3 37.5 0.8
CD2 C:PHE77 4.4 74.0 1.0
C2A C:FWL401 4.4 40.0 0.8
CZ C:ARG26 4.6 57.1 1.0
CE2 C:PHE77 4.6 74.3 1.0
CHB C:DPM402 4.6 33.5 1.0
NH2 C:ARG26 4.6 57.0 1.0
CD1 C:LEU68 4.7 62.5 1.0
NH1 C:ARG26 4.8 51.0 1.0
NE C:ARG26 4.9 55.6 1.0
NB C:DPM402 4.9 34.4 1.0
C9A C:FWL401 4.9 43.5 0.8

Reference:

H.Sato, M.Sugishima, M.Tsukaguchi, T.Masuko, M.Iijima, M.Takano, Y.Omata, K.Hirabayashi, K.Wada, Y.Hisaeda, K.Yamamoto. Crystal Structures of Hydroxymethylbilane Synthase Complexed with A Substrate Analog: A Single Substrate-Binding Site For Four Consecutive Condensation Steps. Biochem.J. V. 478 1023 2021.
ISSN: ESSN 1470-8728
PubMed: 33600566
DOI: 10.1042/BCJ20200996
Page generated: Sat Apr 3 16:03:05 2021

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