Iron in PDB 8u5a: Improving Protein Expression, Stability, and Function with Proteinmpnn

The structure of Improving Protein Expression, Stability, and Function with Proteinmpnn, PDB code: 8u5a was solved by I.Kalvet, A.K.Bera, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.64 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.589, 41.669, 128.439, 90, 95.13, 90
R / Rfree (%)	22.8 / 26.1

The binding sites of Iron atom in the Improving Protein Expression, Stability, and Function with Proteinmpnn (pdb code 8u5a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Improving Protein Expression, Stability, and Function with Proteinmpnn, PDB code: 8u5a:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Improving Protein Expression, Stability, and Function with Proteinmpnn


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Improving Protein Expression, Stability, and Function with Proteinmpnn within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:26.9 occ:0.94 FE A:HEM201 0.0 26.9 0.9 NC A:HEM201 2.1 27.4 0.9 NB A:HEM201 2.1 24.2 0.9 ND A:HEM201 2.1 28.8 0.9 NA A:HEM201 2.1 27.8 0.9 O A:HOH309 2.1 23.6 1.0 NE2 A:HIS94 2.6 27.4 1.0 C4C A:HEM201 3.0 29.7 0.9 C1C A:HEM201 3.0 29.4 0.9 C4B A:HEM201 3.1 27.5 0.9 C1D A:HEM201 3.1 32.5 0.9 C4D A:HEM201 3.1 27.7 0.9 C1B A:HEM201 3.1 25.8 0.9 C4A A:HEM201 3.1 29.7 0.9 C1A A:HEM201 3.1 30.7 0.9 CD2 A:HIS94 3.3 23.7 1.0 CHD A:HEM201 3.4 28.8 0.9 CHC A:HEM201 3.4 24.6 0.9 CHB A:HEM201 3.5 23.3 0.9 CHA A:HEM201 3.5 29.3 0.9 CE1 A:HIS94 3.7 32.9 1.0 NE2 A:HIS62 4.1 30.9 1.0 C3C A:HEM201 4.2 30.2 0.9 C2C A:HEM201 4.2 25.8 0.9 C2D A:HEM201 4.3 30.6 0.9 C3D A:HEM201 4.3 37.0 0.9 C3B A:HEM201 4.3 23.2 0.9 C2B A:HEM201 4.3 25.7 0.9 C3A A:HEM201 4.3 32.8 0.9 C2A A:HEM201 4.3 32.1 0.9 CG A:HIS94 4.5 32.7 1.0 CE1 A:HIS62 4.6 30.1 1.0 ND1 A:HIS94 4.7 28.9 1.0 CG2 A:VAL66 4.8 26.4 1.0 CD2 A:HIS98 5.0 34.9 1.0

Iron binding site 2 out of 2 in the Improving Protein Expression, Stability, and Function with Proteinmpnn


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Improving Protein Expression, Stability, and Function with Proteinmpnn within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:40.9 occ:1.00 FE B:HEM201 0.0 40.9 1.0 NE2 B:HIS94 2.0 41.8 1.0 NA B:HEM201 2.0 42.0 1.0 ND B:HEM201 2.0 45.2 1.0 NB B:HEM201 2.1 38.6 1.0 NC B:HEM201 2.1 38.3 1.0 CE1 B:HIS94 2.6 41.4 1.0 O B:HOH312 2.8 50.9 1.0 C4C B:HEM201 3.0 48.7 1.0 C4A B:HEM201 3.1 47.5 1.0 C1A B:HEM201 3.1 49.8 1.0 C4D B:HEM201 3.1 47.3 1.0 C1C B:HEM201 3.1 42.9 1.0 C1D B:HEM201 3.1 44.3 1.0 C1B B:HEM201 3.1 40.6 1.0 C4B B:HEM201 3.1 38.6 1.0 CD2 B:HIS94 3.3 47.3 1.0 CHD B:HEM201 3.4 46.1 1.0 CHB B:HEM201 3.4 45.0 1.0 CHA B:HEM201 3.4 45.1 1.0 CHC B:HEM201 3.5 42.1 1.0 ND1 B:HIS94 3.9 41.5 1.0 CE1 B:HIS62 4.1 48.2 1.0 CG B:HIS94 4.2 40.7 1.0 C3C B:HEM201 4.3 48.8 1.0 C2C B:HEM201 4.3 46.4 1.0 C3A B:HEM201 4.3 47.5 1.0 C3D B:HEM201 4.3 49.6 1.0 C2A B:HEM201 4.3 46.0 1.0 C2D B:HEM201 4.3 47.3 1.0 C2B B:HEM201 4.3 44.4 1.0 C3B B:HEM201 4.3 41.0 1.0 NE2 B:HIS62 4.3 45.2 1.0 CG2 B:VAL66 4.6 41.0 1.0 ND1 B:HIS98 4.9 50.3 1.0

K.H.Sumida, R.Nunez-Franco, I.Kalvet, S.J.Pellock, B.I.M.Wicky, L.F.Milles, J.Dauparas, J.Wang, Y.Kipnis, N.Jameson, A.Kang, J.De La Cruz, B.Sankaran, A.K.Bera, G.Jimenez-Oses, D.Baker. Improving Protein Expression, Stability, and Function with Proteinmpnn. J.Am.Chem.Soc. 2024.
ISSN: ESSN 1520-5126
PubMed: 38194293
DOI: 10.1021/JACS.3C10941