Magnesium in PDB 7w50: Crystal Structure of Fragmin Domain-1 in Complex with Actin (Adp-Pi- Form)

The structure of Crystal Structure of Fragmin Domain-1 in Complex with Actin (Adp-Pi- Form), PDB code: 7w50 was solved by S.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.62 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.21, 91.06, 115.02, 90, 90, 90
R / Rfree (%)	14.2 / 16.2

The structure of Crystal Structure of Fragmin Domain-1 in Complex with Actin (Adp-Pi- Form) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Fragmin Domain-1 in Complex with Actin (Adp-Pi- Form) (pdb code 7w50). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Fragmin Domain-1 in Complex with Actin (Adp-Pi- Form), PDB code: 7w50:

Magnesium binding site 1 out of 1 in the Crystal Structure of Fragmin Domain-1 in Complex with Actin (Adp-Pi- Form)


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 Fragmin Domain-1 in Complex with Actin (Adp-Pi- Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:9.9 occ:1.00 O2B A:ADP401 2.0 11.9 1.0 O A:HOH583 2.1 11.2 1.0 O A:HOH650 2.1 10.0 1.0 O A:HOH609 2.1 10.3 1.0 O A:HOH551 2.1 10.0 1.0 O4 A:PO4402 2.1 12.5 1.0 PB A:ADP401 3.3 11.7 1.0 P A:PO4402 3.6 12.6 1.0 O1B A:ADP401 3.6 13.0 1.0 O A:HOH533 3.7 10.7 1.0 O2 A:PO4402 3.9 13.6 1.0 O A:HOH607 4.0 11.8 1.0 O3A A:ADP401 4.0 11.4 1.0 O1A A:ADP401 4.1 10.4 1.0 CA A:GLY13 4.2 11.8 1.0 NZ A:LYS18 4.3 11.9 1.0 OE1 A:GLN137 4.3 12.6 1.0 OD2 A:ASP11 4.3 10.2 1.0 OD1 A:ASP11 4.3 10.6 1.0 OD2 A:ASP154 4.4 11.8 1.0 O3 A:PO4402 4.4 12.3 1.0 O1 A:PO4402 4.5 12.2 1.0 O A:HOH577 4.5 14.1 1.0 O3B A:ADP401 4.5 11.6 1.0 CA A:GLY156 4.5 10.3 1.0 CD A:GLN137 4.5 11.6 1.0 PA A:ADP401 4.6 10.2 1.0 NE2 A:GLN137 4.7 11.8 1.0 CG A:ASP11 4.8 9.6 1.0 O A:HOH541 5.0 11.8 1.0

Y.Kanematsu, A.Narita, T.Oda, R.Koike, M.Ota, Y.Takano, K.Moritsugu, I.Fujiwara, K.Tanaka, H.Komatsu, T.Nagae, N.Watanabe, M.Iwasa, Y.Maeda, S.Takeda. Structures and Mechanisms of Actin Atp Hydrolysis. Proc.Natl.Acad.Sci.Usa V. 119 41119 2022.
ISSN: ESSN 1091-6490
PubMed: 36252034
DOI: 10.1073/PNAS.2122641119