Magnesium in PDB 7uk7: Yjfc From Escherichia Coli K-12 in Complex with Adp, MG2+ and SO4

The structure of Yjfc From Escherichia Coli K-12 in Complex with Adp, MG2+ and SO4, PDB code: 7uk7 was solved by J.L.Pederick, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.99 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.01, 68.885, 114.309, 90, 90, 90
R / Rfree (%)	15.8 / 19.2

The binding sites of Magnesium atom in the Yjfc From Escherichia Coli K-12 in Complex with Adp, MG2+ and SO4 (pdb code 7uk7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Yjfc From Escherichia Coli K-12 in Complex with Adp, MG2+ and SO4, PDB code: 7uk7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Yjfc From Escherichia Coli K-12 in Complex with Adp, MG2+ and SO4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yjfc From Escherichia Coli K-12 in Complex with Adp, MG2+ and SO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:19.4 occ:0.95 O1 A:SO4405 2.0 18.9 0.9 O2B A:ADP401 2.0 21.7 1.0 O A:HOH565 2.0 19.5 1.0 OD1 A:ASN118 2.1 21.3 1.0 OE1 A:GLU116 2.1 19.2 1.0 OE2 A:GLU116 2.3 20.1 1.0 CD A:GLU116 2.5 20.9 1.0 CG A:ASN118 3.1 21.9 1.0 PB A:ADP401 3.2 19.3 1.0 S A:SO4405 3.2 23.7 0.9 O3B A:ADP401 3.3 21.2 1.0 O3 A:SO4405 3.5 17.9 0.9 ND2 A:ASN118 3.6 19.8 1.0 MG A:MG403 3.7 18.8 0.9 NZ A:LYS265 3.9 17.6 1.0 O3A A:ADP401 4.0 20.7 1.0 O4 A:SO4405 4.0 21.0 0.9 CG A:GLU116 4.0 19.4 1.0 O A:HOH759 4.1 37.5 1.0 CA A:ARG307 4.1 22.6 1.0 O A:SER306 4.2 21.6 1.0 O A:HOH784 4.2 24.6 1.0 O2 A:SO4405 4.3 19.9 0.9 O A:HOH635 4.4 21.9 1.0 O1B A:ADP401 4.4 21.5 1.0 CB A:ASN118 4.4 17.9 1.0 CB A:ARG307 4.5 19.6 1.0 OD2 A:ASP103 4.6 19.3 1.0 O2A A:ADP401 4.6 19.3 1.0 CE A:LYS265 4.6 25.9 1.0 N A:GLU308 4.6 20.9 1.0 PA A:ADP401 4.9 20.5 1.0 CB A:GLU116 4.9 19.8 1.0 C A:ARG307 4.9 22.8 1.0 CA A:ASN118 5.0 17.6 1.0 C A:SER306 5.0 22.3 1.0

Magnesium binding site 2 out of 2 in the Yjfc From Escherichia Coli K-12 in Complex with Adp, MG2+ and SO4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yjfc From Escherichia Coli K-12 in Complex with Adp, MG2+ and SO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:18.8 occ:0.90 OD2 A:ASP103 2.0 19.3 1.0 O2A A:ADP401 2.0 19.3 1.0 O3 A:SO4405 2.1 17.9 0.9 O A:HOH700 2.1 20.6 1.0 OE1 A:GLU116 2.1 19.2 1.0 O3B A:ADP401 2.2 21.2 1.0 CD A:GLU116 3.2 20.9 1.0 CG A:ASP103 3.2 20.7 1.0 PA A:ADP401 3.3 20.5 1.0 PB A:ADP401 3.3 19.3 1.0 S A:SO4405 3.3 23.7 0.9 O3A A:ADP401 3.6 20.7 1.0 CG A:GLU116 3.6 19.4 1.0 O A:HOH690 3.7 22.6 1.0 O1 A:SO4405 3.7 18.9 0.9 MG A:MG402 3.7 19.4 0.9 O2B A:ADP401 3.9 21.7 1.0 ND2 A:ASN118 3.9 19.8 1.0 CB A:ASP103 4.0 16.6 1.0 O2 A:SO4405 4.1 19.9 0.9 OD1 A:ASP103 4.1 19.9 1.0 C5' A:ADP401 4.2 16.7 1.0 NH2 A:ARG367 4.2 23.4 1.0 O5' A:ADP401 4.3 20.1 1.0 OE2 A:GLU116 4.3 20.1 1.0 O4 A:SO4405 4.3 21.0 0.9 O3' A:ADP401 4.4 16.5 1.0 O1A A:ADP401 4.5 22.6 1.0 OD1 A:ASN118 4.5 21.3 1.0 NH2 A:ARG101 4.5 21.4 1.0 O1B A:ADP401 4.6 21.5 1.0 CD2 A:LEU351 4.6 24.4 1.0 CG A:ASN118 4.7 21.9 1.0 C3' A:ADP401 4.8 16.7 1.0

J.L.Pederick, J.Klose, B.Jovcevski, T.L.Pukala, J.B.Bruning. Escherichia Coli Ygic and Yjfc Possess Peptide─Spermidine Ligase Activity. Biochemistry 2023.
ISSN: ISSN 0006-2960
PubMed: 36745518
DOI: 10.1021/ACS.BIOCHEM.2C00592