Magnesium in PDB 5jmv: Crystal Structure of MJKAE1-PFUPCC1 Complex

All present enzymatic activity of Crystal Structure of MJKAE1-PFUPCC1 Complex:
2.3.1.234; 2.7.11.1;

The structure of Crystal Structure of MJKAE1-PFUPCC1 Complex, PDB code: 5jmv was solved by L.Wan, F.Sicheri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.24 / 3.39
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	121.913, 121.913, 310.613, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.3

The binding sites of Magnesium atom in the Crystal Structure of MJKAE1-PFUPCC1 Complex (pdb code 5jmv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of MJKAE1-PFUPCC1 Complex, PDB code: 5jmv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of MJKAE1-PFUPCC1 Complex


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 MJKAE1-PFUPCC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:38.1 occ:1.00 OD1 A:ASP284 2.0 81.2 1.0 OH A:TYR127 2.2 57.0 1.0 NE2 A:HIS110 2.4 58.5 1.0 NE2 A:HIS106 2.5 67.0 1.0 CG A:ASP284 3.1 82.9 1.0 CE1 A:HIS110 3.2 66.6 1.0 CD2 A:HIS110 3.3 52.1 1.0 O2P A:AMP401 3.3 59.9 1.0 CE1 A:HIS106 3.4 55.4 1.0 CZ A:TYR127 3.4 51.5 1.0 CD2 A:HIS106 3.5 70.1 1.0 OD2 A:ASP284 3.6 83.0 1.0 OG A:SER129 3.7 80.5 1.0 CE1 A:TYR127 3.9 38.0 1.0 CB A:SER129 4.2 73.0 1.0 ND1 A:HIS110 4.3 60.0 1.0 CG A:HIS110 4.4 58.2 1.0 CB A:ASP284 4.4 78.0 1.0 N A:ASP284 4.5 51.6 1.0 ND1 A:HIS106 4.5 56.9 1.0 CA A:ASP284 4.5 58.3 1.0 P A:AMP401 4.5 87.2 1.0 CE2 A:TYR127 4.6 58.9 1.0 CG A:HIS106 4.6 60.2 1.0 O3P A:AMP401 4.8 92.9 1.0 CE A:MET288 4.9 53.5 1.0 ND2 A:ASN132 5.0 61.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of MJKAE1-PFUPCC1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of MJKAE1-PFUPCC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:36.4 occ:1.00 OD1 B:ASP284 2.1 80.0 1.0 OH B:TYR127 2.4 32.6 1.0 NE2 B:HIS110 2.6 68.5 1.0 NE2 B:HIS106 2.9 64.4 1.0 CG B:ASP284 3.1 78.8 1.0 CE1 B:HIS110 3.3 68.5 1.0 OG B:SER129 3.3 67.1 1.0 OD2 B:ASP284 3.5 75.9 1.0 CZ B:TYR127 3.5 42.1 1.0 CD2 B:HIS110 3.6 62.9 1.0 O2P B:AMP401 3.6 78.1 1.0 CE1 B:TYR127 3.7 44.9 1.0 CB B:SER129 3.7 63.9 1.0 CE1 B:HIS106 3.8 55.9 1.0 O3P B:AMP401 3.9 98.3 1.0 CD2 B:HIS106 3.9 63.5 1.0 P B:AMP401 4.1 95.5 1.0 N B:ASP284 4.3 56.0 1.0 ND1 B:HIS110 4.4 62.2 1.0 CB B:ASP284 4.4 74.9 1.0 CA B:ASP284 4.5 62.0 1.0 CG B:HIS110 4.6 55.2 1.0 O1P B:AMP401 4.6 92.2 1.0 CE2 B:TYR127 4.7 43.8 1.0 CA B:SER129 4.9 65.0 1.0 C B:GLY283 5.0 62.8 1.0 ND1 B:HIS106 5.0 53.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of MJKAE1-PFUPCC1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of MJKAE1-PFUPCC1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:18.5 occ:1.00 OD1 C:ASP284 2.2 92.1 1.0 NE2 C:HIS106 2.4 61.2 1.0 NE2 C:HIS110 2.4 46.5 1.0 OH C:TYR127 2.5 54.4 1.0 CE1 C:HIS106 3.3 58.4 1.0 CG C:ASP284 3.3 86.0 1.0 CE1 C:HIS110 3.3 53.6 1.0 CD2 C:HIS110 3.3 46.2 1.0 OG C:SER129 3.4 81.7 1.0 CD2 C:HIS106 3.4 67.9 1.0 CZ C:TYR127 3.6 60.9 1.0 O2P C:AMP401 3.7 57.6 1.0 OD2 C:ASP284 3.7 99.2 1.0 CE1 C:TYR127 4.0 61.7 1.0 CB C:SER129 4.0 61.5 1.0 P C:AMP401 4.3 71.0 1.0 O1P C:AMP401 4.3 78.0 1.0 ND1 C:HIS110 4.3 49.4 1.0 CG C:HIS110 4.4 48.2 1.0 ND1 C:HIS106 4.4 61.2 1.0 CG C:HIS106 4.5 67.6 1.0 CB C:ASP284 4.5 61.5 1.0 O3P C:AMP401 4.7 66.7 1.0 N C:ASP284 4.7 57.2 1.0 CA C:ASP284 4.7 51.5 1.0 CE2 C:TYR127 4.8 52.8 1.0 CE C:MET288 4.9 80.5 1.0 ND2 C:ASN132 5.0 0.5 1.0

L.C.Wan, M.C.Pillon, N.Thevakumaran, Y.Sun, A.Chakrabartty, A.Guarne, I.Kurinov, D.Durocher, F.Sicheri. Structural and Functional Characterization of Keops Dimerization By PCC1 and Its Role in T6A Biosynthesis. Nucleic Acids Res. V. 44 6971 2016.
ISSN: ESSN 1362-4962
PubMed: 27302132
DOI: 10.1093/NAR/GKW542