Magnesium in PDB 5mqj: Crystal Structure of Dck Mutant C3S

All present enzymatic activity of Crystal Structure of Dck Mutant C3S:
2.7.1.74;

The structure of Crystal Structure of Dck Mutant C3S, PDB code: 5mqj was solved by M.Saez-Ayala, E.Rebuffet, K.Hammam, L.Gros, S.Lopez, B.Hajem, M.Humbert, E.Baudelet, S.Audebert, S.Betzi, A.Lugari, S.Combes, D.Pez, S.Letard, C.Mansfield, A.Moussy, P.De Sepulveda, X.Morelli, P.Dubreuil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.06 / 3.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.695, 92.695, 338.083, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 25.1

The binding sites of Magnesium atom in the Crystal Structure of Dck Mutant C3S (pdb code 5mqj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Dck Mutant C3S, PDB code: 5mqj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Dck Mutant C3S


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 Dck Mutant C3S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:64.7 occ:1.00 OP1 A:UMP302 2.0 0.8 1.0 P A:UMP302 3.3 0.6 1.0 OE2 A:GLU127 3.3 0.3 1.0 O5' A:UMP302 3.4 0.1 1.0 O2B A:UDP301 3.4 0.6 1.0 NH1 A:ARG192 3.6 0.7 1.0 O1B A:UDP301 3.6 0.7 1.0 OE1 A:GLU53 3.9 0.2 1.0 OP3 A:UMP302 4.1 1.0 1.0 NH2 A:ARG194 4.1 0.5 1.0 PB A:UDP301 4.2 0.7 1.0 NH1 A:ARG194 4.2 0.1 1.0 CD A:GLU127 4.3 0.6 1.0 OP2 A:UMP302 4.4 0.5 1.0 C5' A:UMP302 4.5 0.7 1.0 O1A A:UDP301 4.5 0.7 1.0 OG A:SER35 4.6 0.5 1.0 CG A:GLU53 4.6 0.9 1.0 CZ A:ARG192 4.6 0.1 1.0 CZ A:ARG194 4.7 0.9 1.0 CD A:GLU53 4.7 0.9 1.0 CG1 A:VAL55 4.9 0.7 1.0 NH2 A:ARG192 4.9 0.9 1.0 OE1 A:GLU127 4.9 0.3 1.0 NZ A:LYS34 4.9 89.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Dck Mutant C3S


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 Dck Mutant C3S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:55.8 occ:1.00 OP2 B:UMP302 1.9 0.1 1.0 OE2 B:GLU127 2.8 0.3 1.0 OE1 B:GLU53 2.9 0.3 1.0 O2B B:UDP301 3.3 0.2 1.0 P B:UMP302 3.3 0.1 1.0 OG B:SER35 3.4 1.0 1.0 O3B B:UDP301 3.6 0.8 1.0 NH2 B:ARG194 3.6 0.9 1.0 O5' B:UMP302 3.8 0.9 1.0 CD B:GLU127 3.8 0.3 1.0 CD B:GLU53 3.9 0.1 1.0 C5' B:UMP302 3.9 0.1 1.0 CG1 B:VAL55 4.0 0.2 1.0 OP3 B:UMP302 4.1 0.3 1.0 PB B:UDP301 4.1 0.2 1.0 OE1 B:GLU127 4.2 0.3 1.0 NH2 B:ARG192 4.2 0.4 1.0 CG B:GLU53 4.2 0.1 1.0 OP1 B:UMP302 4.4 0.3 1.0 O2A B:UDP301 4.5 0.4 1.0 CZ B:ARG194 4.5 0.6 1.0 NH1 B:ARG194 4.6 0.2 1.0 CB B:SER35 4.6 0.9 1.0 CB B:VAL55 4.6 0.4 1.0 CG2 B:VAL55 4.9 0.6 1.0 NZ B:LYS34 4.9 85.4 1.0 OE2 B:GLU53 5.0 0.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Dck Mutant C3S


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 Dck Mutant C3S within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:91.6 occ:1.00 OP2 C:UMP302 2.2 0.3 1.0 OE2 C:GLU127 2.8 0.2 1.0 NH1 C:ARG192 3.2 0.9 1.0 O5' C:UMP302 3.3 0.8 1.0 P C:UMP302 3.4 0.1 1.0 OG C:SER35 3.4 0.3 1.0 OE1 C:GLU53 3.6 0.3 1.0 CG1 C:VAL55 3.8 0.9 1.0 O3B C:UDP301 4.0 0.3 1.0 CD C:GLU127 4.0 0.2 1.0 O2B C:UDP301 4.2 1.0 1.0 OP3 C:UMP302 4.2 0.2 1.0 C5' C:UMP302 4.3 0.5 1.0 OE1 C:GLU127 4.4 0.7 1.0 CB C:GLU53 4.4 0.9 1.0 NH2 C:ARG194 4.5 56.2 0.5 OP1 C:UMP302 4.5 0.3 1.0 CZ C:ARG192 4.5 0.5 1.0 NH1 C:ARG194 4.5 54.7 0.5 CB C:VAL55 4.6 0.9 1.0 O2A C:UDP301 4.7 0.8 1.0 CD C:GLU53 4.7 0.5 1.0 CB C:SER35 4.7 0.6 1.0 PB C:UDP301 4.8 0.6 1.0 CZ C:ARG194 5.0 73.3 0.5

Magnesium binding site 4 out of 4 in the Crystal Structure of Dck Mutant C3S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Dck Mutant C3S within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg303 b:66.5 occ:1.00 OP2 D:UMP302 2.0 0.7 1.0 O1B D:UDP301 3.0 0.1 1.0 P D:UMP302 3.2 0.3 1.0 NH2 D:ARG194 3.4 0.1 1.0 OE1 D:GLU53 3.5 0.2 1.0 OP1 D:UMP302 3.6 0.8 1.0 OE1 D:GLU127 3.7 0.5 1.0 CB D:GLU53 3.9 0.1 1.0 OG D:SER35 3.9 0.4 1.0 NH1 D:ARG192 3.9 0.8 1.0 O5' D:UMP302 4.0 0.5 1.0 C5' D:UMP302 4.0 0.1 1.0 CD D:GLU53 4.1 0.5 1.0 CG1 D:VAL55 4.2 0.1 1.0 CG D:GLU53 4.2 0.1 1.0 NH1 D:ARG194 4.2 0.8 1.0 CZ D:ARG194 4.3 0.9 1.0 OE2 D:GLU127 4.4 0.3 1.0 CD D:GLU127 4.4 0.8 1.0 OP3 D:UMP302 4.4 0.9 1.0 PB D:UDP301 4.4 1.0 1.0 CB D:VAL55 4.7 0.1 1.0 CZ D:ARG192 4.9 0.9 1.0 CG2 D:VAL55 5.0 0.7 1.0

K.Hammam, M.Saez-Ayala, E.Rebuffet, L.Gros, S.Lopez, B.Hajem, M.Humbert, E.Baudelet, S.Audebert, S.Betzi, A.Lugari, S.Combes, S.Letard, N.Casteran, C.Mansfield, A.Moussy, P.De Sepulveda, X.Morelli, P.Dubreuil. Dual Protein Kinase and Nucleoside Kinase Modulators For Rationally Designed Polypharmacology. Nat Commun V. 8 1420 2017.
ISSN: ESSN 2041-1723
PubMed: 29127277
DOI: 10.1038/S41467-017-01582-5