Magnesium in PDB 6grg: E. Coli Microcin Synthetase Mcbbcd Complex with Pro-MCCB17, Adp and Phosphate Bound

The structure of E. Coli Microcin Synthetase Mcbbcd Complex with Pro-MCCB17, Adp and Phosphate Bound, PDB code: 6grg was solved by D.Ghilarov, C.E.M.Stevenson, D.Y.Travin, J.Piskunova, M.Serebryakova, A.Maxwell, D.M.Lawson, K.Severinov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.76 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.640, 83.280, 86.790, 90.00, 91.43, 90.00
R / Rfree (%)	16.5 / 22.6

The structure of E. Coli Microcin Synthetase Mcbbcd Complex with Pro-MCCB17, Adp and Phosphate Bound also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the E. Coli Microcin Synthetase Mcbbcd Complex with Pro-MCCB17, Adp and Phosphate Bound (pdb code 6grg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the E. Coli Microcin Synthetase Mcbbcd Complex with Pro-MCCB17, Adp and Phosphate Bound, PDB code: 6grg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the E. Coli Microcin Synthetase Mcbbcd Complex with Pro-MCCB17, Adp and Phosphate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Microcin Synthetase Mcbbcd Complex with Pro-MCCB17, Adp and Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:45.0 occ:1.00 O D:HOH811 2.1 42.8 1.0 OE2 D:GLU261 2.2 40.9 1.0 O1 D:PO4703 2.2 36.9 1.0 O D:HOH804 2.2 50.6 1.0 O1B D:ADP702 2.2 42.2 1.0 O D:HOH803 2.2 42.2 1.0 CD D:GLU261 3.0 50.1 1.0 OE1 D:GLU261 3.2 52.3 1.0 PB D:ADP702 3.4 42.3 1.0 OE1 D:GLU170 3.4 50.2 1.0 P D:PO4703 3.5 38.4 1.0 O D:LEU245 3.8 43.2 1.0 O2B D:ADP702 3.9 45.4 1.0 NZ D:LYS257 3.9 44.6 1.0 O4 D:PO4703 3.9 36.7 1.0 NH2 D:ARG171 4.0 48.4 1.0 O D:HOH818 4.3 39.8 1.0 CD D:GLU170 4.3 46.4 1.0 O3B D:ADP702 4.3 37.4 1.0 OE2 D:GLU170 4.3 55.2 1.0 OE1 D:GLU167 4.4 44.9 1.0 O2 D:PO4703 4.4 47.8 1.0 CG D:GLU261 4.5 48.5 1.0 O3A D:ADP702 4.5 48.8 1.0 O3 D:PO4703 4.5 44.5 1.0 CE D:LYS257 4.8 46.3 1.0 MG D:MG706 4.8 42.9 1.0 MG D:MG705 4.9 39.8 1.0 C D:LEU245 5.0 44.1 1.0

Magnesium binding site 2 out of 3 in the E. Coli Microcin Synthetase Mcbbcd Complex with Pro-MCCB17, Adp and Phosphate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Microcin Synthetase Mcbbcd Complex with Pro-MCCB17, Adp and Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg705 b:39.8 occ:1.00 OE1 D:GLU167 2.2 44.9 1.0 O2B D:ADP702 2.2 45.4 1.0 O D:HOH813 2.2 37.8 1.0 O D:HOH822 2.2 39.8 1.0 O D:HOH817 2.2 38.7 1.0 O4 D:PO4703 2.2 36.7 1.0 CD D:GLU167 3.2 48.1 1.0 PB D:ADP702 3.3 42.3 1.0 O3B D:ADP702 3.5 37.4 1.0 OE2 D:GLU167 3.6 54.1 1.0 P D:PO4703 3.6 38.4 1.0 O D:CYS151 3.7 46.2 1.0 OE1 D:GLU60 3.8 44.1 1.0 O D:HOH854 3.8 44.5 1.0 NH2 D:ARG61 3.8 45.9 1.0 O D:HOH811 3.9 42.8 1.0 OE2 D:GLU60 4.1 56.6 1.0 O3 D:PO4703 4.2 44.5 1.0 O1 D:PO4703 4.2 36.9 1.0 O1B D:ADP702 4.2 42.2 1.0 O D:HOH844 4.3 42.6 1.0 CD D:GLU60 4.3 50.3 1.0 O3A D:ADP702 4.5 48.8 1.0 CG D:GLU167 4.5 45.7 1.0 C3' D:ADP702 4.7 36.3 1.0 O2 D:PO4703 4.7 47.8 1.0 MG D:MG704 4.9 45.0 1.0 C D:CYS151 4.9 50.0 1.0 OE1 D:GLU57 4.9 49.0 1.0 C5' D:ADP702 4.9 34.5 1.0 O3' D:ADP702 5.0 37.6 1.0 MG D:MG706 5.0 42.9 1.0

Magnesium binding site 3 out of 3 in the E. Coli Microcin Synthetase Mcbbcd Complex with Pro-MCCB17, Adp and Phosphate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Microcin Synthetase Mcbbcd Complex with Pro-MCCB17, Adp and Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg706 b:42.9 occ:1.00 O3B D:ADP702 2.1 37.4 1.0 O D:HOH809 2.1 33.0 1.0 O D:HOH818 2.1 39.8 1.0 OE1 D:GLU57 2.2 49.0 1.0 O3 D:PO4703 2.2 44.5 1.0 O D:HOH808 2.2 43.1 1.0 PB D:ADP702 3.3 42.3 1.0 P D:PO4703 3.3 38.4 1.0 CD D:GLU57 3.3 48.9 1.0 O1 D:PO4703 3.5 36.9 1.0 O1B D:ADP702 3.5 42.2 1.0 O D:HOH813 3.8 37.8 1.0 O2A D:ADP702 3.8 34.7 1.0 OE2 D:GLU57 3.9 44.5 1.0 O D:SER42 4.0 37.4 1.0 OE1 D:GLN264 4.0 46.6 1.0 O4 D:PO4703 4.0 36.7 1.0 OE2 D:GLU261 4.2 40.9 1.0 NE2 D:GLN264 4.3 44.1 1.0 O3A D:ADP702 4.3 48.8 1.0 O2B D:ADP702 4.4 45.4 1.0 O2 D:PO4703 4.5 47.8 1.0 CG D:GLU57 4.6 47.0 1.0 CD D:GLN264 4.6 42.9 1.0 C5' D:ADP702 4.6 34.5 1.0 PA D:ADP702 4.7 36.9 1.0 NH2 D:ARG61 4.8 45.9 1.0 MG D:MG704 4.8 45.0 1.0 MG D:MG705 5.0 39.8 1.0

D.Ghilarov, C.E.M.Stevenson, D.Y.Travin, J.Piskunova, M.Serebryakova, A.Maxwell, D.M.Lawson, K.Severinov. Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting A Ribosomally Synthesized Peptide Into A Dna Gyrase Poison. Mol. Cell V. 73 749 2019.
ISSN: ISSN 1097-4164
PubMed: 30661981
DOI: 10.1016/J.MOLCEL.2018.11.032