Manganese in PDB 4edk: The Structure of the S. Aureus Dnag Rna Polymerase Domain Bound to Gtp and Manganese

The structure of The Structure of the S. Aureus Dnag Rna Polymerase Domain Bound to Gtp and Manganese, PDB code: 4edk was solved by R.U.Rymer, F.A.Solorio, C.Chu, J.E.Corn, J.D.Wang, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.94 / 2.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	151.742, 151.742, 38.720, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 20

The binding sites of Manganese atom in the The Structure of the S. Aureus Dnag Rna Polymerase Domain Bound to Gtp and Manganese (pdb code 4edk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Structure of the S. Aureus Dnag Rna Polymerase Domain Bound to Gtp and Manganese, PDB code: 4edk:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the The Structure of the S. Aureus Dnag Rna Polymerase Domain Bound to Gtp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of the S. Aureus Dnag Rna Polymerase Domain Bound to Gtp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn505 b:26.3 occ:1.00 O A:HOH890 2.4 20.9 1.0 O A:HOH891 2.4 29.3 1.0 O A:HOH901 2.5 37.2 1.0 O A:HOH899 2.5 36.9 1.0 O A:HOH903 2.6 37.8 1.0 O A:HOH892 2.6 48.1 1.0 OD2 A:ASP312 3.5 38.9 1.0 OE2 A:GLU266 3.8 31.1 1.0 OD2 A:ASP310 3.9 22.0 1.0 OD1 A:ASP312 3.9 33.0 1.0 O A:HOH907 4.1 43.0 1.0 CG A:ASP312 4.1 36.5 1.0 O A:HOH756 4.1 40.1 1.0 O1A A:GTP504 4.2 26.4 1.0 OE1 A:GLU266 4.3 25.3 1.0 CB A:ALA314 4.4 23.6 1.0 CD A:GLU266 4.5 30.4 1.0 CB A:ASP310 4.5 16.8 1.0 CG A:ASP310 4.5 27.1 1.0 O A:HOH682 4.6 44.8 1.0 N1 A:BEN503 4.6 56.6 1.0 O A:HOH837 4.7 61.0 1.0

Manganese binding site 2 out of 3 in the The Structure of the S. Aureus Dnag Rna Polymerase Domain Bound to Gtp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of the S. Aureus Dnag Rna Polymerase Domain Bound to Gtp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn506 b:26.3 occ:1.00 O A:HOH894 2.2 15.4 1.0 O1A A:GTP504 2.3 26.4 1.0 O2B A:GTP504 2.3 23.0 1.0 OD2 A:ASP343 2.3 22.9 1.0 OD2 A:ASP310 2.4 22.0 1.0 O A:HOH836 2.5 26.2 1.0 CG A:ASP310 3.2 27.1 1.0 PB A:GTP504 3.3 26.0 1.0 CG A:ASP343 3.3 30.0 1.0 PA A:GTP504 3.4 26.3 1.0 OD1 A:ASP310 3.5 23.2 1.0 O3A A:GTP504 3.5 25.2 1.0 MN A:MN507 3.5 26.2 1.0 CB A:ASP343 3.6 21.4 1.0 O A:HOH891 3.8 29.3 1.0 O A:HOH756 3.9 40.1 1.0 O1B A:GTP504 4.0 29.2 1.0 O A:HOH899 4.0 36.9 1.0 O A:HOH657 4.1 23.7 1.0 OD2 A:ASP270 4.1 29.6 1.0 O A:HOH650 4.2 30.3 1.0 O2A A:GTP504 4.3 27.4 1.0 O A:HOH647 4.3 21.9 1.0 OD1 A:ASP343 4.5 32.9 1.0 CB A:ASP310 4.6 16.8 1.0 O5' A:GTP504 4.6 26.4 1.0 O3B A:GTP504 4.6 25.8 1.0 C5' A:GTP504 4.7 26.0 1.0 OD1 A:ASP270 4.8 27.4 1.0 CG A:ASP270 4.9 28.6 1.0

Manganese binding site 3 out of 3 in the The Structure of the S. Aureus Dnag Rna Polymerase Domain Bound to Gtp and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of the S. Aureus Dnag Rna Polymerase Domain Bound to Gtp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn507 b:26.2 occ:1.00 O2B A:GTP504 2.2 23.0 1.0 OD2 A:ASP343 2.3 22.9 1.0 O2G A:GTP504 2.3 20.7 1.0 O A:HOH893 2.4 24.4 1.0 O A:HOH647 2.4 21.9 1.0 O A:HOH657 2.4 23.7 1.0 CG A:ASP343 3.2 30.0 1.0 PB A:GTP504 3.3 26.0 1.0 OD1 A:ASP343 3.3 32.9 1.0 PG A:GTP504 3.5 26.9 1.0 MN A:MN506 3.5 26.3 1.0 O1B A:GTP504 3.5 29.2 1.0 O3B A:GTP504 3.9 25.8 1.0 O A:HOH836 3.9 26.2 1.0 NH2 A:ARG146 4.1 28.7 1.0 O A:HOH941 4.1 42.8 1.0 O A:HOH953 4.1 39.7 1.0 OD2 A:ASP345 4.1 38.2 1.0 O1G A:GTP504 4.2 25.9 1.0 OD1 A:ASP270 4.2 27.4 1.0 CB A:ASP345 4.4 34.2 1.0 OE2 A:GLU346 4.4 36.7 1.0 O A:HOH894 4.5 15.4 1.0 CD A:GLU346 4.5 37.0 1.0 CB A:ASP343 4.6 21.4 1.0 O3G A:GTP504 4.7 30.3 1.0 CG A:GLU346 4.7 34.5 1.0 O3A A:GTP504 4.7 25.2 1.0 O A:HOH817 4.8 35.9 1.0 CG A:ASP345 4.8 40.7 1.0 OD2 A:ASP270 5.0 29.6 1.0

R.U.Rymer, F.A.Solorio, A.K.Tehranchi, C.Chu, J.E.Corn, J.L.Keck, J.D.Wang, J.M.Berger. Binding Mechanism of Metal-Ntp Substrates and Stringent-Response Alarmones to Bacterial Dnag-Type Primases. Structure V. 20 1478 2012.
ISSN: ISSN 0969-2126
PubMed: 22795082
DOI: 10.1016/J.STR.2012.05.017