Magnesium in PDB 7bnk: Crystal Structure of Parb From Myxococcus Xanthus Bound to Cdp and Monothiophosphate

The structure of Crystal Structure of Parb From Myxococcus Xanthus Bound to Cdp and Monothiophosphate, PDB code: 7bnk was solved by F.Altegoer, G.Bange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.28 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.243, 80.706, 143.38, 90, 90, 90
R / Rfree (%)	20.3 / 23.7

The binding sites of Magnesium atom in the Crystal Structure of Parb From Myxococcus Xanthus Bound to Cdp and Monothiophosphate (pdb code 7bnk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Parb From Myxococcus Xanthus Bound to Cdp and Monothiophosphate, PDB code: 7bnk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Parb From Myxococcus Xanthus Bound to Cdp and Monothiophosphate


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 Parb From Myxococcus Xanthus Bound to Cdp and Monothiophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:28.7 occ:1.00 O4P A:TS6403 1.9 34.5 0.7 OD1 A:ASN127 2.0 28.3 1.0 O3B A:CDP404 2.1 24.3 1.0 O2A A:CDP404 2.2 26.4 1.0 OE1 A:GLU126 2.2 29.6 1.0 OE2 A:GLU126 2.5 29.1 1.0 CD A:GLU126 2.7 35.7 1.0 CG A:ASN127 3.1 30.4 1.0 PA A:CDP404 3.2 26.2 1.0 PB A:CDP404 3.2 27.4 1.0 P A:TS6403 3.4 39.4 0.9 O3A A:CDP404 3.4 26.8 1.0 ND2 A:ASN127 3.5 30.9 1.0 NH2 A:ARG54 3.7 31.3 1.0 O2B A:CDP404 3.7 26.8 1.0 O5' A:CDP404 3.7 24.6 1.0 NH1 A:ARG130 3.8 25.1 1.0 O1P A:TS6403 4.0 32.3 0.7 CG A:GLU126 4.2 27.9 1.0 NH2 A:ARG95 4.2 27.2 1.0 O3P A:TS6403 4.3 31.9 0.7 S2P A:TS6403 4.3 54.7 0.6 CB A:ASN127 4.4 25.2 1.0 O1B A:CDP404 4.5 23.9 1.0 O1A A:CDP404 4.5 26.3 1.0 N A:GLY92 4.6 24.5 1.0 H4' A:CDP404 4.7 29.1 1.0 CA A:ASN127 4.7 24.9 1.0 O A:HOH513 4.8 25.1 1.0 CZ A:ARG130 4.8 26.7 1.0 N A:ASN127 4.8 24.5 1.0 CZ A:ARG54 4.9 33.5 1.0 C5' A:CDP404 4.9 26.4 1.0 NH2 A:ARG130 4.9 26.4 1.0 C A:GLU126 5.0 27.4 1.0 H5'2 A:CDP404 5.0 31.7 1.0 CB A:GLU126 5.0 24.9 1.0 O A:GLU126 5.0 24.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Parb From Myxococcus Xanthus Bound to Cdp and Monothiophosphate


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 Parb From Myxococcus Xanthus Bound to Cdp and Monothiophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:29.8 occ:1.00 O3P B:TS6403 2.0 30.8 0.9 OD1 B:ASN127 2.1 25.3 1.0 OE1 B:GLU126 2.1 27.7 1.0 O1B B:CDP404 2.2 22.2 1.0 O1A B:CDP404 2.3 24.3 1.0 OE2 B:GLU126 2.4 27.3 1.0 CD B:GLU126 2.6 31.8 1.0 CG B:ASN127 3.1 30.0 1.0 PB B:CDP404 3.2 24.1 1.0 PA B:CDP404 3.2 22.9 1.0 ND2 B:ASN127 3.5 28.9 1.0 P B:TS6403 3.5 31.9 0.9 O3A B:CDP404 3.5 27.2 1.0 O3B B:CDP404 3.6 29.0 1.0 NH2 B:ARG54 3.7 31.1 1.0 O5' B:CDP404 3.7 25.5 1.0 NH1 B:ARG130 3.8 21.5 1.0 O1P B:TS6403 4.0 33.9 0.8 CG B:GLU126 4.1 28.4 1.0 O4P B:TS6403 4.3 29.0 0.8 NH2 B:ARG95 4.3 24.9 1.0 CB B:ASN127 4.4 25.4 1.0 O2B B:CDP404 4.5 24.8 1.0 O2A B:CDP404 4.6 23.9 1.0 N B:GLY92 4.6 24.9 1.0 CA B:ASN127 4.7 23.4 1.0 H4' B:CDP404 4.8 28.7 1.0 N B:ASN127 4.8 23.0 1.0 O B:HOH525 4.8 24.2 1.0 S2P B:TS6403 4.8 41.6 0.5 CZ B:ARG130 4.9 28.2 1.0 CB B:GLU126 4.9 25.4 1.0 CZ B:ARG54 4.9 32.0 1.0 C B:GLU126 5.0 25.6 1.0 C5' B:CDP404 5.0 24.1 1.0

M.Osorio-Valeriano, F.Altegoer, C.K.Das, W.Steinchen, G.Panis, L.Connolley, G.Giacomelli, H.Feddersen, L.Corrales-Guerrero, P.Giammarinaro, J.Hanssmann, M.Bramkamp, P.H.Viollier, S.Murray, L.V.Schafer, G.Bange, M.Thanbichler. The Ctpase Activity of Parb Acts As A Timing Mechanism to Control the Dynamics and Function of Prokaryotic Dna Partition Complexes Mol.Cell 2021.
ISSN: ISSN 1097-2765