Magnesium in PDB 6hz9: Structure of Mcrbc Without Dna Binding Domains (Class 5)

The binding sites of Magnesium atom in the Structure of Mcrbc Without Dna Binding Domains (Class 5) (pdb code 6hz9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Mcrbc Without Dna Binding Domains (Class 5), PDB code: 6hz9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of Mcrbc Without Dna Binding Domains (Class 5)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Mcrbc Without Dna Binding Domains (Class 5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:0.8 occ:1.00 O3G A:GNP1001 2.0 0.5 1.0 O1B A:GNP1001 2.0 0.5 1.0 OG1 A:THR208 2.1 0.5 1.0 HH12 B:ARG349 2.5 0.6 1.0 N3B A:GNP1001 2.9 0.5 1.0 PG A:GNP1001 3.0 0.5 1.0 PB A:GNP1001 3.0 0.5 1.0 OD2 A:ASP279 3.0 1.0 1.0 NH1 B:ARG349 3.2 0.6 1.0 CB A:THR208 3.3 0.5 1.0 HB A:THR208 3.3 0.5 1.0 HH11 B:ARG349 3.4 0.6 1.0 HNB3 A:GNP1001 3.4 0.5 1.0 O1A A:GNP1001 3.5 0.5 1.0 HH11 B:ARG348 3.5 0.8 1.0 HG21 A:THR208 3.7 0.5 1.0 H A:THR208 3.8 0.5 1.0 O1G A:GNP1001 3.9 0.5 1.0 O2B A:GNP1001 4.0 0.5 1.0 O2G A:GNP1001 4.0 0.5 1.0 CG2 A:THR208 4.0 0.5 1.0 CG A:ASP279 4.0 1.0 1.0 NH1 B:ARG348 4.1 0.8 1.0 HH22 B:ARG349 4.1 0.6 1.0 HH12 B:ARG348 4.1 0.8 1.0 O3A A:GNP1001 4.1 0.5 1.0 PA A:GNP1001 4.3 0.5 1.0 CZ B:ARG349 4.3 0.6 1.0 OD1 A:ASP279 4.3 1.0 1.0 N A:THR208 4.4 0.5 1.0 HE2 B:LYS301 4.4 0.9 1.0 CA A:THR208 4.4 0.5 1.0 HB2 B:MET295 4.5 0.8 1.0 HG23 A:THR208 4.5 0.5 1.0 O2A A:GNP1001 4.5 0.5 1.0 NH2 B:ARG349 4.6 0.6 1.0 HB2 A:LYS207 4.6 0.6 1.0 HA A:THR208 4.7 0.5 1.0 OE1 A:GLU280 4.8 0.4 1.0 HE2 A:LYS207 4.8 0.6 1.0 HG22 A:THR208 4.8 0.5 1.0 HD13 A:LEU331 4.9 0.2 1.0

Magnesium binding site 2 out of 6 in the Structure of Mcrbc Without Dna Binding Domains (Class 5)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Mcrbc Without Dna Binding Domains (Class 5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:0.9 occ:1.00 O2B B:GNP1001 2.0 0.9 1.0 OG1 B:THR208 2.1 0.9 1.0 N3B B:GNP1001 2.1 0.9 1.0 HNB3 B:GNP1001 2.3 0.9 1.0 O3G B:GNP1001 2.3 0.9 1.0 PB B:GNP1001 2.5 0.9 1.0 O2A B:GNP1001 2.5 0.9 1.0 PG B:GNP1001 2.8 0.9 1.0 HH12 C:ARG349 3.0 0.5 1.0 HB B:THR208 3.2 0.9 1.0 CB B:THR208 3.2 0.9 1.0 HH11 C:ARG349 3.3 0.5 1.0 H B:THR208 3.4 0.9 1.0 HE2 C:LYS301 3.4 0.6 1.0 O3A B:GNP1001 3.4 0.9 1.0 NH1 C:ARG349 3.4 0.5 1.0 PA B:GNP1001 3.4 0.9 1.0 HH21 C:ARG348 3.5 0.7 1.0 O2G B:GNP1001 3.7 0.9 1.0 O1B B:GNP1001 3.7 0.9 1.0 HG21 B:THR208 3.9 0.9 1.0 O1G B:GNP1001 3.9 0.9 1.0 O1A B:GNP1001 3.9 0.9 1.0 N B:THR208 4.1 0.9 1.0 CG2 B:THR208 4.1 0.9 1.0 NH2 C:ARG348 4.1 0.7 1.0 HH22 C:ARG348 4.2 0.7 1.0 CA B:THR208 4.2 0.9 1.0 OD2 B:ASP279 4.3 0.3 1.0 HZ1 C:LYS301 4.3 0.6 1.0 CE C:LYS301 4.3 0.6 1.0 HB2 B:LYS207 4.3 0.7 1.0 HG23 B:THR208 4.5 0.9 1.0 CZ C:ARG349 4.6 0.5 1.0 HA B:THR208 4.7 0.9 1.0 HE3 C:LYS301 4.7 0.6 1.0 HE2 B:LYS207 4.7 0.7 1.0 HG3 C:MET295 4.7 1.0 1.0 H5'1 B:GNP1001 4.8 0.9 1.0 NZ C:LYS301 4.8 0.6 1.0 HB2 C:MET295 4.8 1.0 1.0 O5' B:GNP1001 4.9 0.9 1.0 H B:GLY204 4.9 0.8 1.0 HG22 B:THR208 4.9 0.9 1.0 HH22 C:ARG349 4.9 0.5 1.0 OD1 B:ASP279 4.9 0.3 1.0 HA C:MET295 5.0 1.0 1.0

Magnesium binding site 3 out of 6 in the Structure of Mcrbc Without Dna Binding Domains (Class 5)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Mcrbc Without Dna Binding Domains (Class 5) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:0.4 occ:1.00 O2B C:GNP1001 2.0 0.5 1.0 O3G C:GNP1001 2.0 0.5 1.0 O2A C:GNP1001 2.0 0.5 1.0 OG1 C:THR208 2.1 0.4 1.0 N3B C:GNP1001 2.7 0.5 1.0 PB C:GNP1001 2.7 0.5 1.0 PG C:GNP1001 2.8 0.5 1.0 PA C:GNP1001 3.0 0.5 1.0 H C:THR208 3.1 0.4 1.0 HB C:THR208 3.2 0.4 1.0 CB C:THR208 3.2 0.4 1.0 O3A C:GNP1001 3.3 0.5 1.0 HNB3 C:GNP1001 3.3 0.5 1.0 O1A C:GNP1001 3.4 0.5 1.0 HH21 D:ARG348 3.5 0.9 1.0 O1G C:GNP1001 3.6 0.5 1.0 HH22 D:ARG348 3.9 0.9 1.0 N C:THR208 3.9 0.4 1.0 NH2 D:ARG348 4.0 0.9 1.0 HG21 C:THR208 4.0 0.4 1.0 HZ1 D:LYS301 4.0 0.4 1.0 OD2 C:ASP279 4.0 0.2 1.0 O2G C:GNP1001 4.0 0.5 1.0 O1B C:GNP1001 4.1 0.5 1.0 HB2 C:LYS207 4.1 0.9 1.0 CG2 C:THR208 4.2 0.4 1.0 CA C:THR208 4.2 0.4 1.0 HH12 D:ARG349 4.2 0.1 1.0 HE2 D:LYS301 4.2 0.4 1.0 O5' C:GNP1001 4.4 0.5 1.0 HH11 D:ARG349 4.4 0.1 1.0 H5'1 C:GNP1001 4.4 0.5 1.0 NH1 D:ARG349 4.5 0.1 1.0 HG23 C:THR208 4.5 0.4 1.0 OD1 C:ASP279 4.5 0.2 1.0 HG2 D:MET295 4.6 0.9 1.0 HZ3 D:LYS301 4.6 0.4 1.0 HA C:THR208 4.7 0.4 1.0 NZ D:LYS301 4.7 0.4 1.0 HG3 D:MET295 4.7 0.9 1.0 H5'2 C:GNP1001 4.7 0.5 1.0 HE2 C:LYS207 4.7 0.9 1.0 CG C:ASP279 4.7 0.2 1.0 C5' C:GNP1001 4.8 0.5 1.0 H C:LYS207 4.8 0.9 1.0 H C:GLY204 4.9 0.1 1.0 HG22 C:THR208 5.0 0.4 1.0 CE D:LYS301 5.0 0.4 1.0

Magnesium binding site 4 out of 6 in the Structure of Mcrbc Without Dna Binding Domains (Class 5)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Mcrbc Without Dna Binding Domains (Class 5) within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg1002 b:0.7 occ:1.00 O3G G:GNP1001 2.0 0.1 1.0 O1B G:GNP1001 2.0 0.1 1.0 OG1 G:THR208 2.1 0.4 1.0 HH12 H:ARG349 2.6 0.7 1.0 N3B G:GNP1001 2.9 0.1 1.0 PG G:GNP1001 3.0 0.1 1.0 PB G:GNP1001 3.0 0.1 1.0 OD2 G:ASP279 3.0 0.9 1.0 CB G:THR208 3.3 0.4 1.0 NH1 H:ARG349 3.3 0.7 1.0 HB G:THR208 3.3 0.4 1.0 HH11 H:ARG349 3.4 0.7 1.0 HNB3 G:GNP1001 3.4 0.1 1.0 O1A G:GNP1001 3.5 0.1 1.0 HG21 G:THR208 3.7 0.4 1.0 H G:THR208 3.8 0.4 1.0 HH11 H:ARG348 3.9 0.2 1.0 O1G G:GNP1001 3.9 0.1 1.0 O2B G:GNP1001 4.0 0.1 1.0 O2G G:GNP1001 4.0 0.1 1.0 CG2 G:THR208 4.0 0.4 1.0 CG G:ASP279 4.0 0.9 1.0 O3A G:GNP1001 4.1 0.1 1.0 HB2 H:MET295 4.2 0.6 1.0 PA G:GNP1001 4.3 0.1 1.0 HH22 H:ARG349 4.3 0.7 1.0 OD1 G:ASP279 4.3 0.9 1.0 N G:THR208 4.4 0.4 1.0 CA G:THR208 4.4 0.4 1.0 HE2 H:LYS301 4.4 0.6 1.0 CZ H:ARG349 4.4 0.7 1.0 NH1 H:ARG348 4.5 0.2 1.0 HG23 G:THR208 4.5 0.4 1.0 HH12 H:ARG348 4.5 0.2 1.0 O2A G:GNP1001 4.5 0.1 1.0 HB2 G:LYS207 4.6 0.2 1.0 HA G:THR208 4.7 0.4 1.0 OE1 G:GLU280 4.8 0.4 1.0 NH2 H:ARG349 4.8 0.7 1.0 HE2 G:LYS207 4.8 0.2 1.0 HG22 G:THR208 4.8 0.4 1.0 HD13 G:LEU331 4.9 0.8 1.0

Magnesium binding site 5 out of 6 in the Structure of Mcrbc Without Dna Binding Domains (Class 5)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Mcrbc Without Dna Binding Domains (Class 5) within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg1002 b:0.9 occ:1.00 O2B H:GNP1001 2.0 0.2 1.0 OG1 H:THR208 2.1 0.3 1.0 N3B H:GNP1001 2.1 0.2 1.0 HNB3 H:GNP1001 2.3 0.2 1.0 O3G H:GNP1001 2.3 0.2 1.0 PB H:GNP1001 2.5 0.2 1.0 O2A H:GNP1001 2.5 0.2 1.0 PG H:GNP1001 2.8 0.2 1.0 HH12 I:ARG349 3.1 0.8 1.0 HB H:THR208 3.2 0.3 1.0 CB H:THR208 3.2 0.3 1.0 HH21 I:ARG348 3.3 0.1 1.0 H H:THR208 3.4 0.3 1.0 O3A H:GNP1001 3.4 0.2 1.0 PA H:GNP1001 3.4 0.2 1.0 HH11 I:ARG349 3.5 0.8 1.0 HE2 I:LYS301 3.5 0.2 1.0 NH1 I:ARG349 3.6 0.8 1.0 O2G H:GNP1001 3.7 0.2 1.0 O1B H:GNP1001 3.7 0.2 1.0 HG21 H:THR208 3.9 0.3 1.0 O1G H:GNP1001 3.9 0.2 1.0 O1A H:GNP1001 3.9 0.2 1.0 NH2 I:ARG348 4.0 0.1 1.0 N H:THR208 4.1 0.3 1.0 HH22 I:ARG348 4.1 0.1 1.0 CG2 H:THR208 4.1 0.3 1.0 CA H:THR208 4.2 0.3 1.0 OD2 H:ASP279 4.3 0.7 1.0 HZ1 I:LYS301 4.3 0.2 1.0 HB2 H:LYS207 4.3 0.7 1.0 CE I:LYS301 4.5 0.2 1.0 HG23 H:THR208 4.5 0.3 1.0 CZ I:ARG349 4.7 0.8 1.0 HA H:THR208 4.7 0.3 1.0 HE2 H:LYS207 4.7 0.7 1.0 H5'1 H:GNP1001 4.8 0.2 1.0 HE I:ARG348 4.8 0.1 1.0 NZ I:LYS301 4.8 0.2 1.0 O5' H:GNP1001 4.9 0.2 1.0 HH22 I:ARG349 4.9 0.8 1.0 HG22 H:THR208 4.9 0.3 1.0 H H:GLY204 4.9 0.3 1.0 HE3 I:LYS301 4.9 0.2 1.0 OD1 H:ASP279 4.9 0.7 1.0

Magnesium binding site 6 out of 6 in the Structure of Mcrbc Without Dna Binding Domains (Class 5)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Mcrbc Without Dna Binding Domains (Class 5) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg1002 b:0.8 occ:1.00 O2B I:GNP1001 2.0 0.7 1.0 O3G I:GNP1001 2.0 0.7 1.0 O2A I:GNP1001 2.0 0.7 1.0 OG1 I:THR208 2.1 1.0 1.0 N3B I:GNP1001 2.7 0.7 1.0 PB I:GNP1001 2.7 0.7 1.0 PG I:GNP1001 2.8 0.7 1.0 PA I:GNP1001 3.0 0.7 1.0 H I:THR208 3.1 1.0 1.0 HB I:THR208 3.2 1.0 1.0 CB I:THR208 3.2 1.0 1.0 HH21 J:ARG348 3.3 0.3 1.0 O3A I:GNP1001 3.3 0.7 1.0 HNB3 I:GNP1001 3.3 0.7 1.0 O1A I:GNP1001 3.4 0.7 1.0 O1G I:GNP1001 3.6 0.7 1.0 HH22 J:ARG348 3.7 0.3 1.0 NH2 J:ARG348 3.8 0.3 1.0 N I:THR208 3.9 1.0 1.0 HZ1 J:LYS301 3.9 0.7 1.0 HG21 I:THR208 4.0 1.0 1.0 OD2 I:ASP279 4.0 0.4 1.0 O2G I:GNP1001 4.0 0.7 1.0 HH12 J:ARG349 4.1 0.3 1.0 O1B I:GNP1001 4.1 0.7 1.0 HB2 I:LYS207 4.1 0.3 1.0 CG2 I:THR208 4.2 1.0 1.0 CA I:THR208 4.2 1.0 1.0 HE2 J:LYS301 4.2 0.7 1.0 HH11 J:ARG349 4.3 0.3 1.0 O5' I:GNP1001 4.4 0.7 1.0 NH1 J:ARG349 4.4 0.3 1.0 H5'1 I:GNP1001 4.4 0.7 1.0 HG23 I:THR208 4.5 1.0 1.0 HZ3 J:LYS301 4.5 0.7 1.0 OD1 I:ASP279 4.5 0.4 1.0 HG2 J:MET295 4.6 0.7 1.0 NZ J:LYS301 4.6 0.7 1.0 HA I:THR208 4.7 1.0 1.0 H5'2 I:GNP1001 4.7 0.7 1.0 HE2 I:LYS207 4.7 0.3 1.0 HG3 J:MET295 4.7 0.7 1.0 CG I:ASP279 4.7 0.4 1.0 C5' I:GNP1001 4.8 0.7 1.0 H I:LYS207 4.8 0.3 1.0 CE J:LYS301 4.9 0.7 1.0 H I:GLY204 4.9 0.8 1.0 HG22 I:THR208 5.0 1.0 1.0

N.Nirwan, Y.Itoh, P.Singh, S.Bandyopadhyay, K.R.Vinothkumar, A.Amunts, K.Saikrishnan. Structure-Based Mechanism For Activation of the Aaa+ Gtpase Mcrb By the Endonuclease Mcrc. Nat Commun V. 10 3058 2019.
ISSN: ESSN 2041-1723
PubMed: 31296862
DOI: 10.1038/S41467-019-11084-1