Magnesium in PDB 4r7z: Pfmcm-Aaa Double-Octamer

The structure of Pfmcm-Aaa Double-Octamer, PDB code: 4r7z was solved by J.M.Miller, B.T.Arachea, L.B.Epling, E.J.Enemark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.37 / 3.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	124.956, 127.082, 128.025, 71.85, 72.82, 80.39
R / Rfree (%)	30.1 / 31.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Pfmcm-Aaa Double-Octamer (pdb code 4r7z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Pfmcm-Aaa Double-Octamer, PDB code: 4r7z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Pfmcm-Aaa Double-Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pfmcm-Aaa Double-Octamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:81.5 occ:1.00 O3B A:ADP1001 1.9 72.5 1.0 OG A:SER335 2.1 48.1 1.0 PB A:ADP1001 3.2 72.5 1.0 CB A:SER335 3.5 48.1 1.0 O2B A:ADP1001 3.5 72.5 1.0 OE2 A:GLU760 3.6 0.0 1.0 O1B A:ADP1001 3.8 72.5 1.0 OD2 A:ASP759 3.9 73.9 1.0 OD1 A:ASP759 3.9 73.9 1.0 N A:SER335 4.3 85.5 1.0 CG A:ASP759 4.3 73.9 1.0 CA A:SER335 4.4 85.5 1.0 CD A:GLU760 4.4 0.0 1.0 O3A A:ADP1001 4.5 72.5 1.0 O2A A:ADP1001 4.5 72.5 1.0 OE1 A:GLU760 4.7 0.0 1.0 OD1 A:ASN803 4.8 0.7 1.0 ND2 A:ASN803 4.9 0.7 1.0

Magnesium binding site 2 out of 16 in the Pfmcm-Aaa Double-Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pfmcm-Aaa Double-Octamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:81.5 occ:1.00 O3B B:ADP1001 1.9 72.5 1.0 OG B:SER335 2.1 48.1 1.0 PB B:ADP1001 3.2 72.5 1.0 CB B:SER335 3.5 48.1 1.0 O2B B:ADP1001 3.5 72.5 1.0 OE2 B:GLU760 3.6 0.0 1.0 O1B B:ADP1001 3.8 72.5 1.0 OD2 B:ASP759 3.9 73.9 1.0 OD1 B:ASP759 3.9 73.9 1.0 N B:SER335 4.3 85.5 1.0 CG B:ASP759 4.3 73.9 1.0 CA B:SER335 4.4 85.5 1.0 CD B:GLU760 4.4 0.0 1.0 O3A B:ADP1001 4.5 72.5 1.0 O2A B:ADP1001 4.5 72.5 1.0 OE1 B:GLU760 4.7 0.0 1.0 OD1 B:ASN803 4.8 0.7 1.0 ND2 B:ASN803 4.9 0.7 1.0

Magnesium binding site 3 out of 16 in the Pfmcm-Aaa Double-Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pfmcm-Aaa Double-Octamer within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:81.5 occ:1.00 O3B C:ADP1001 1.9 72.5 1.0 OG C:SER335 2.1 48.1 1.0 PB C:ADP1001 3.2 72.5 1.0 CB C:SER335 3.5 48.1 1.0 O2B C:ADP1001 3.5 72.5 1.0 OE2 C:GLU760 3.6 0.0 1.0 O1B C:ADP1001 3.8 72.5 1.0 OD2 C:ASP759 3.9 73.9 1.0 OD1 C:ASP759 3.9 73.9 1.0 N C:SER335 4.3 85.5 1.0 CG C:ASP759 4.3 73.9 1.0 CA C:SER335 4.4 85.5 1.0 CD C:GLU760 4.4 0.0 1.0 O3A C:ADP1001 4.5 72.5 1.0 O2A C:ADP1001 4.5 72.5 1.0 OE1 C:GLU760 4.7 0.0 1.0 OD1 C:ASN803 4.8 0.7 1.0 ND2 C:ASN803 4.9 0.7 1.0

Magnesium binding site 4 out of 16 in the Pfmcm-Aaa Double-Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pfmcm-Aaa Double-Octamer within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:81.5 occ:1.00 O3B D:ADP1001 1.9 72.5 1.0 OG D:SER335 2.1 48.1 1.0 PB D:ADP1001 3.2 72.5 1.0 CB D:SER335 3.5 48.1 1.0 O2B D:ADP1001 3.5 72.5 1.0 OE2 D:GLU760 3.6 0.0 1.0 O1B D:ADP1001 3.8 72.5 1.0 OD2 D:ASP759 3.9 73.9 1.0 OD1 D:ASP759 3.9 73.9 1.0 N D:SER335 4.3 85.5 1.0 CG D:ASP759 4.3 73.9 1.0 CA D:SER335 4.4 85.5 1.0 CD D:GLU760 4.4 0.0 1.0 O3A D:ADP1001 4.5 72.5 1.0 O2A D:ADP1001 4.5 72.5 1.0 OE1 D:GLU760 4.7 0.0 1.0 OD1 D:ASN803 4.8 0.7 1.0 ND2 D:ASN803 4.9 0.7 1.0

Magnesium binding site 5 out of 16 in the Pfmcm-Aaa Double-Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pfmcm-Aaa Double-Octamer within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1002 b:81.5 occ:1.00 O3B E:ADP1001 1.9 72.5 1.0 OG E:SER335 2.1 48.1 1.0 PB E:ADP1001 3.2 72.5 1.0 CB E:SER335 3.5 48.1 1.0 O2B E:ADP1001 3.5 72.5 1.0 OE2 E:GLU760 3.6 0.0 1.0 O1B E:ADP1001 3.8 72.5 1.0 OD2 E:ASP759 3.9 73.9 1.0 OD1 E:ASP759 3.9 73.9 1.0 N E:SER335 4.3 85.5 1.0 CG E:ASP759 4.3 73.9 1.0 CA E:SER335 4.4 85.5 1.0 CD E:GLU760 4.4 0.0 1.0 O3A E:ADP1001 4.5 72.5 1.0 O2A E:ADP1001 4.5 72.5 1.0 OE1 E:GLU760 4.7 0.0 1.0 OD1 E:ASN803 4.8 0.7 1.0 ND2 E:ASN803 4.9 0.7 1.0

Magnesium binding site 6 out of 16 in the Pfmcm-Aaa Double-Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pfmcm-Aaa Double-Octamer within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1002 b:81.5 occ:1.00 O3B F:ADP1001 1.9 72.5 1.0 OG F:SER335 2.1 48.1 1.0 PB F:ADP1001 3.2 72.5 1.0 CB F:SER335 3.5 48.1 1.0 O2B F:ADP1001 3.5 72.5 1.0 OE2 F:GLU760 3.6 0.0 1.0 O1B F:ADP1001 3.8 72.5 1.0 OD2 F:ASP759 3.9 73.9 1.0 OD1 F:ASP759 3.9 73.9 1.0 N F:SER335 4.3 85.5 1.0 CG F:ASP759 4.3 73.9 1.0 CA F:SER335 4.4 85.5 1.0 CD F:GLU760 4.4 0.0 1.0 O3A F:ADP1001 4.5 72.5 1.0 O2A F:ADP1001 4.5 72.5 1.0 OE1 F:GLU760 4.7 0.0 1.0 OD1 F:ASN803 4.8 0.7 1.0 ND2 F:ASN803 4.9 0.7 1.0

Magnesium binding site 7 out of 16 in the Pfmcm-Aaa Double-Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pfmcm-Aaa Double-Octamer within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg1002 b:81.5 occ:1.00 O3B G:ADP1001 1.9 72.5 1.0 OG G:SER335 2.1 48.1 1.0 PB G:ADP1001 3.2 72.5 1.0 CB G:SER335 3.5 48.1 1.0 O2B G:ADP1001 3.5 72.5 1.0 OE2 G:GLU760 3.6 0.0 1.0 O1B G:ADP1001 3.8 72.5 1.0 OD2 G:ASP759 3.9 73.9 1.0 OD1 G:ASP759 3.9 73.9 1.0 N G:SER335 4.3 85.5 1.0 CG G:ASP759 4.3 73.9 1.0 CA G:SER335 4.4 85.5 1.0 CD G:GLU760 4.4 0.0 1.0 O3A G:ADP1001 4.5 72.5 1.0 O2A G:ADP1001 4.5 72.5 1.0 OE1 G:GLU760 4.7 0.0 1.0 OD1 G:ASN803 4.8 0.7 1.0 ND2 G:ASN803 4.9 0.7 1.0

Magnesium binding site 8 out of 16 in the Pfmcm-Aaa Double-Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pfmcm-Aaa Double-Octamer within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg1002 b:81.5 occ:1.00 O3B H:ADP1001 1.9 72.5 1.0 OG H:SER335 2.1 48.1 1.0 PB H:ADP1001 3.2 72.5 1.0 CB H:SER335 3.5 48.1 1.0 O2B H:ADP1001 3.5 72.5 1.0 OE2 H:GLU760 3.6 0.0 1.0 O1B H:ADP1001 3.8 72.5 1.0 OD2 H:ASP759 3.9 73.9 1.0 OD1 H:ASP759 3.9 73.9 1.0 N H:SER335 4.3 85.5 1.0 CG H:ASP759 4.3 73.9 1.0 CA H:SER335 4.4 85.5 1.0 CD H:GLU760 4.4 0.0 1.0 O3A H:ADP1001 4.5 72.5 1.0 O2A H:ADP1001 4.5 72.5 1.0 OE1 H:GLU760 4.7 0.0 1.0 OD1 H:ASN803 4.8 0.7 1.0 ND2 H:ASN803 4.9 0.7 1.0

Magnesium binding site 9 out of 16 in the Pfmcm-Aaa Double-Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pfmcm-Aaa Double-Octamer within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg1002 b:81.5 occ:1.00 O3B I:ADP1001 1.9 72.5 1.0 OG I:SER335 2.1 48.1 1.0 PB I:ADP1001 3.2 72.5 1.0 CB I:SER335 3.5 48.1 1.0 O2B I:ADP1001 3.5 72.5 1.0 OE2 I:GLU760 3.6 0.0 1.0 O1B I:ADP1001 3.8 72.5 1.0 OD2 I:ASP759 3.9 73.9 1.0 OD1 I:ASP759 3.9 73.9 1.0 N I:SER335 4.3 85.5 1.0 CG I:ASP759 4.3 73.9 1.0 CA I:SER335 4.4 85.5 1.0 CD I:GLU760 4.4 0.0 1.0 O3A I:ADP1001 4.5 72.5 1.0 O2A I:ADP1001 4.5 72.5 1.0 OE1 I:GLU760 4.7 0.0 1.0 OD1 I:ASN803 4.8 0.7 1.0 ND2 I:ASN803 4.9 0.7 1.0

Magnesium binding site 10 out of 16 in the Pfmcm-Aaa Double-Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Pfmcm-Aaa Double-Octamer within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg1002 b:81.5 occ:1.00 O3B J:ADP1001 1.9 72.5 1.0 OG J:SER335 2.1 48.1 1.0 PB J:ADP1001 3.2 72.5 1.0 CB J:SER335 3.5 48.1 1.0 O2B J:ADP1001 3.5 72.5 1.0 OE2 J:GLU760 3.6 0.0 1.0 O1B J:ADP1001 3.8 72.5 1.0 OD2 J:ASP759 3.9 73.9 1.0 OD1 J:ASP759 3.9 73.9 1.0 N J:SER335 4.3 85.5 1.0 CG J:ASP759 4.3 73.9 1.0 CA J:SER335 4.4 85.5 1.0 CD J:GLU760 4.4 0.0 1.0 O3A J:ADP1001 4.5 72.5 1.0 O2A J:ADP1001 4.5 72.5 1.0 OE1 J:GLU760 4.7 0.0 1.0 OD1 J:ASN803 4.8 0.7 1.0 ND2 J:ASN803 4.9 0.7 1.0

J.M.Miller, B.T.Arachea, L.B.Epling, E.J.Enemark. Analysis of the Crystal Structure of An Active Mcm Hexamer. Elife V. 3 2014.
ISSN: ESSN 2050-084X
PubMed: 25262915
DOI: 10.7554/ELIFE.03433