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

Protein crystallography data

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

Magnesium Binding Sites:

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 4r7z

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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 4r7z

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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 4r7z

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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 4r7z

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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 4r7z

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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 4r7z

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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 4r7z

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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 4r7z

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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 4r7z

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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 4r7z

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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

Reference:

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
Page generated: Tue Aug 20 02:54:46 2024

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