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
Go back to
Magnesium Binding Sites List in 4r7z
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
Go back to
Magnesium Binding Sites List in 4r7z
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
Go back to
Magnesium Binding Sites List in 4r7z
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
Go back to
Magnesium Binding Sites List in 4r7z
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
Go back to
Magnesium Binding Sites List in 4r7z
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
Go back to
Magnesium Binding Sites List in 4r7z
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
Go back to
Magnesium Binding Sites List in 4r7z
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
Go back to
Magnesium Binding Sites List in 4r7z
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
Go back to
Magnesium Binding Sites List in 4r7z
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
Go back to
Magnesium Binding Sites List in 4r7z
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
|