Magnesium in PDB 1pf9: Groel-Groes-Adp
Protein crystallography data
The structure of Groel-Groes-Adp, PDB code: 1pf9
was solved by
C.Chaudhry,
G.W.Farr,
M.J.Todd,
H.S.Rye,
A.T.Brunger,
P.D.Adams,
A.L.Horwich,
P.B.Sigler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.16 /
2.99
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
255.260,
265.250,
184.400,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
26.9 /
28.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Groel-Groes-Adp
(pdb code 1pf9). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Groel-Groes-Adp, PDB code: 1pf9:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 1pf9
Go back to
Magnesium Binding Sites List in 1pf9
Magnesium binding site 1 out
of 7 in the Groel-Groes-Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Groel-Groes-Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:2.0
occ:1.00
|
O2A
|
A:ADP700
|
1.9
|
7.6
|
1.0
|
O1B
|
A:ADP700
|
2.0
|
8.3
|
1.0
|
OD1
|
A:ASP87
|
2.2
|
9.4
|
1.0
|
PB
|
A:ADP700
|
3.0
|
11.1
|
1.0
|
PA
|
A:ADP700
|
3.1
|
7.9
|
1.0
|
CG
|
A:ASP87
|
3.2
|
8.3
|
1.0
|
O3B
|
A:ADP700
|
3.3
|
10.2
|
1.0
|
OD2
|
A:ASP87
|
3.4
|
8.4
|
1.0
|
O5'
|
A:ADP700
|
3.5
|
7.9
|
1.0
|
O3A
|
A:ADP700
|
3.6
|
8.9
|
1.0
|
O
|
A:HOH800
|
3.7
|
64.0
|
1.0
|
OD2
|
A:ASP398
|
4.1
|
12.9
|
1.0
|
N
|
A:GLY88
|
4.2
|
6.5
|
1.0
|
O1A
|
A:ADP700
|
4.4
|
6.0
|
1.0
|
O2B
|
A:ADP700
|
4.4
|
7.7
|
1.0
|
O
|
A:SER151
|
4.5
|
7.0
|
1.0
|
CB
|
A:ASP87
|
4.6
|
7.4
|
1.0
|
CA
|
A:GLY88
|
4.8
|
6.7
|
1.0
|
C5'
|
A:ADP700
|
4.8
|
8.2
|
1.0
|
CA
|
A:SER151
|
4.9
|
6.2
|
1.0
|
CA
|
A:ASP87
|
4.9
|
7.4
|
1.0
|
OG
|
A:SER151
|
5.0
|
7.4
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 1pf9
Go back to
Magnesium Binding Sites List in 1pf9
Magnesium binding site 2 out
of 7 in the Groel-Groes-Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Groel-Groes-Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:2.0
occ:1.00
|
O2A
|
B:ADP701
|
1.9
|
7.7
|
1.0
|
O1B
|
B:ADP701
|
2.0
|
8.0
|
1.0
|
OD1
|
B:ASP87
|
2.2
|
9.5
|
1.0
|
PB
|
B:ADP701
|
3.0
|
10.4
|
1.0
|
PA
|
B:ADP701
|
3.1
|
8.3
|
1.0
|
CG
|
B:ASP87
|
3.2
|
8.2
|
1.0
|
OD2
|
B:ASP87
|
3.4
|
8.4
|
1.0
|
O5'
|
B:ADP701
|
3.4
|
8.0
|
1.0
|
O3B
|
B:ADP701
|
3.4
|
10.2
|
1.0
|
O3A
|
B:ADP701
|
3.5
|
8.8
|
1.0
|
O
|
B:HOH801
|
3.9
|
63.9
|
1.0
|
OD2
|
B:ASP398
|
4.0
|
12.7
|
1.0
|
N
|
B:GLY88
|
4.2
|
6.7
|
1.0
|
O1A
|
B:ADP701
|
4.4
|
6.4
|
1.0
|
O
|
B:SER151
|
4.4
|
7.0
|
1.0
|
O2B
|
B:ADP701
|
4.4
|
7.6
|
1.0
|
CB
|
B:ASP87
|
4.6
|
7.3
|
1.0
|
C5'
|
B:ADP701
|
4.8
|
8.3
|
1.0
|
OG
|
B:SER151
|
4.8
|
7.2
|
1.0
|
CA
|
B:SER151
|
4.9
|
6.4
|
1.0
|
CA
|
B:GLY88
|
4.9
|
6.7
|
1.0
|
CA
|
B:ASP87
|
5.0
|
7.2
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 1pf9
Go back to
Magnesium Binding Sites List in 1pf9
Magnesium binding site 3 out
of 7 in the Groel-Groes-Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Groel-Groes-Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg603
b:2.0
occ:1.00
|
O2A
|
C:ADP702
|
1.9
|
7.3
|
1.0
|
O1B
|
C:ADP702
|
2.0
|
8.3
|
1.0
|
OD1
|
C:ASP87
|
2.2
|
9.7
|
1.0
|
PB
|
C:ADP702
|
3.0
|
10.8
|
1.0
|
PA
|
C:ADP702
|
3.0
|
8.0
|
1.0
|
CG
|
C:ASP87
|
3.3
|
8.3
|
1.0
|
O3B
|
C:ADP702
|
3.3
|
10.2
|
1.0
|
O5'
|
C:ADP702
|
3.4
|
7.9
|
1.0
|
OD2
|
C:ASP87
|
3.5
|
8.2
|
1.0
|
O3A
|
C:ADP702
|
3.5
|
8.8
|
1.0
|
O
|
C:HOH802
|
3.7
|
64.1
|
1.0
|
OD2
|
C:ASP398
|
4.0
|
12.8
|
1.0
|
N
|
C:GLY88
|
4.2
|
6.6
|
1.0
|
O1A
|
C:ADP702
|
4.4
|
6.2
|
1.0
|
O2B
|
C:ADP702
|
4.4
|
7.7
|
1.0
|
O
|
C:SER151
|
4.5
|
7.0
|
1.0
|
CB
|
C:ASP87
|
4.6
|
7.4
|
1.0
|
C5'
|
C:ADP702
|
4.8
|
8.2
|
1.0
|
OG
|
C:SER151
|
4.8
|
7.2
|
1.0
|
CA
|
C:GLY88
|
4.9
|
6.7
|
1.0
|
CA
|
C:ASP87
|
4.9
|
7.4
|
1.0
|
CA
|
C:SER151
|
5.0
|
6.4
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 1pf9
Go back to
Magnesium Binding Sites List in 1pf9
Magnesium binding site 4 out
of 7 in the Groel-Groes-Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Groel-Groes-Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg604
b:2.0
occ:1.00
|
O2A
|
D:ADP703
|
1.8
|
7.4
|
1.0
|
O1B
|
D:ADP703
|
2.0
|
8.1
|
1.0
|
OD1
|
D:ASP87
|
2.1
|
9.5
|
1.0
|
PB
|
D:ADP703
|
3.0
|
10.4
|
1.0
|
PA
|
D:ADP703
|
3.0
|
8.1
|
1.0
|
CG
|
D:ASP87
|
3.2
|
8.3
|
1.0
|
O3B
|
D:ADP703
|
3.2
|
10.2
|
1.0
|
OD2
|
D:ASP87
|
3.4
|
8.4
|
1.0
|
O5'
|
D:ADP703
|
3.4
|
8.0
|
1.0
|
O3A
|
D:ADP703
|
3.5
|
8.7
|
1.0
|
O
|
D:HOH803
|
3.8
|
63.9
|
1.0
|
OD2
|
D:ASP398
|
4.2
|
12.9
|
1.0
|
N
|
D:GLY88
|
4.2
|
6.6
|
1.0
|
O1A
|
D:ADP703
|
4.3
|
6.2
|
1.0
|
O2B
|
D:ADP703
|
4.4
|
7.4
|
1.0
|
O
|
D:SER151
|
4.5
|
7.0
|
1.0
|
CB
|
D:ASP87
|
4.6
|
7.5
|
1.0
|
C5'
|
D:ADP703
|
4.8
|
8.2
|
1.0
|
CA
|
D:GLY88
|
4.8
|
6.5
|
1.0
|
OG
|
D:SER151
|
4.9
|
7.2
|
1.0
|
CA
|
D:ASP87
|
4.9
|
7.3
|
1.0
|
CA
|
D:SER151
|
5.0
|
6.3
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 1pf9
Go back to
Magnesium Binding Sites List in 1pf9
Magnesium binding site 5 out
of 7 in the Groel-Groes-Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Groel-Groes-Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg605
b:2.0
occ:1.00
|
O1B
|
E:ADP704
|
1.9
|
8.0
|
1.0
|
O2A
|
E:ADP704
|
1.9
|
7.6
|
1.0
|
OD1
|
E:ASP87
|
2.2
|
9.6
|
1.0
|
PB
|
E:ADP704
|
3.0
|
10.4
|
1.0
|
PA
|
E:ADP704
|
3.0
|
8.5
|
1.0
|
CG
|
E:ASP87
|
3.2
|
8.3
|
1.0
|
O5'
|
E:ADP704
|
3.3
|
7.9
|
1.0
|
O3B
|
E:ADP704
|
3.3
|
10.1
|
1.0
|
OD2
|
E:ASP87
|
3.4
|
8.3
|
1.0
|
O3A
|
E:ADP704
|
3.5
|
8.8
|
1.0
|
O
|
E:HOH804
|
3.8
|
64.0
|
1.0
|
OD2
|
E:ASP398
|
4.0
|
12.7
|
1.0
|
N
|
E:GLY88
|
4.2
|
6.5
|
1.0
|
O1A
|
E:ADP704
|
4.3
|
6.4
|
1.0
|
O2B
|
E:ADP704
|
4.3
|
7.8
|
1.0
|
O
|
E:SER151
|
4.5
|
7.0
|
1.0
|
CB
|
E:ASP87
|
4.6
|
7.4
|
1.0
|
C5'
|
E:ADP704
|
4.7
|
8.1
|
1.0
|
CA
|
E:GLY88
|
4.8
|
6.5
|
1.0
|
OG
|
E:SER151
|
4.9
|
7.0
|
1.0
|
CA
|
E:ASP87
|
4.9
|
7.3
|
1.0
|
CA
|
E:SER151
|
5.0
|
6.4
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 1pf9
Go back to
Magnesium Binding Sites List in 1pf9
Magnesium binding site 6 out
of 7 in the Groel-Groes-Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Groel-Groes-Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg606
b:2.0
occ:1.00
|
O2A
|
F:ADP705
|
1.7
|
7.3
|
1.0
|
O1B
|
F:ADP705
|
1.9
|
8.2
|
1.0
|
OD1
|
F:ASP87
|
2.3
|
9.4
|
1.0
|
PA
|
F:ADP705
|
2.8
|
7.8
|
1.0
|
PB
|
F:ADP705
|
2.9
|
10.5
|
1.0
|
O5'
|
F:ADP705
|
3.2
|
7.9
|
1.0
|
O3B
|
F:ADP705
|
3.3
|
10.2
|
1.0
|
O3A
|
F:ADP705
|
3.3
|
8.8
|
1.0
|
CG
|
F:ASP87
|
3.4
|
8.2
|
1.0
|
OD2
|
F:ASP87
|
3.5
|
8.3
|
1.0
|
O
|
F:HOH805
|
3.8
|
64.1
|
1.0
|
O1A
|
F:ADP705
|
4.1
|
6.3
|
1.0
|
OD2
|
F:ASP398
|
4.2
|
12.8
|
1.0
|
N
|
F:GLY88
|
4.3
|
6.7
|
1.0
|
O2B
|
F:ADP705
|
4.3
|
7.7
|
1.0
|
O
|
F:SER151
|
4.5
|
7.0
|
1.0
|
C5'
|
F:ADP705
|
4.6
|
8.3
|
1.0
|
CB
|
F:ASP87
|
4.7
|
7.4
|
1.0
|
CA
|
F:GLY88
|
4.9
|
6.7
|
1.0
|
OG
|
F:SER151
|
5.0
|
7.2
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 1pf9
Go back to
Magnesium Binding Sites List in 1pf9
Magnesium binding site 7 out
of 7 in the Groel-Groes-Adp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Groel-Groes-Adp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg607
b:2.0
occ:1.00
|
O2A
|
G:ADP706
|
1.8
|
7.3
|
1.0
|
O1B
|
G:ADP706
|
2.1
|
8.3
|
1.0
|
OD1
|
G:ASP87
|
2.2
|
9.4
|
1.0
|
PA
|
G:ADP706
|
3.0
|
7.8
|
1.0
|
PB
|
G:ADP706
|
3.1
|
10.3
|
1.0
|
CG
|
G:ASP87
|
3.2
|
8.3
|
1.0
|
O3B
|
G:ADP706
|
3.3
|
10.2
|
1.0
|
OD2
|
G:ASP87
|
3.4
|
8.5
|
1.0
|
O5'
|
G:ADP706
|
3.4
|
8.2
|
1.0
|
O3A
|
G:ADP706
|
3.6
|
8.6
|
1.0
|
O
|
G:HOH806
|
3.9
|
63.9
|
1.0
|
OD2
|
G:ASP398
|
4.0
|
12.8
|
1.0
|
N
|
G:GLY88
|
4.3
|
6.5
|
1.0
|
O1A
|
G:ADP706
|
4.3
|
6.2
|
1.0
|
O2B
|
G:ADP706
|
4.5
|
7.5
|
1.0
|
O
|
G:SER151
|
4.5
|
7.1
|
1.0
|
CB
|
G:ASP87
|
4.7
|
7.5
|
1.0
|
C5'
|
G:ADP706
|
4.8
|
8.1
|
1.0
|
OG
|
G:SER151
|
4.8
|
7.2
|
1.0
|
CA
|
G:SER151
|
4.9
|
6.3
|
1.0
|
CA
|
G:GLY88
|
5.0
|
6.6
|
1.0
|
|
Reference:
C.Chaudhry,
G.W.Farr,
M.J.Todd,
H.S.Rye,
A.T.Brunger,
P.D.Adams,
A.L.Horwich,
P.B.Sigler.
Role of the Gamma-Phosphate of Atp in Triggering Protein Folding By Groel-Groes: Function, Structure and Energetics. Embo J. V. 22 4877 2003.
ISSN: ISSN 0261-4189
PubMed: 14517228
DOI: 10.1093/EMBOJ/CDG477
Page generated: Tue Aug 13 10:51:23 2024
|