Sodium in PDB 7knf: 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)
Enzymatic activity of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)
All present enzymatic activity of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh):
5.4.2.12;
Protein crystallography data
The structure of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh), PDB code: 7knf
was solved by
S.Lovell,
M.M.Kashipathy,
K.P.Battaile,
M.Weidmann,
P.Dranchak,
M.Aitha,
B.Queme,
C.D.Collmus,
L.Kanter,
L.Lamy,
D.Tao,
G.Rai,
H.Suga,
J.Inglese,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.13 /
1.80
|
Space group
|
P 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.669,
75.846,
100.424,
90,
98.31,
90
|
R / Rfree (%)
|
15.2 /
19.4
|
Other elements in 7knf:
The structure of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh) also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)
(pdb code 7knf). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh), PDB code: 7knf:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 7knf
Go back to
Sodium Binding Sites List in 7knf
Sodium binding site 1 out
of 4 in the 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na603
b:19.4
occ:1.00
|
O
|
A:ALA53
|
2.4
|
16.7
|
1.0
|
OG1
|
A:THR55
|
2.4
|
16.7
|
1.0
|
O
|
A:HOH779
|
2.4
|
18.6
|
1.0
|
O
|
A:ILE50
|
2.4
|
15.9
|
1.0
|
O
|
A:HOH741
|
2.7
|
20.7
|
1.0
|
O
|
A:LEU51
|
2.7
|
19.8
|
1.0
|
C
|
A:LEU51
|
3.3
|
19.6
|
1.0
|
CB
|
A:THR55
|
3.5
|
15.8
|
1.0
|
C
|
A:ALA53
|
3.5
|
17.5
|
1.0
|
C
|
A:ILE50
|
3.5
|
15.8
|
1.0
|
CA
|
A:LEU51
|
3.6
|
16.5
|
1.0
|
N
|
A:THR55
|
3.7
|
15.2
|
1.0
|
CG2
|
A:THR55
|
3.7
|
15.3
|
1.0
|
N
|
A:LEU51
|
4.0
|
15.9
|
1.0
|
N
|
A:ALA53
|
4.0
|
19.5
|
1.0
|
OD1
|
A:ASP59
|
4.1
|
18.9
|
1.0
|
CA
|
A:THR55
|
4.1
|
15.9
|
1.0
|
CA
|
A:ALA53
|
4.2
|
18.4
|
1.0
|
N
|
A:ASN52
|
4.2
|
19.0
|
1.0
|
OD2
|
A:ASP59
|
4.4
|
21.2
|
1.0
|
O
|
A:HOH1064
|
4.4
|
40.0
|
1.0
|
C
|
A:GLN54
|
4.4
|
15.8
|
1.0
|
C
|
A:ASN52
|
4.5
|
20.4
|
1.0
|
N
|
A:GLN54
|
4.5
|
17.2
|
1.0
|
CB
|
A:ALA53
|
4.6
|
17.9
|
1.0
|
CA
|
A:GLN54
|
4.6
|
22.5
|
1.0
|
CG
|
A:ASP59
|
4.7
|
20.4
|
1.0
|
CA
|
A:ILE50
|
4.8
|
15.4
|
1.0
|
CA
|
A:ASN52
|
4.8
|
19.6
|
1.0
|
C
|
A:THR55
|
4.8
|
13.5
|
1.0
|
O
|
A:THR55
|
4.9
|
18.3
|
1.0
|
O
|
A:HOH901
|
4.9
|
32.6
|
1.0
|
CB
|
A:LEU51
|
5.0
|
20.9
|
1.0
|
|
Sodium binding site 2 out
of 4 in 7knf
Go back to
Sodium Binding Sites List in 7knf
Sodium binding site 2 out
of 4 in the 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na604
b:15.4
occ:1.00
|
OD1
|
A:ASN470
|
2.7
|
14.5
|
1.0
|
O
|
A:LYS473
|
2.8
|
17.1
|
1.0
|
O
|
A:ALA484
|
2.8
|
17.1
|
1.0
|
O
|
A:HIS482
|
2.8
|
19.8
|
1.0
|
O
|
A:ASN470
|
2.8
|
13.8
|
1.0
|
ND1
|
A:HIS482
|
3.1
|
22.5
|
1.0
|
C
|
A:HIS482
|
3.6
|
20.6
|
1.0
|
C
|
A:ASN470
|
3.6
|
17.9
|
1.0
|
N
|
A:ALA484
|
3.7
|
20.8
|
1.0
|
CG
|
A:ASN470
|
3.7
|
16.8
|
1.0
|
C
|
A:LYS473
|
3.8
|
16.6
|
1.0
|
CE1
|
A:HIS482
|
3.9
|
25.7
|
1.0
|
C
|
A:ALA484
|
3.9
|
17.4
|
1.0
|
SD
|
A:MET474
|
3.9
|
17.8
|
1.0
|
CG
|
A:HIS482
|
4.0
|
21.3
|
1.0
|
C
|
A:THR483
|
4.0
|
22.7
|
1.0
|
CA
|
A:ASN470
|
4.1
|
12.2
|
1.0
|
N
|
A:THR483
|
4.2
|
19.9
|
1.0
|
CA
|
A:THR483
|
4.2
|
17.3
|
1.0
|
CB
|
A:HIS482
|
4.3
|
22.1
|
1.0
|
CA
|
A:MET474
|
4.4
|
14.8
|
1.0
|
CA
|
A:ALA484
|
4.4
|
19.0
|
1.0
|
O
|
A:GLY429
|
4.5
|
15.4
|
1.0
|
N
|
A:MET474
|
4.5
|
15.8
|
1.0
|
CB
|
A:ASN470
|
4.5
|
12.0
|
1.0
|
ND2
|
A:ASN470
|
4.6
|
16.9
|
1.0
|
CA
|
A:HIS482
|
4.6
|
20.4
|
1.0
|
N
|
A:ALA471
|
4.6
|
15.1
|
1.0
|
CA
|
A:LYS473
|
4.8
|
15.2
|
1.0
|
O
|
A:THR483
|
4.8
|
24.8
|
1.0
|
CE
|
A:MET474
|
4.8
|
20.3
|
1.0
|
CA
|
A:ALA471
|
4.9
|
14.3
|
1.0
|
N
|
A:LYS473
|
4.9
|
15.3
|
1.0
|
CB
|
A:LYS473
|
4.9
|
17.8
|
1.0
|
C
|
A:GLY429
|
4.9
|
18.3
|
1.0
|
NE2
|
A:HIS482
|
5.0
|
27.1
|
1.0
|
|
Sodium binding site 3 out
of 4 in 7knf
Go back to
Sodium Binding Sites List in 7knf
Sodium binding site 3 out
of 4 in the 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na603
b:22.2
occ:1.00
|
O
|
B:ALA53
|
2.3
|
19.3
|
1.0
|
O
|
B:HOH770
|
2.4
|
23.8
|
1.0
|
O
|
B:ILE50
|
2.4
|
18.8
|
1.0
|
OG1
|
B:THR55
|
2.4
|
19.3
|
1.0
|
O
|
B:HOH748
|
2.5
|
23.8
|
1.0
|
O
|
B:LEU51
|
2.6
|
24.1
|
1.0
|
C
|
B:LEU51
|
3.2
|
24.4
|
1.0
|
C
|
B:ALA53
|
3.4
|
19.2
|
1.0
|
CB
|
B:THR55
|
3.6
|
23.0
|
1.0
|
C
|
B:ILE50
|
3.6
|
26.9
|
1.0
|
CA
|
B:LEU51
|
3.6
|
23.2
|
1.0
|
N
|
B:THR55
|
3.6
|
20.7
|
1.0
|
CG2
|
B:THR55
|
3.7
|
17.5
|
1.0
|
N
|
B:ALA53
|
3.9
|
26.8
|
1.0
|
N
|
B:LEU51
|
4.1
|
22.9
|
1.0
|
OD1
|
B:ASP59
|
4.1
|
26.0
|
1.0
|
CA
|
B:ALA53
|
4.2
|
23.1
|
1.0
|
CA
|
B:THR55
|
4.2
|
20.9
|
1.0
|
N
|
B:ASN52
|
4.2
|
24.6
|
1.0
|
C
|
B:ASN52
|
4.4
|
26.3
|
1.0
|
OD2
|
B:ASP59
|
4.4
|
26.6
|
1.0
|
C
|
B:GLN54
|
4.4
|
25.8
|
1.0
|
N
|
B:GLN54
|
4.5
|
21.9
|
1.0
|
CB
|
B:ALA53
|
4.6
|
20.1
|
1.0
|
CA
|
B:GLN54
|
4.6
|
24.2
|
1.0
|
CG
|
B:ASP59
|
4.7
|
26.5
|
1.0
|
CA
|
B:ASN52
|
4.7
|
25.1
|
1.0
|
CA
|
B:ILE50
|
4.8
|
21.3
|
1.0
|
C
|
B:THR55
|
4.9
|
18.8
|
1.0
|
O
|
B:THR55
|
4.9
|
21.9
|
1.0
|
O
|
B:ASN52
|
5.0
|
25.0
|
1.0
|
|
Sodium binding site 4 out
of 4 in 7knf
Go back to
Sodium Binding Sites List in 7knf
Sodium binding site 4 out
of 4 in the 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na604
b:18.8
occ:1.00
|
O
|
B:LYS473
|
2.7
|
19.9
|
1.0
|
OD1
|
B:ASN470
|
2.7
|
20.9
|
1.0
|
O
|
B:ALA484
|
2.8
|
24.1
|
1.0
|
O
|
B:HIS482
|
2.9
|
22.6
|
1.0
|
O
|
B:ASN470
|
2.9
|
18.4
|
1.0
|
ND1
|
B:HIS482
|
3.1
|
30.4
|
1.0
|
C
|
B:HIS482
|
3.6
|
24.1
|
1.0
|
C
|
B:ASN470
|
3.6
|
22.4
|
1.0
|
N
|
B:ALA484
|
3.7
|
22.9
|
1.0
|
C
|
B:LYS473
|
3.7
|
19.7
|
1.0
|
CG
|
B:ASN470
|
3.7
|
22.1
|
1.0
|
CE1
|
B:HIS482
|
3.8
|
30.6
|
1.0
|
SD
|
B:MET474
|
3.9
|
20.6
|
1.0
|
C
|
B:ALA484
|
3.9
|
20.4
|
1.0
|
C
|
B:THR483
|
4.1
|
25.7
|
1.0
|
CG
|
B:HIS482
|
4.1
|
30.3
|
1.0
|
CA
|
B:ASN470
|
4.1
|
14.7
|
1.0
|
CA
|
B:THR483
|
4.2
|
21.4
|
1.0
|
N
|
B:THR483
|
4.2
|
22.9
|
1.0
|
CA
|
B:MET474
|
4.3
|
17.9
|
1.0
|
CB
|
B:HIS482
|
4.4
|
20.8
|
1.0
|
N
|
B:MET474
|
4.4
|
16.4
|
1.0
|
CA
|
B:ALA484
|
4.5
|
21.4
|
1.0
|
CB
|
B:ASN470
|
4.5
|
18.4
|
1.0
|
O
|
B:GLY429
|
4.6
|
19.1
|
1.0
|
N
|
B:ALA471
|
4.6
|
18.0
|
1.0
|
CA
|
B:HIS482
|
4.6
|
19.2
|
1.0
|
ND2
|
B:ASN470
|
4.6
|
19.5
|
1.0
|
CA
|
B:LYS473
|
4.7
|
19.9
|
1.0
|
CE
|
B:MET474
|
4.8
|
17.9
|
1.0
|
N
|
B:LYS473
|
4.8
|
18.9
|
1.0
|
CB
|
B:LYS473
|
4.9
|
18.7
|
1.0
|
O
|
B:THR483
|
4.9
|
26.2
|
1.0
|
CA
|
B:ALA471
|
4.9
|
17.5
|
1.0
|
C
|
B:GLY429
|
5.0
|
21.2
|
1.0
|
|
Reference:
M.Weidmann,
P.Dranchak,
M.Aitha,
B.Queme,
C.D.Collmus,
L.Kanter,
L.Lamy,
D.Tao,
M.M.Kashipathy,
K.P.Battaile,
G.Rai,
S.Lovell,
H.Suga,
J.Inglese.
Structure-Activity Relationship of Ipglycermide Binding to Phosphoglycerate Mutases J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Sat Apr 17 17:09:01 2021
|