Sodium in PDB 7kng: 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)
Enzymatic activity of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)
All present enzymatic activity of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F):
5.4.2.12;
Protein crystallography data
The structure of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F), PDB code: 7kng
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)
|
44.69 /
2.10
|
Space group
|
P 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.862,
75.471,
101.36,
90,
99.11,
90
|
R / Rfree (%)
|
16.7 /
22
|
Other elements in 7kng:
The structure of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F) also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)
(pdb code 7kng). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F), PDB code: 7kng:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 7kng
Go back to
Sodium Binding Sites List in 7kng
Sodium binding site 1 out
of 4 in the 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na603
b:26.6
occ:1.00
|
O
|
A:ALA53
|
2.2
|
28.5
|
1.0
|
O
|
A:HOH784
|
2.3
|
25.1
|
1.0
|
O
|
A:ILE50
|
2.4
|
27.7
|
1.0
|
OG1
|
A:THR55
|
2.4
|
22.4
|
1.0
|
O
|
A:LEU51
|
2.4
|
30.7
|
1.0
|
O
|
A:HOH728
|
2.6
|
29.1
|
1.0
|
C
|
A:LEU51
|
3.1
|
30.7
|
1.0
|
C
|
A:ALA53
|
3.4
|
26.9
|
1.0
|
CA
|
A:LEU51
|
3.5
|
30.4
|
1.0
|
C
|
A:ILE50
|
3.5
|
32.4
|
1.0
|
CB
|
A:THR55
|
3.6
|
29.5
|
1.0
|
N
|
A:THR55
|
3.7
|
27.6
|
1.0
|
CG2
|
A:THR55
|
3.9
|
25.6
|
1.0
|
N
|
A:LEU51
|
3.9
|
26.4
|
1.0
|
N
|
A:ALA53
|
3.9
|
27.8
|
1.0
|
N
|
A:ASN52
|
4.0
|
28.1
|
1.0
|
CA
|
A:ALA53
|
4.2
|
31.1
|
1.0
|
CA
|
A:THR55
|
4.2
|
20.9
|
1.0
|
OD1
|
A:ASP59
|
4.3
|
33.7
|
1.0
|
C
|
A:ASN52
|
4.3
|
33.6
|
1.0
|
C
|
A:GLN54
|
4.4
|
22.5
|
1.0
|
N
|
A:GLN54
|
4.4
|
26.0
|
1.0
|
OD2
|
A:ASP59
|
4.5
|
29.9
|
1.0
|
CA
|
A:GLN54
|
4.6
|
24.9
|
1.0
|
CA
|
A:ASN52
|
4.6
|
26.0
|
1.0
|
CB
|
A:ALA53
|
4.6
|
25.1
|
1.0
|
CA
|
A:ILE50
|
4.8
|
28.8
|
1.0
|
CG
|
A:ASP59
|
4.8
|
30.0
|
1.0
|
CB
|
A:LEU51
|
4.9
|
33.7
|
1.0
|
O
|
A:ASN52
|
4.9
|
36.8
|
1.0
|
C
|
A:THR55
|
4.9
|
25.3
|
1.0
|
|
Sodium binding site 2 out
of 4 in 7kng
Go back to
Sodium Binding Sites List in 7kng
Sodium binding site 2 out
of 4 in the 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na604
b:19.8
occ:1.00
|
O
|
A:HIS482
|
2.6
|
31.9
|
1.0
|
O
|
A:LYS473
|
2.6
|
29.6
|
1.0
|
O
|
A:ALA484
|
2.7
|
26.2
|
1.0
|
OD1
|
A:ASN470
|
2.7
|
26.4
|
1.0
|
O
|
A:ASN470
|
2.8
|
26.4
|
1.0
|
ND1
|
A:HIS482
|
3.0
|
34.9
|
1.0
|
C
|
A:HIS482
|
3.6
|
31.2
|
1.0
|
N
|
A:ALA484
|
3.6
|
30.3
|
1.0
|
C
|
A:ASN470
|
3.6
|
28.6
|
1.0
|
C
|
A:LYS473
|
3.7
|
28.9
|
1.0
|
CE1
|
A:HIS482
|
3.7
|
36.8
|
1.0
|
CG
|
A:ASN470
|
3.8
|
28.3
|
1.0
|
C
|
A:ALA484
|
3.8
|
28.5
|
1.0
|
CG
|
A:HIS482
|
3.9
|
32.4
|
1.0
|
SD
|
A:MET474
|
3.9
|
26.6
|
1.0
|
CA
|
A:ASN470
|
4.1
|
25.8
|
1.0
|
CB
|
A:HIS482
|
4.2
|
34.7
|
1.0
|
C
|
A:THR483
|
4.2
|
29.2
|
1.0
|
N
|
A:THR483
|
4.2
|
33.1
|
1.0
|
CA
|
A:ALA484
|
4.3
|
30.1
|
1.0
|
CA
|
A:THR483
|
4.3
|
24.8
|
1.0
|
CA
|
A:MET474
|
4.4
|
25.1
|
1.0
|
N
|
A:MET474
|
4.4
|
24.3
|
1.0
|
CA
|
A:HIS482
|
4.5
|
27.1
|
1.0
|
CB
|
A:ASN470
|
4.5
|
25.5
|
1.0
|
N
|
A:ALA471
|
4.6
|
23.8
|
1.0
|
CA
|
A:LYS473
|
4.7
|
25.0
|
1.0
|
NE2
|
A:HIS482
|
4.7
|
33.4
|
1.0
|
ND2
|
A:ASN470
|
4.7
|
27.2
|
1.0
|
O
|
A:GLY429
|
4.7
|
25.2
|
1.0
|
CD2
|
A:HIS482
|
4.8
|
40.2
|
1.0
|
N
|
A:LYS473
|
4.8
|
28.1
|
1.0
|
CE
|
A:MET474
|
4.8
|
21.3
|
1.0
|
CB
|
A:LYS473
|
4.9
|
25.3
|
1.0
|
CA
|
A:ALA471
|
4.9
|
26.3
|
1.0
|
N
|
A:HIS485
|
4.9
|
24.1
|
1.0
|
|
Sodium binding site 3 out
of 4 in 7kng
Go back to
Sodium Binding Sites List in 7kng
Sodium binding site 3 out
of 4 in the 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na603
b:27.8
occ:1.00
|
O
|
B:HOH819
|
2.1
|
31.7
|
1.0
|
O
|
B:ALA53
|
2.2
|
27.0
|
1.0
|
O
|
B:ILE50
|
2.3
|
28.3
|
1.0
|
OG1
|
B:THR55
|
2.4
|
23.3
|
1.0
|
O
|
B:HOH739
|
2.5
|
32.2
|
1.0
|
O
|
B:LEU51
|
2.5
|
30.7
|
1.0
|
C
|
B:LEU51
|
3.1
|
24.3
|
1.0
|
C
|
B:ALA53
|
3.4
|
28.1
|
1.0
|
C
|
B:ILE50
|
3.5
|
25.6
|
1.0
|
CB
|
B:THR55
|
3.5
|
30.9
|
1.0
|
CA
|
B:LEU51
|
3.5
|
25.1
|
1.0
|
CG2
|
B:THR55
|
3.6
|
25.0
|
1.0
|
N
|
B:THR55
|
3.7
|
26.5
|
1.0
|
N
|
B:ALA53
|
3.9
|
32.6
|
1.0
|
N
|
B:LEU51
|
4.0
|
29.8
|
1.0
|
N
|
B:ASN52
|
4.1
|
23.4
|
1.0
|
CA
|
B:THR55
|
4.1
|
27.4
|
1.0
|
OD1
|
B:ASP59
|
4.2
|
31.6
|
1.0
|
CA
|
B:ALA53
|
4.2
|
30.0
|
1.0
|
C
|
B:ASN52
|
4.3
|
32.0
|
1.0
|
OD2
|
B:ASP59
|
4.3
|
32.7
|
1.0
|
C
|
B:GLN54
|
4.4
|
29.4
|
1.0
|
N
|
B:GLN54
|
4.4
|
30.4
|
1.0
|
CA
|
B:GLN54
|
4.6
|
30.4
|
1.0
|
CA
|
B:ASN52
|
4.6
|
24.3
|
1.0
|
CB
|
B:ALA53
|
4.7
|
31.1
|
1.0
|
CG
|
B:ASP59
|
4.7
|
27.0
|
1.0
|
O
|
B:HOH871
|
4.7
|
39.9
|
1.0
|
CA
|
B:ILE50
|
4.7
|
25.8
|
1.0
|
O
|
B:ASN52
|
4.8
|
33.1
|
1.0
|
C
|
B:THR55
|
4.8
|
28.2
|
1.0
|
O
|
B:THR55
|
4.9
|
29.0
|
1.0
|
CB
|
B:LEU51
|
5.0
|
30.8
|
1.0
|
CG2
|
B:ILE50
|
5.0
|
33.4
|
1.0
|
|
Sodium binding site 4 out
of 4 in 7kng
Go back to
Sodium Binding Sites List in 7kng
Sodium binding site 4 out
of 4 in the 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na604
b:18.2
occ:1.00
|
O
|
B:ASN470
|
2.6
|
22.9
|
1.0
|
O
|
B:LYS473
|
2.6
|
34.5
|
1.0
|
OD1
|
B:ASN470
|
2.6
|
20.0
|
1.0
|
O
|
B:ALA484
|
2.8
|
25.5
|
1.0
|
O
|
B:HIS482
|
2.8
|
29.8
|
1.0
|
ND1
|
B:HIS482
|
2.9
|
37.8
|
1.0
|
C
|
B:ASN470
|
3.5
|
28.9
|
1.0
|
C
|
B:LYS473
|
3.6
|
28.7
|
1.0
|
CE1
|
B:HIS482
|
3.6
|
32.9
|
1.0
|
C
|
B:HIS482
|
3.7
|
30.0
|
1.0
|
CG
|
B:ASN470
|
3.7
|
22.6
|
1.0
|
N
|
B:ALA484
|
3.7
|
27.9
|
1.0
|
CG
|
B:HIS482
|
3.9
|
36.1
|
1.0
|
SD
|
B:MET474
|
3.9
|
28.2
|
1.0
|
C
|
B:ALA484
|
3.9
|
26.4
|
1.0
|
CA
|
B:ASN470
|
4.0
|
23.1
|
1.0
|
C
|
B:THR483
|
4.2
|
30.0
|
1.0
|
CB
|
B:HIS482
|
4.2
|
31.1
|
1.0
|
CA
|
B:MET474
|
4.3
|
28.4
|
1.0
|
N
|
B:THR483
|
4.3
|
34.7
|
1.0
|
CA
|
B:THR483
|
4.3
|
29.6
|
1.0
|
N
|
B:MET474
|
4.3
|
29.5
|
1.0
|
CB
|
B:ASN470
|
4.5
|
24.3
|
1.0
|
CA
|
B:ALA484
|
4.5
|
26.8
|
1.0
|
N
|
B:ALA471
|
4.5
|
27.0
|
1.0
|
ND2
|
B:ASN470
|
4.6
|
27.7
|
1.0
|
CA
|
B:LYS473
|
4.6
|
27.5
|
1.0
|
CA
|
B:HIS482
|
4.6
|
34.6
|
1.0
|
NE2
|
B:HIS482
|
4.7
|
32.4
|
1.0
|
N
|
B:LYS473
|
4.8
|
30.4
|
1.0
|
O
|
B:GLY429
|
4.8
|
20.5
|
1.0
|
CE
|
B:MET474
|
4.8
|
22.5
|
1.0
|
CB
|
B:LYS473
|
4.8
|
32.2
|
1.0
|
CA
|
B:ALA471
|
4.9
|
25.4
|
1.0
|
CD2
|
B:HIS482
|
4.9
|
34.0
|
1.0
|
CG2
|
B:THR486
|
4.9
|
30.8
|
1.0
|
CG
|
B:MET474
|
5.0
|
33.4
|
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 17:08:58 2021
|