Zinc 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:
Zinc Binding Sites:
The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7kng
Go back to
Zinc Binding Sites List in 7kng
Zinc 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 Zinc with other atoms in the Zn 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:Zn605
b:26.9
occ:1.00
|
OD1
|
A:ASP37
|
2.0
|
28.1
|
1.0
|
OD2
|
A:ASP467
|
2.0
|
23.9
|
1.0
|
OG
|
A:SER86
|
2.0
|
27.8
|
1.0
|
NE2
|
A:HIS468
|
2.1
|
26.1
|
1.0
|
OD2
|
A:ASP37
|
2.5
|
22.3
|
1.0
|
CG
|
A:ASP37
|
2.5
|
27.2
|
1.0
|
CG
|
A:ASP467
|
2.8
|
27.4
|
1.0
|
CB
|
A:SER86
|
2.9
|
28.5
|
1.0
|
CE1
|
A:HIS468
|
3.0
|
21.2
|
1.0
|
CD2
|
A:HIS468
|
3.0
|
24.9
|
1.0
|
OD1
|
A:ASP467
|
3.0
|
27.0
|
1.0
|
CA
|
A:SER86
|
3.2
|
22.6
|
1.0
|
N
|
A:SER86
|
3.6
|
21.3
|
1.0
|
NZ
|
A:LYS359
|
3.7
|
27.3
|
1.0
|
OD2
|
A:ASP426
|
3.9
|
23.7
|
1.0
|
CB
|
A:ASP37
|
4.0
|
24.1
|
1.0
|
ND1
|
A:HIS468
|
4.1
|
23.1
|
1.0
|
CG
|
A:ASP426
|
4.1
|
27.4
|
1.0
|
CG
|
A:HIS468
|
4.1
|
25.4
|
1.0
|
CB
|
A:ASP467
|
4.2
|
21.7
|
1.0
|
CE
|
A:LYS359
|
4.3
|
27.4
|
1.0
|
CA
|
A:ASP37
|
4.4
|
25.4
|
1.0
|
C
|
A:ASN85
|
4.4
|
21.2
|
1.0
|
N
|
A:GLY38
|
4.4
|
25.9
|
1.0
|
OD1
|
A:ASP426
|
4.5
|
23.0
|
1.0
|
CB
|
A:ASP426
|
4.5
|
22.1
|
1.0
|
CE1
|
A:HIS90
|
4.6
|
31.6
|
1.0
|
ZN
|
A:ZN606
|
4.6
|
26.0
|
1.0
|
C
|
A:SER86
|
4.6
|
20.2
|
1.0
|
C
|
A:ASP37
|
4.7
|
28.9
|
1.0
|
O
|
A:ASN85
|
4.8
|
21.6
|
1.0
|
CD
|
A:LYS359
|
4.9
|
21.3
|
1.0
|
ND1
|
A:HIS90
|
4.9
|
27.0
|
1.0
|
CE1
|
A:HIS485
|
4.9
|
32.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7kng
Go back to
Zinc Binding Sites List in 7kng
Zinc 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 Zinc with other atoms in the Zn 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:Zn606
b:26.0
occ:1.00
|
NE2
|
A:HIS430
|
2.0
|
22.4
|
1.0
|
NE2
|
A:HIS485
|
2.0
|
28.5
|
1.0
|
OD2
|
A:ASP426
|
2.0
|
23.7
|
1.0
|
SG
|
C:CYS14
|
2.3
|
25.7
|
1.0
|
OD1
|
A:ASP426
|
2.5
|
23.0
|
1.0
|
CG
|
A:ASP426
|
2.6
|
27.4
|
1.0
|
CE1
|
A:HIS485
|
2.8
|
32.0
|
1.0
|
CE1
|
A:HIS430
|
2.8
|
24.7
|
1.0
|
CD2
|
A:HIS430
|
3.1
|
23.6
|
1.0
|
CD2
|
A:HIS485
|
3.2
|
31.6
|
1.0
|
CB
|
C:CYS14
|
3.2
|
36.9
|
1.0
|
O
|
C:CYS14
|
3.6
|
38.5
|
1.0
|
ND1
|
A:HIS485
|
4.0
|
26.4
|
1.0
|
C
|
C:CYS14
|
4.0
|
36.5
|
1.0
|
ND1
|
A:HIS430
|
4.0
|
19.6
|
1.0
|
NZ
|
A:LYS359
|
4.0
|
27.3
|
1.0
|
CB
|
A:ASP426
|
4.1
|
22.1
|
1.0
|
CE1
|
A:HIS468
|
4.2
|
21.2
|
1.0
|
CG
|
A:HIS430
|
4.2
|
22.2
|
1.0
|
OG
|
A:SER86
|
4.2
|
27.8
|
1.0
|
CG
|
A:HIS485
|
4.2
|
27.0
|
1.0
|
CA
|
C:CYS14
|
4.2
|
31.8
|
1.0
|
O
|
A:HOH798
|
4.3
|
25.3
|
1.0
|
ND2
|
A:ASN470
|
4.4
|
27.2
|
1.0
|
NE2
|
A:HIS468
|
4.5
|
26.1
|
1.0
|
OD1
|
A:ASP37
|
4.6
|
28.1
|
1.0
|
ZN
|
A:ZN605
|
4.6
|
26.9
|
1.0
|
O
|
A:ASP426
|
4.8
|
19.3
|
1.0
|
N
|
C:NH215
|
4.9
|
31.5
|
1.0
|
C
|
A:ASP426
|
4.9
|
26.0
|
1.0
|
N
|
C:CYS14
|
4.9
|
34.7
|
1.0
|
CA
|
A:ASP426
|
4.9
|
22.4
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7kng
Go back to
Zinc Binding Sites List in 7kng
Zinc 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 Zinc with other atoms in the Zn 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:Zn605
b:26.2
occ:1.00
|
OD2
|
B:ASP467
|
1.9
|
22.3
|
1.0
|
OG
|
B:SER86
|
2.0
|
31.5
|
1.0
|
OD1
|
B:ASP37
|
2.0
|
25.3
|
1.0
|
NE2
|
B:HIS468
|
2.1
|
24.7
|
1.0
|
OD2
|
B:ASP37
|
2.5
|
21.5
|
1.0
|
CG
|
B:ASP37
|
2.6
|
26.6
|
1.0
|
CG
|
B:ASP467
|
2.8
|
28.6
|
1.0
|
CB
|
B:SER86
|
2.9
|
22.4
|
1.0
|
CD2
|
B:HIS468
|
2.9
|
24.6
|
1.0
|
CE1
|
B:HIS468
|
3.0
|
28.8
|
1.0
|
OD1
|
B:ASP467
|
3.1
|
24.9
|
1.0
|
CA
|
B:SER86
|
3.2
|
21.7
|
1.0
|
N
|
B:SER86
|
3.6
|
24.5
|
1.0
|
NZ
|
B:LYS359
|
3.7
|
23.2
|
1.0
|
OD2
|
B:ASP426
|
3.9
|
27.0
|
1.0
|
CB
|
B:ASP37
|
4.0
|
26.8
|
1.0
|
CG
|
B:HIS468
|
4.1
|
23.3
|
1.0
|
ND1
|
B:HIS468
|
4.1
|
29.4
|
1.0
|
CG
|
B:ASP426
|
4.1
|
27.4
|
1.0
|
CB
|
B:ASP467
|
4.2
|
22.4
|
1.0
|
CE
|
B:LYS359
|
4.3
|
28.4
|
1.0
|
CA
|
B:ASP37
|
4.4
|
23.7
|
1.0
|
C
|
B:ASN85
|
4.4
|
24.1
|
1.0
|
OD1
|
B:ASP426
|
4.5
|
26.7
|
1.0
|
N
|
B:GLY38
|
4.5
|
20.6
|
1.0
|
CB
|
B:ASP426
|
4.5
|
26.2
|
1.0
|
CE1
|
B:HIS90
|
4.5
|
23.6
|
1.0
|
C
|
B:SER86
|
4.6
|
21.9
|
1.0
|
ZN
|
B:ZN606
|
4.7
|
26.2
|
1.0
|
C
|
B:ASP37
|
4.8
|
24.2
|
1.0
|
ND1
|
B:HIS90
|
4.9
|
19.0
|
1.0
|
NE2
|
B:HIS485
|
4.9
|
24.2
|
1.0
|
O
|
B:ASN85
|
4.9
|
26.2
|
1.0
|
CD
|
B:LYS359
|
4.9
|
22.1
|
1.0
|
CE1
|
B:HIS485
|
4.9
|
28.3
|
1.0
|
O
|
B:SER86
|
5.0
|
23.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7kng
Go back to
Zinc Binding Sites List in 7kng
Zinc 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 Zinc with other atoms in the Zn 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:Zn606
b:26.2
occ:1.00
|
NE2
|
B:HIS485
|
2.0
|
24.2
|
1.0
|
NE2
|
B:HIS430
|
2.0
|
26.3
|
1.0
|
OD2
|
B:ASP426
|
2.1
|
27.0
|
1.0
|
OD1
|
B:ASP426
|
2.4
|
26.7
|
1.0
|
SG
|
D:CYS14
|
2.4
|
32.1
|
1.0
|
CG
|
B:ASP426
|
2.6
|
27.4
|
1.0
|
CE1
|
B:HIS485
|
2.9
|
28.3
|
1.0
|
CE1
|
B:HIS430
|
3.0
|
27.9
|
1.0
|
CD2
|
B:HIS430
|
3.1
|
23.6
|
1.0
|
CD2
|
B:HIS485
|
3.1
|
28.3
|
1.0
|
CB
|
D:CYS14
|
3.2
|
34.4
|
1.0
|
O
|
D:CYS14
|
3.7
|
31.2
|
1.0
|
C
|
D:CYS14
|
4.0
|
34.7
|
1.0
|
ND1
|
B:HIS485
|
4.0
|
30.1
|
1.0
|
ND1
|
B:HIS430
|
4.1
|
27.7
|
1.0
|
NZ
|
B:LYS359
|
4.1
|
23.2
|
1.0
|
CB
|
B:ASP426
|
4.1
|
26.2
|
1.0
|
OG
|
B:SER86
|
4.1
|
31.5
|
1.0
|
CG
|
B:HIS485
|
4.2
|
26.3
|
1.0
|
CG
|
B:HIS430
|
4.2
|
26.6
|
1.0
|
CE1
|
B:HIS468
|
4.2
|
28.8
|
1.0
|
CA
|
D:CYS14
|
4.2
|
28.0
|
1.0
|
O
|
B:HOH776
|
4.4
|
26.2
|
1.0
|
ND2
|
B:ASN470
|
4.4
|
27.7
|
1.0
|
NE2
|
B:HIS468
|
4.5
|
24.7
|
1.0
|
OD1
|
B:ASP37
|
4.6
|
25.3
|
1.0
|
ZN
|
B:ZN605
|
4.7
|
26.2
|
1.0
|
O
|
B:ASP426
|
4.7
|
20.7
|
1.0
|
N
|
D:NH215
|
4.8
|
35.0
|
1.0
|
C
|
B:ASP426
|
4.9
|
23.9
|
1.0
|
N
|
D:CYS14
|
4.9
|
34.8
|
1.0
|
CA
|
B:ASP426
|
5.0
|
24.7
|
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 17:48:41 2021
|