Zinc 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:
Zinc Binding Sites:
The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7knf
Go back to
Zinc Binding Sites List in 7knf
Zinc 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 Zinc with other atoms in the Zn 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:Zn601
b:14.4
occ:1.00
|
OD2
|
A:ASP467
|
1.9
|
11.5
|
1.0
|
OG
|
A:SER86
|
2.0
|
13.4
|
1.0
|
OD1
|
A:ASP37
|
2.0
|
12.0
|
1.0
|
NE2
|
A:HIS468
|
2.1
|
12.3
|
1.0
|
CG
|
A:ASP37
|
2.6
|
13.8
|
1.0
|
OD2
|
A:ASP37
|
2.6
|
13.4
|
1.0
|
CG
|
A:ASP467
|
2.8
|
14.6
|
1.0
|
OD1
|
A:ASP467
|
3.0
|
12.7
|
1.0
|
CE1
|
A:HIS468
|
3.0
|
14.0
|
1.0
|
CD2
|
A:HIS468
|
3.0
|
11.9
|
1.0
|
CB
|
A:SER86
|
3.0
|
16.9
|
1.0
|
CA
|
A:SER86
|
3.2
|
17.5
|
1.0
|
O
|
C:HOA101
|
3.4
|
19.5
|
1.0
|
N
|
A:SER86
|
3.7
|
14.2
|
1.0
|
NZ
|
A:LYS359
|
3.9
|
15.3
|
1.0
|
CB
|
A:ASP37
|
4.0
|
10.4
|
1.0
|
ND1
|
A:HIS468
|
4.1
|
12.9
|
1.0
|
CG
|
A:HIS468
|
4.1
|
12.6
|
1.0
|
OD2
|
A:ASP426
|
4.1
|
14.0
|
1.0
|
CB
|
A:ASP467
|
4.2
|
12.8
|
1.0
|
CG
|
A:ASP426
|
4.2
|
16.8
|
1.0
|
CA
|
A:ASP37
|
4.3
|
11.2
|
1.0
|
C
|
A:ASN85
|
4.3
|
13.4
|
1.0
|
N
|
A:GLY38
|
4.3
|
11.5
|
1.0
|
OD1
|
A:ASP426
|
4.5
|
15.8
|
1.0
|
C
|
A:SER86
|
4.5
|
12.8
|
1.0
|
CE
|
A:LYS359
|
4.6
|
17.1
|
1.0
|
CE1
|
A:HIS90
|
4.6
|
18.9
|
1.0
|
CB
|
A:ASP426
|
4.6
|
13.8
|
1.0
|
C
|
A:ASP37
|
4.6
|
12.8
|
1.0
|
N
|
C:HOA101
|
4.6
|
22.4
|
1.0
|
O
|
A:ASN85
|
4.7
|
12.5
|
1.0
|
ZN
|
A:ZN602
|
4.8
|
17.9
|
1.0
|
O
|
A:SER86
|
4.9
|
12.9
|
1.0
|
ND1
|
A:HIS90
|
4.9
|
13.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7knf
Go back to
Zinc Binding Sites List in 7knf
Zinc 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 Zinc with other atoms in the Zn 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:Zn602
b:17.9
occ:1.00
|
NE2
|
A:HIS430
|
2.1
|
15.7
|
1.0
|
NE2
|
A:HIS485
|
2.1
|
17.2
|
1.0
|
O
|
C:THR13
|
2.1
|
22.0
|
1.0
|
OD2
|
A:ASP426
|
2.2
|
14.0
|
1.0
|
O
|
C:HOA101
|
2.3
|
19.5
|
1.0
|
OD1
|
A:ASP426
|
2.5
|
15.8
|
1.0
|
CG
|
A:ASP426
|
2.7
|
16.8
|
1.0
|
C
|
C:THR13
|
2.9
|
24.1
|
1.0
|
CE1
|
A:HIS485
|
2.9
|
19.4
|
1.0
|
N
|
C:HOA101
|
3.0
|
22.4
|
1.0
|
CE1
|
A:HIS430
|
3.0
|
19.6
|
1.0
|
CD2
|
A:HIS430
|
3.1
|
14.3
|
1.0
|
CD2
|
A:HIS485
|
3.2
|
16.8
|
1.0
|
O
|
C:HOH206
|
3.9
|
29.5
|
1.0
|
ND1
|
A:HIS485
|
4.1
|
18.6
|
1.0
|
ND1
|
A:HIS430
|
4.1
|
15.6
|
1.0
|
CE1
|
A:HIS468
|
4.2
|
14.0
|
1.0
|
OG
|
A:SER86
|
4.2
|
13.4
|
1.0
|
CG
|
A:HIS430
|
4.2
|
15.3
|
1.0
|
CB
|
A:ASP426
|
4.2
|
13.8
|
1.0
|
CG
|
A:HIS485
|
4.2
|
17.9
|
1.0
|
NZ
|
A:LYS359
|
4.3
|
15.3
|
1.0
|
CA
|
C:THR13
|
4.4
|
21.2
|
1.0
|
ND2
|
A:ASN470
|
4.5
|
16.9
|
1.0
|
NE2
|
A:HIS468
|
4.6
|
12.3
|
1.0
|
ZN
|
A:ZN601
|
4.8
|
14.4
|
1.0
|
O
|
A:ASP426
|
4.8
|
12.4
|
1.0
|
OD1
|
A:ASP37
|
4.9
|
12.0
|
1.0
|
O
|
C:HOH204
|
4.9
|
23.9
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7knf
Go back to
Zinc Binding Sites List in 7knf
Zinc 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 Zinc with other atoms in the Zn 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:Zn601
b:18.1
occ:1.00
|
OD2
|
B:ASP467
|
1.9
|
13.8
|
1.0
|
OG
|
B:SER86
|
2.0
|
21.4
|
1.0
|
OD1
|
B:ASP37
|
2.1
|
14.5
|
1.0
|
NE2
|
B:HIS468
|
2.1
|
16.8
|
1.0
|
OD2
|
B:ASP37
|
2.5
|
18.5
|
1.0
|
CG
|
B:ASP37
|
2.6
|
14.8
|
1.0
|
CG
|
B:ASP467
|
2.8
|
17.9
|
1.0
|
CB
|
B:SER86
|
2.9
|
20.1
|
1.0
|
OD1
|
B:ASP467
|
3.0
|
15.2
|
1.0
|
CD2
|
B:HIS468
|
3.0
|
17.2
|
1.0
|
CE1
|
B:HIS468
|
3.1
|
18.9
|
1.0
|
CA
|
B:SER86
|
3.1
|
18.9
|
1.0
|
O
|
D:HOA101
|
3.4
|
25.1
|
1.0
|
N
|
B:SER86
|
3.6
|
19.2
|
1.0
|
NZ
|
B:LYS359
|
3.8
|
19.1
|
1.0
|
CB
|
B:ASP37
|
4.0
|
17.2
|
1.0
|
CG
|
B:HIS468
|
4.1
|
18.0
|
1.0
|
CB
|
B:ASP467
|
4.1
|
16.0
|
1.0
|
OD2
|
B:ASP426
|
4.1
|
15.8
|
1.0
|
ND1
|
B:HIS468
|
4.2
|
15.6
|
1.0
|
CG
|
B:ASP426
|
4.2
|
17.8
|
1.0
|
C
|
B:ASN85
|
4.3
|
14.3
|
1.0
|
CA
|
B:ASP37
|
4.3
|
16.0
|
1.0
|
N
|
B:GLY38
|
4.3
|
16.4
|
1.0
|
OD1
|
B:ASP426
|
4.5
|
15.3
|
1.0
|
C
|
B:SER86
|
4.5
|
18.7
|
1.0
|
CB
|
B:ASP426
|
4.5
|
13.4
|
1.0
|
CE
|
B:LYS359
|
4.6
|
17.4
|
1.0
|
CE1
|
B:HIS90
|
4.6
|
21.0
|
1.0
|
N
|
D:HOA101
|
4.6
|
20.8
|
1.0
|
C
|
B:ASP37
|
4.6
|
17.4
|
1.0
|
O
|
B:ASN85
|
4.7
|
14.4
|
1.0
|
ZN
|
B:ZN602
|
4.7
|
20.6
|
1.0
|
ND1
|
B:HIS90
|
4.9
|
19.5
|
1.0
|
O
|
B:SER86
|
4.9
|
17.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7knf
Go back to
Zinc Binding Sites List in 7knf
Zinc 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 Zinc with other atoms in the Zn 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:Zn602
b:20.6
occ:1.00
|
NE2
|
B:HIS430
|
2.1
|
18.9
|
1.0
|
NE2
|
B:HIS485
|
2.1
|
19.5
|
1.0
|
O
|
D:THR13
|
2.2
|
27.8
|
1.0
|
OD2
|
B:ASP426
|
2.2
|
15.8
|
1.0
|
O
|
D:HOA101
|
2.3
|
25.1
|
1.0
|
OD1
|
B:ASP426
|
2.5
|
15.3
|
1.0
|
CG
|
B:ASP426
|
2.7
|
17.8
|
1.0
|
C
|
D:THR13
|
2.9
|
23.5
|
1.0
|
CE1
|
B:HIS485
|
3.0
|
20.6
|
1.0
|
N
|
D:HOA101
|
3.0
|
20.8
|
1.0
|
CE1
|
B:HIS430
|
3.0
|
17.7
|
1.0
|
CD2
|
B:HIS430
|
3.1
|
17.1
|
1.0
|
CD2
|
B:HIS485
|
3.2
|
18.7
|
1.0
|
O
|
D:HOH205
|
3.8
|
31.8
|
1.0
|
OG
|
B:SER86
|
4.1
|
21.4
|
1.0
|
CE1
|
B:HIS468
|
4.1
|
18.9
|
1.0
|
ND1
|
B:HIS485
|
4.1
|
22.9
|
1.0
|
ND1
|
B:HIS430
|
4.2
|
22.2
|
1.0
|
CB
|
B:ASP426
|
4.2
|
13.4
|
1.0
|
CG
|
B:HIS430
|
4.2
|
18.1
|
1.0
|
CG
|
B:HIS485
|
4.3
|
20.4
|
1.0
|
NZ
|
B:LYS359
|
4.3
|
19.1
|
1.0
|
CA
|
D:THR13
|
4.4
|
22.8
|
1.0
|
ND2
|
B:ASN470
|
4.4
|
19.5
|
1.0
|
NE2
|
B:HIS468
|
4.4
|
16.8
|
1.0
|
ZN
|
B:ZN601
|
4.7
|
18.1
|
1.0
|
O
|
B:ASP426
|
4.8
|
15.7
|
1.0
|
OD1
|
B:ASP37
|
4.9
|
14.5
|
1.0
|
O
|
D:HOH202
|
5.0
|
24.9
|
1.0
|
CA
|
B:ASP426
|
5.0
|
17.5
|
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 17:48:28 2021
|