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Zinc in PDB 7tl7: 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)

Enzymatic activity of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)

All present enzymatic activity of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2):
5.4.2.12;

Protein crystallography data

The structure of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2), PDB code: 7tl7 was solved by L.Liu, S.Lovell, K.P.Battaile, P.Dranchak, B.Queme, M.Aitha, R.H.P.Vanneer, H.Kimura, T.Katho, H.Suga, J.Inglese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.84 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.999, 87.624, 151.341, 90, 97.13, 90
R / Rfree (%) 17.1 / 21.6

Other elements in 7tl7:

The structure of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) (pdb code 7tl7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2), PDB code: 7tl7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7tl7

Go back to Zinc Binding Sites List in 7tl7
Zinc binding site 1 out of 8 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:23.3
occ:1.00
 OD2 A:ASP426 2.0 25.1 1.0
NE2 A:HIS485 2.0 22.2 1.0
NE2 A:HIS430 2.1 26.9 1.0
SG a:CYS14 2.3 27.0 1.0
CG A:ASP426 2.7 26.6 1.0
OD1 A:ASP426 2.8 21.4 1.0
CE1 A:HIS485 3.0 22.9 1.0
CD2 A:HIS430 3.0 23.1 1.0
CD2 A:HIS485 3.1 20.4 1.0
CE1 A:HIS430 3.1 33.5 1.0
CB a:CYS14 3.4 24.5 1.0
NZ A:LYS359 4.0 26.2 1.0
OG A:SER86 4.1 21.3 1.0
ND1 A:HIS485 4.1 24.8 1.0
CG A:HIS430 4.2 25.4 1.0
CB A:ASP426 4.2 25.5 1.0
ND1 A:HIS430 4.2 22.0 1.0
CG A:HIS485 4.2 23.6 1.0
CE1 A:HIS468 4.3 25.1 1.0
O A:HOH788 4.3 21.5 1.0
C a:CYS14 4.4 36.6 1.0
O a:CYS14 4.4 39.7 1.0
NE2 A:HIS468 4.5 22.1 1.0
CA a:CYS14 4.5 26.4 1.0
ND2 A:ASN470 4.5 24.3 1.0
O A:ASP426 4.7 24.4 1.0
ZN A:ZN602 4.8 28.1 1.0
N a:NH215 4.8 28.9 1.0
OD1 A:ASP37 4.8 20.5 1.0
C A:ASP426 4.9 25.6 1.0

Zinc binding site 2 out of 8 in 7tl7

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Zinc binding site 2 out of 8 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:28.1
occ:1.00
 OD1 A:ASP37 1.9 20.5 1.0
OG A:SER86 1.9 21.3 1.0
OD2 A:ASP467 2.0 21.8 1.0
NE2 A:HIS468 2.1 22.1 1.0
CG A:ASP37 2.6 22.6 1.0
CB A:SER86 2.8 21.3 1.0
CG A:ASP467 2.8 22.2 1.0
OD2 A:ASP37 2.8 23.3 1.0
CD2 A:HIS468 2.9 23.5 1.0
OD1 A:ASP467 3.1 21.8 1.0
CE1 A:HIS468 3.1 25.1 1.0
CA A:SER86 3.1 19.3 1.0
N A:SER86 3.6 21.4 1.0
NZ A:LYS359 3.7 26.2 1.0
CB A:ASP37 4.0 23.6 1.0
CG A:HIS468 4.0 20.8 1.0
OD2 A:ASP426 4.1 25.1 1.0
ND1 A:HIS468 4.1 22.5 1.0
CG A:ASP426 4.2 26.6 1.0
CB A:ASP467 4.2 18.2 1.0
CA A:ASP37 4.3 22.9 1.0
C A:ASN85 4.4 21.6 1.0
N A:GLY38 4.4 21.4 1.0
CE A:LYS359 4.4 29.0 1.0
C A:SER86 4.5 22.1 1.0
OD1 A:ASP426 4.5 21.4 1.0
CB A:ASP426 4.6 25.5 1.0
C A:ASP37 4.7 22.4 1.0
CE1 A:HIS90 4.7 21.8 1.0
ZN A:ZN601 4.8 23.3 1.0
O A:ASN85 4.8 21.7 1.0
O A:SER86 4.9 22.2 1.0
ND1 A:HIS90 5.0 20.9 1.0

Zinc binding site 3 out of 8 in 7tl7

Go back to Zinc Binding Sites List in 7tl7
Zinc binding site 3 out of 8 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:28.5
occ:1.00
 NE2 B:HIS485 2.0 23.2 1.0
NE2 B:HIS430 2.0 36.3 1.0
SG b:CYS14 2.2 30.6 1.0
OD2 B:ASP426 2.3 29.6 1.0
OD1 B:ASP426 2.6 31.0 1.0
CE1 B:HIS485 2.7 26.1 1.0
CG B:ASP426 2.8 31.3 1.0
CE1 B:HIS430 3.0 30.2 1.0
CD2 B:HIS430 3.1 35.7 1.0
CB b:CYS14 3.1 33.5 1.0
CD2 B:HIS485 3.2 30.5 1.0
ND1 B:HIS485 3.9 23.2 1.0
NZ B:LYS359 4.1 35.5 1.0
ND1 B:HIS430 4.1 36.7 1.0
OG B:SER86 4.1 31.0 1.0
CG B:HIS485 4.2 23.0 1.0
CG B:HIS430 4.2 32.8 1.0
CE1 B:HIS468 4.2 27.9 1.0
ND2 B:ASN470 4.2 33.5 1.0
O B:HOH800 4.3 23.6 1.0
CA b:CYS14 4.3 35.4 1.0
C b:CYS14 4.3 40.8 1.0
CB B:ASP426 4.3 33.2 1.0
NE2 B:HIS468 4.5 26.7 1.0
N b:NH215 4.6 38.3 1.0
O b:CYS14 4.6 43.2 1.0
ZN B:ZN602 4.7 34.1 1.0
OD1 B:ASP37 4.8 24.3 1.0
O B:ASP426 4.8 29.2 1.0

Zinc binding site 4 out of 8 in 7tl7

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Zinc binding site 4 out of 8 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:34.1
occ:1.00
 OG B:SER86 1.9 31.0 1.0
OD1 B:ASP37 2.0 24.3 1.0
NE2 B:HIS468 2.1 26.7 1.0
OD2 B:ASP467 2.1 25.0 1.0
CG B:ASP37 2.6 26.6 1.0
OD2 B:ASP37 2.8 25.8 1.0
CB B:SER86 2.8 29.4 1.0
CD2 B:HIS468 2.9 23.5 1.0
CG B:ASP467 3.0 20.7 1.0
CA B:SER86 3.1 25.6 1.0
CE1 B:HIS468 3.2 27.9 1.0
OD1 B:ASP467 3.2 22.9 1.0
N B:SER86 3.5 24.4 1.0
NZ B:LYS359 4.0 35.5 1.0
CB B:ASP37 4.0 24.8 1.0
OD2 B:ASP426 4.0 29.6 1.0
CG B:HIS468 4.1 20.1 1.0
ND1 B:HIS468 4.1 24.0 1.0
CG B:ASP426 4.2 31.3 1.0
C B:ASN85 4.3 26.1 1.0
CB B:ASP467 4.3 21.8 1.0
CA B:ASP37 4.3 23.2 1.0
CE B:LYS359 4.4 33.5 1.0
N B:GLY38 4.4 29.5 1.0
C B:SER86 4.5 25.3 1.0
OD1 B:ASP426 4.5 31.0 1.0
CB B:ASP426 4.7 33.2 1.0
C B:ASP37 4.7 31.6 1.0
ZN B:ZN601 4.7 28.5 1.0
CE1 B:HIS90 4.8 23.7 1.0
O B:ASN85 4.8 24.6 1.0
CD B:LYS359 4.9 28.0 1.0
O B:SER86 4.9 21.6 1.0
NE2 B:HIS485 5.0 23.2 1.0

Zinc binding site 5 out of 8 in 7tl7

Go back to Zinc Binding Sites List in 7tl7
Zinc binding site 5 out of 8 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:19.7
occ:1.00
 NE2 C:HIS485 2.0 19.2 1.0
NE2 C:HIS430 2.0 20.4 1.0
OD2 C:ASP426 2.1 19.1 1.0
SG c:CYS14 2.3 21.1 1.0
OD1 C:ASP426 2.7 18.2 1.0
CG C:ASP426 2.7 19.7 1.0
CE1 C:HIS485 2.9 21.5 1.0
CD2 C:HIS430 3.0 20.2 1.0
CE1 C:HIS430 3.0 23.8 1.0
CD2 C:HIS485 3.1 24.0 1.0
CB c:CYS14 3.1 25.0 1.0
NZ C:LYS359 4.0 19.9 1.0
ND1 C:HIS485 4.1 21.3 1.0
ND1 C:HIS430 4.1 21.0 1.0
CG C:HIS430 4.1 21.4 1.0
CG C:HIS485 4.2 24.9 1.0
OG C:SER86 4.2 19.8 1.0
CB C:ASP426 4.2 17.2 1.0
CE1 C:HIS468 4.2 17.5 1.0
NE2 C:HIS468 4.4 17.4 1.0
O C:HOH788 4.4 19.6 1.0
CA c:CYS14 4.4 26.8 1.0
ND2 C:ASN470 4.4 23.8 1.0
C c:CYS14 4.6 31.6 1.0
O C:ASP426 4.8 22.9 1.0
ZN C:ZN603 4.8 25.9 1.0
OD1 C:ASP37 4.8 19.7 1.0
O c:CYS14 4.8 41.3 1.0
N c:NH215 4.9 39.0 1.0
C C:ASP426 4.9 18.4 1.0
CA C:ASP426 5.0 18.4 1.0

Zinc binding site 6 out of 8 in 7tl7

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Zinc binding site 6 out of 8 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn603

b:25.9
occ:1.00
 OD1 C:ASP37 1.9 19.7 1.0
OD2 C:ASP467 2.0 20.6 1.0
OG C:SER86 2.0 19.8 1.0
NE2 C:HIS468 2.2 17.4 1.0
CG C:ASP37 2.6 18.0 1.0
CG C:ASP467 2.8 17.3 1.0
OD2 C:ASP37 2.9 21.2 1.0
CD2 C:HIS468 2.9 19.6 1.0
CB C:SER86 2.9 21.8 1.0
OD1 C:ASP467 3.0 18.2 1.0
CA C:SER86 3.1 16.4 1.0
CE1 C:HIS468 3.2 17.5 1.0
N C:SER86 3.6 20.6 1.0
NZ C:LYS359 3.9 19.9 1.0
CB C:ASP37 4.0 20.8 1.0
OD2 C:ASP426 4.0 19.1 1.0
CG C:HIS468 4.1 15.2 1.0
CG C:ASP426 4.1 19.7 1.0
ND1 C:HIS468 4.2 21.6 1.0
CB C:ASP467 4.2 16.8 1.0
CA C:ASP37 4.3 16.6 1.0
C C:ASN85 4.3 16.9 1.0
N C:GLY38 4.4 18.2 1.0
OD1 C:ASP426 4.5 18.2 1.0
CE C:LYS359 4.5 20.6 1.0
C C:SER86 4.5 21.0 1.0
CB C:ASP426 4.6 17.2 1.0
C C:ASP37 4.7 16.1 1.0
O C:ASN85 4.8 17.4 1.0
ZN C:ZN602 4.8 19.7 1.0
CE1 C:HIS90 4.8 23.2 1.0
O C:SER86 4.9 18.0 1.0
CD C:LYS359 5.0 20.9 1.0

Zinc binding site 7 out of 8 in 7tl7

Go back to Zinc Binding Sites List in 7tl7
Zinc binding site 7 out of 8 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:27.9
occ:1.00
 NE2 D:HIS485 2.0 26.9 1.0
NE2 D:HIS430 2.1 35.8 1.0
SG d:CYS14 2.2 30.3 1.0
OD2 D:ASP426 2.2 32.0 1.0
OD1 D:ASP426 2.6 27.8 1.0
CG D:ASP426 2.7 28.3 1.0
CE1 D:HIS485 2.8 32.4 1.0
CD2 D:HIS430 3.0 40.2 1.0
CE1 D:HIS430 3.1 43.6 1.0
CB d:CYS14 3.1 31.3 1.0
CD2 D:HIS485 3.2 26.0 1.0
ND1 D:HIS485 4.0 30.3 1.0
OG D:SER86 4.1 28.3 1.0
NZ D:LYS359 4.1 27.9 1.0
ND1 D:HIS430 4.2 43.1 1.0
CG D:HIS430 4.2 40.6 1.0
CG D:HIS485 4.2 29.4 1.0
CB D:ASP426 4.2 29.6 1.0
N d:NH215 4.3 39.8 1.0
C d:CYS14 4.3 36.0 1.0
CA d:CYS14 4.3 38.8 1.0
CE1 D:HIS468 4.3 26.5 1.0
O D:HOH765 4.3 24.5 1.0
ND2 D:ASN470 4.4 34.4 1.0
NE2 D:HIS468 4.5 27.4 1.0
O d:CYS14 4.6 45.0 1.0
ZN D:ZN603 4.8 32.6 1.0
OD1 D:ASP37 4.9 30.4 1.0
O D:ASP426 4.9 29.9 1.0
C D:ASP426 5.0 28.3 1.0

Zinc binding site 8 out of 8 in 7tl7

Go back to Zinc Binding Sites List in 7tl7
Zinc binding site 8 out of 8 in the 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 1.90A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Sa-D2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:32.6
occ:1.00
 OD1 D:ASP37 1.9 30.4 1.0
OG D:SER86 2.1 28.3 1.0
OD2 D:ASP467 2.1 27.7 1.0
NE2 D:HIS468 2.1 27.4 1.0
CG D:ASP37 2.7 25.3 1.0
CD2 D:HIS468 2.9 25.1 1.0
OD2 D:ASP37 2.9 28.9 1.0
CG D:ASP467 2.9 20.8 1.0
CB D:SER86 2.9 28.5 1.0
OD1 D:ASP467 3.0 23.1 1.0
CA D:SER86 3.1 21.0 1.0
CE1 D:HIS468 3.2 26.5 1.0
N D:SER86 3.5 20.2 1.0
NZ D:LYS359 3.9 27.9 1.0
OD2 D:ASP426 3.9 32.0 1.0
CB D:ASP37 4.0 29.1 1.0
CG D:HIS468 4.0 17.9 1.0
ND1 D:HIS468 4.2 23.0 1.0
CG D:ASP426 4.2 28.3 1.0
C D:ASN85 4.2 27.7 1.0
CB D:ASP467 4.3 25.3 1.0
CA D:ASP37 4.3 29.8 1.0
N D:GLY38 4.3 26.7 1.0
C D:SER86 4.5 27.4 1.0
CE D:LYS359 4.5 29.0 1.0
CB D:ASP426 4.6 29.6 1.0
OD1 D:ASP426 4.6 27.8 1.0
C D:ASP37 4.7 28.2 1.0
O D:ASN85 4.7 23.7 1.0
CE1 D:HIS90 4.8 29.1 1.0
ZN D:ZN602 4.8 27.9 1.0
O D:SER86 4.9 21.9 1.0
NE2 D:HIS485 5.0 26.9 1.0
ND1 D:HIS90 5.0 25.5 1.0

Reference:

R.H.P.Van Neer, P.K.Dranchak, L.Liu, M.Aitha, B.Queme, H.Kimura, T.Katoh, K.P.Battaile, S.Lovell, J.Inglese, H.Suga. Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases. Acs Chem.Biol. V. 17 2284 2022.
ISSN: ESSN 1554-8937
PubMed: 35904259
DOI: 10.1021/ACSCHEMBIO.2C00403
Page generated: Wed Oct 30 11:37:57 2024

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