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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:

Chlorine (Cl) 4 atoms
Sodium (Na) 4 atoms

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: Tue Oct 29 22:24:21 2024

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