Atomistry » Zinc » PDB 7khc-7kuq » 7kng
Atomistry »
  Zinc »
    PDB 7khc-7kuq »
      7kng »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy