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

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:

Sodium (Na) 4 atoms

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: Tue Oct 29 22:24:22 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy