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: Sat Apr 17 17:48:28 2021

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