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Zinc in PDB 5kgl: 2.45A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Orthorhombic Form)

Enzymatic activity of 2.45A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Orthorhombic Form)

All present enzymatic activity of 2.45A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Orthorhombic Form):
5.4.2.12;

Protein crystallography data

The structure of 2.45A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Orthorhombic Form), PDB code: 5kgl was solved by S.Lovell, N.Mehzabeen, K.P.Battaile, H.Yu, P.Dranchak, R.Macarthur, Z.Li, T.Carlow, H.Suga, J.Inglese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.44 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.321, 98.852, 173.144, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 26

Other elements in 5kgl:

The structure of 2.45A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Orthorhombic Form) also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.45A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Orthorhombic Form) (pdb code 5kgl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the 2.45A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Orthorhombic Form), PDB code: 5kgl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5kgl

Go back to Zinc Binding Sites List in 5kgl
Zinc binding site 1 out of 2 in the 2.45A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Orthorhombic Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.45A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:24.5
occ:1.00
OD1 A:ASP467 2.0 15.1 1.0
OD1 A:ASP37 2.0 19.6 1.0
OG A:SER86 2.1 18.2 1.0
NE2 A:HIS468 2.1 23.1 1.0
CG A:ASP37 2.6 20.7 1.0
OD2 A:ASP37 2.8 18.0 1.0
CB A:SER86 2.8 16.4 1.0
CG A:ASP467 3.0 17.1 1.0
CD2 A:HIS468 3.0 13.3 1.0
CA A:SER86 3.1 24.0 1.0
CE1 A:HIS468 3.1 18.7 1.0
OD2 A:ASP467 3.4 14.7 1.0
N A:SER86 3.5 16.5 1.0
NZ A:LYS359 3.6 22.7 1.0
CB A:ASP37 4.1 19.4 1.0
CG A:ASP426 4.1 21.9 1.0
ND1 A:HIS468 4.1 16.7 1.0
CG A:HIS468 4.1 16.4 1.0
OD2 A:ASP426 4.2 25.1 1.0
OD1 A:ASP426 4.2 27.0 1.0
CB A:ASP467 4.3 18.5 1.0
C A:ASN85 4.3 20.9 1.0
CE A:LYS359 4.3 21.8 1.0
C A:SER86 4.4 16.9 1.0
CA A:ASP37 4.5 18.6 1.0
CB A:ASP426 4.6 28.7 1.0
MN A:MN602 4.6 32.5 1.0
N A:GLY38 4.6 16.9 1.0
O A:ASN85 4.7 20.8 1.0
C A:ASP37 4.8 19.9 1.0
CE1 A:HIS90 4.8 21.4 1.0
O A:SER86 4.8 18.9 1.0
CE1 A:HIS485 4.9 20.2 1.0
NE2 A:HIS485 5.0 20.5 1.0

Zinc binding site 2 out of 2 in 5kgl

Go back to Zinc Binding Sites List in 5kgl
Zinc binding site 2 out of 2 in the 2.45A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Orthorhombic Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.45A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:29.6
occ:1.00
OD1 B:ASP37 1.9 21.7 1.0
OD2 B:ASP467 2.0 26.7 1.0
NE2 B:HIS468 2.1 23.2 1.0
OG B:SER86 2.1 33.0 1.0
CG B:ASP37 2.7 23.2 1.0
CD2 B:HIS468 2.9 26.4 1.0
OD2 B:ASP37 2.9 24.9 1.0
CB B:SER86 2.9 30.0 1.0
CG B:ASP467 2.9 26.4 1.0
CE1 B:HIS468 3.1 20.9 1.0
OD1 B:ASP467 3.1 20.3 1.0
CA B:SER86 3.1 27.5 1.0
N B:SER86 3.6 31.9 1.0
NZ B:LYS359 3.7 31.7 1.0
OD2 B:ASP426 3.9 36.7 1.0
CG B:HIS468 4.0 25.8 1.0
CB B:ASP37 4.0 25.7 1.0
CG B:ASP426 4.0 30.8 1.0
ND1 B:HIS468 4.1 18.7 1.0
C B:ASN85 4.3 27.6 1.0
CB B:ASP467 4.3 22.3 1.0
CA B:ASP37 4.4 24.6 1.0
OD1 B:ASP426 4.4 22.6 1.0
N B:GLY38 4.4 16.2 1.0
CB B:ASP426 4.5 26.8 1.0
MN B:MN602 4.5 44.4 1.0
C B:SER86 4.5 25.7 1.0
CE B:LYS359 4.6 36.6 1.0
O B:ASN85 4.7 20.9 1.0
C B:ASP37 4.7 17.1 1.0
CE1 B:HIS485 4.9 30.4 1.0
O B:SER86 4.9 34.5 1.0
CE1 B:HIS90 5.0 38.0 1.0
NE2 B:HIS485 5.0 30.6 1.0

Reference:

H.Yu, P.Dranchak, Z.Li, R.Macarthur, M.S.Munson, N.Mehzabeen, N.J.Baird, K.P.Battalie, D.Ross, S.Lovell, C.K.Carlow, H.Suga, J.Inglese. Macrocycle Peptides Delineate Locked-Open Inhibition Mechanism For Microorganism Phosphoglycerate Mutases. Nat Commun V. 8 14932 2017.
ISSN: ESSN 2041-1723
PubMed: 28368002
DOI: 10.1038/NCOMMS14932
Page generated: Wed Dec 16 06:27:19 2020

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