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Nickel in PDB 1iid: Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla

Enzymatic activity of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla

All present enzymatic activity of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla:
2.3.1.97;

Protein crystallography data

The structure of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla, PDB code: 1iid was solved by T.A.Farazi, J.I.Gordon, G.Waksman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 75.129, 97.060, 141.809, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 28.8

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla (pdb code 1iid). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla, PDB code: 1iid:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1iid

Go back to Nickel Binding Sites List in 1iid
Nickel binding site 1 out of 2 in the Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1

b:67.9
occ:1.00
OD1 A:ASP37 2.2 63.7 1.0
O A:ALA34 2.3 66.1 1.0
NE2 A:HIS38 2.5 51.2 1.0
CA A:ALA34 2.6 67.0 1.0
OD2 A:ASP37 2.6 63.7 1.0
C A:ALA34 2.7 66.6 1.0
CG A:ASP37 2.7 63.2 1.0
CE1 A:HIS38 2.9 51.0 1.0
N A:ALA34 3.3 66.8 1.0
CD2 A:HIS38 3.5 50.7 1.0
CB A:ALA34 3.8 67.5 1.0
N A:MET35 3.9 66.0 1.0
ND1 A:HIS38 3.9 50.3 1.0
CB A:ASP37 4.2 62.0 1.0
CG A:HIS38 4.3 52.2 1.0
O A:VAL209 4.5 47.3 1.0
N A:ASP37 4.6 61.3 1.0
O A:ASP37 4.7 59.0 1.0
CA A:MET35 4.7 66.2 1.0
CA A:ASP37 4.8 60.5 1.0
C A:ASP37 4.8 59.2 1.0
CE1 A:PHE49 4.9 33.5 1.0

Nickel binding site 2 out of 2 in 1iid

Go back to Nickel Binding Sites List in 1iid
Nickel binding site 2 out of 2 in the Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni2

b:62.4
occ:1.00
ND1 A:HIS296 2.4 47.5 1.0
O A:HOH534 2.4 41.3 1.0
O A:HOH552 2.7 50.4 1.0
CG A:HIS296 3.3 47.4 1.0
CE1 A:HIS296 3.4 47.5 1.0
CB A:HIS296 3.5 45.4 1.0
O A:HOH535 4.1 40.5 1.0
CA A:HIS296 4.1 43.0 1.0
O A:LYS125 4.2 48.7 1.0
CD2 A:HIS296 4.4 47.5 1.0
NE2 A:HIS296 4.5 48.5 1.0
O A:HIS296 5.0 41.3 1.0
C A:HIS296 5.0 42.8 1.0

Reference:

T.A.Farazi, G.Waksman, J.I.Gordon. Structures of Saccharomyces Cerevisiae N-Myristoyltransferase with Bound Myristoylcoa and Peptide Provide Insights About Substrate Recognition and Catalysis. Biochemistry V. 40 6335 2001.
ISSN: ISSN 0006-2960
PubMed: 11371195
DOI: 10.1021/BI0101401
Page generated: Fri Sep 25 07:55:00 2020
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