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Sodium in PDB 1c23: E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex

Enzymatic activity of E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex

All present enzymatic activity of E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex:
3.4.11.18;

Protein crystallography data

The structure of E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex, PDB code: 1c23 was solved by W.T.Lowther, Y.Zhang, P.B.Sampson, J.F.Honek, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.20 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.221, 67.518, 48.823, 90.00, 111.20, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1c23:

The structure of E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex (pdb code 1c23). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex, PDB code: 1c23:

Sodium binding site 1 out of 1 in 1c23

Go back to Sodium Binding Sites List in 1c23
Sodium binding site 1 out of 1 in the E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli Methionine Aminopeptidase: Methionine Phosphonate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:12.1
occ:1.00
 O A:VAL76 2.6 14.0 1.0
O A:SER231 2.6 17.7 1.0
O A:ASN74 2.7 18.2 1.0
O A:HOH586 2.8 16.9 1.0
O A:SER72 3.4 14.5 1.0
C A:ASN74 3.5 15.9 1.0
N A:ASN74 3.6 7.5 1.0
C A:SER231 3.7 16.7 1.0
C A:VAL76 3.8 16.3 1.0
C A:ILE73 3.8 10.3 1.0
CA A:ASN74 3.9 9.0 1.0
C A:SER72 4.0 19.5 1.0
O A:ILE73 4.2 15.2 1.0
N A:VAL76 4.3 11.9 1.0
CE A:MET112 4.3 15.0 1.0
CB A:SER72 4.3 10.6 1.0
O A:HOH507 4.3 15.3 1.0
CA A:ILE73 4.4 12.7 1.0
N A:SER231 4.4 14.1 1.0
CA A:SER231 4.4 10.4 1.0
N A:ILE73 4.4 12.8 1.0
CB A:SER231 4.4 16.0 1.0
CA A:VAL76 4.6 13.7 1.0
N A:GLU75 4.6 11.6 1.0
O A:ILE93 4.6 20.7 1.0
N A:ALA232 4.6 9.2 1.0
CG1 A:ILE93 4.7 17.9 1.0
N A:VAL77 4.8 15.0 1.0
CA A:ALA232 4.8 8.7 1.0
C A:GLU75 4.8 18.5 1.0
CD1 A:ILE93 4.8 16.2 1.0
O A:VAL77 4.8 17.8 1.0
CB A:VAL76 4.8 16.6 1.0
CA A:SER72 4.8 10.6 1.0
CA A:VAL77 5.0 17.9 1.0

Reference:

W.T.Lowther, Y.Zhang, P.B.Sampson, J.F.Honek, B.W.Matthews. Insights Into the Mechanism of Escherichia Coli Methionine Aminopeptidase From the Structural Analysis of Reaction Products and Phosphorus-Based Transition-State Analogues. Biochemistry V. 38 14810 1999.
ISSN: ISSN 0006-2960
PubMed: 10555963
DOI: 10.1021/BI991711G
Page generated: Sun Oct 6 17:57:45 2024

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