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Cobalt in PDB 1yj3: Crystal Structure Analysis of Product Bound Methionine Aminopeptidase Type 1C From Mycobacterium Tuberculosis

Enzymatic activity of Crystal Structure Analysis of Product Bound Methionine Aminopeptidase Type 1C From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure Analysis of Product Bound Methionine Aminopeptidase Type 1C From Mycobacterium Tuberculosis:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure Analysis of Product Bound Methionine Aminopeptidase Type 1C From Mycobacterium Tuberculosis, PDB code: 1yj3 was solved by A.Addlagatta, M.L.Quillin, O.Omotoso, J.O.Liu, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.360, 48.160, 56.540, 90.00, 95.05, 90.00
R / Rfree (%) 20.3 / 24.7

Other elements in 1yj3:

The structure of Crystal Structure Analysis of Product Bound Methionine Aminopeptidase Type 1C From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Potassium (K) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure Analysis of Product Bound Methionine Aminopeptidase Type 1C From Mycobacterium Tuberculosis (pdb code 1yj3). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure Analysis of Product Bound Methionine Aminopeptidase Type 1C From Mycobacterium Tuberculosis, PDB code: 1yj3:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 1yj3

Go back to Cobalt Binding Sites List in 1yj3
Cobalt binding site 1 out of 2 in the Crystal Structure Analysis of Product Bound Methionine Aminopeptidase Type 1C From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure Analysis of Product Bound Methionine Aminopeptidase Type 1C From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:10.8
occ:1.00
O A:MET500 1.9 12.0 1.0
OE1 A:GLU269 2.0 6.4 1.0
NE2 A:HIS205 2.1 6.5 1.0
OE2 A:GLU238 2.1 8.9 1.0
OD1 A:ASP142 2.2 9.1 1.0
C A:MET500 2.7 14.4 1.0
CD A:GLU269 3.0 6.6 1.0
OXT A:MET500 3.0 16.3 1.0
CD2 A:HIS205 3.0 5.0 1.0
CD A:GLU238 3.1 10.4 1.0
CG A:ASP142 3.1 9.2 1.0
CE1 A:HIS205 3.1 6.4 1.0
CO A:CO402 3.3 11.4 1.0
OE2 A:GLU269 3.4 7.5 1.0
OE1 A:GLU238 3.5 11.0 1.0
OD2 A:ASP142 3.6 8.4 1.0
OG1 A:THR236 3.6 5.7 1.0
CG2 A:THR236 3.7 9.1 1.0
CB A:THR236 4.0 9.3 1.0
O A:HOH767 4.0 20.8 0.5
CA A:MET500 4.1 14.8 1.0
CG A:HIS205 4.2 5.1 1.0
ND1 A:HIS205 4.2 7.2 1.0
CB A:ASP142 4.2 7.0 1.0
CG A:GLU269 4.3 6.9 1.0
CG A:GLU238 4.3 8.6 1.0
N A:MET500 4.3 10.0 1.0
NE2 A:HIS212 4.8 17.6 1.0
CB A:GLU238 4.8 8.5 1.0
O A:HOH556 4.8 18.4 1.0
OD2 A:ASP131 4.9 9.6 1.0

Cobalt binding site 2 out of 2 in 1yj3

Go back to Cobalt Binding Sites List in 1yj3
Cobalt binding site 2 out of 2 in the Crystal Structure Analysis of Product Bound Methionine Aminopeptidase Type 1C From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure Analysis of Product Bound Methionine Aminopeptidase Type 1C From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:11.4
occ:1.00
O A:MET500 2.1 12.0 1.0
OD2 A:ASP142 2.1 8.4 1.0
OE2 A:GLU269 2.1 7.5 1.0
OD1 A:ASP131 2.2 8.9 1.0
N A:MET500 2.2 10.0 1.0
OD2 A:ASP131 2.2 9.6 1.0
CG A:ASP131 2.5 9.8 1.0
C A:MET500 2.8 14.4 1.0
CA A:MET500 2.8 14.8 1.0
CG A:ASP142 2.9 9.2 1.0
CD A:GLU269 3.0 6.6 1.0
OD1 A:ASP142 3.2 9.1 1.0
CO A:CO401 3.3 10.8 1.0
OE1 A:GLU269 3.3 6.4 1.0
OXT A:MET500 4.0 16.3 1.0
OG1 A:THR133 4.0 10.3 1.0
CB A:ASP131 4.0 9.4 1.0
ND2 A:ASN144 4.1 8.1 1.0
CB A:MET500 4.3 15.2 1.0
CB A:ASP142 4.3 7.0 1.0
CG A:GLU269 4.4 6.9 1.0
N A:THR143 4.4 10.3 1.0
O A:HOH509 4.6 10.5 1.0
O A:THR143 4.6 10.5 1.0
OE1 A:GLU238 4.7 11.0 1.0
OE2 A:GLU238 4.7 8.9 1.0
C A:ASP142 4.7 8.1 1.0
O A:HOH556 4.7 18.4 1.0
C A:THR143 4.8 10.0 1.0
CA A:ASP131 4.8 10.7 1.0
CA A:ASP142 4.8 7.0 1.0
CB A:ASN144 4.8 9.0 1.0
CB A:GLU269 4.9 6.5 1.0
O A:VAL132 5.0 12.8 1.0
C A:ASP131 5.0 9.4 1.0
CD A:GLU238 5.0 10.4 1.0

Reference:

A.Addlagatta, M.L.Quillin, O.Omotoso, J.O.Liu, B.W.Matthews. Identification of An SH3-Binding Motif in A New Class of Methionine Aminopeptidases From Mycobacterium Tuberculosis Suggests A Mode of Interaction with the Ribosome. Biochemistry V. 44 7166 2005.
ISSN: ISSN 0006-2960
PubMed: 15882055
DOI: 10.1021/BI0501176
Page generated: Sun Dec 13 10:36:52 2020

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