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Manganese in PDB 1ecc: Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine

Enzymatic activity of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine

All present enzymatic activity of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine:
2.4.2.14;

Protein crystallography data

The structure of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine, PDB code: 1ecc was solved by J.M.Krahn, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.200, 78.200, 308.800, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 26.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine (pdb code 1ecc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine, PDB code: 1ecc:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 1ecc

Go back to Manganese Binding Sites List in 1ecc
Manganese binding site 1 out of 5 in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn506

b:37.2
occ:1.00
 O2 A:PCP505 2.1 33.2 1.0
O3 A:PCP505 2.1 33.7 1.0
O1 A:PCP505 2.2 35.2 1.0
O A:HOH2378 2.2 31.6 1.0
O1B A:PCP505 2.2 33.4 1.0
O A:HOH2379 2.2 33.6 1.0
C2 A:PCP505 2.8 33.1 1.0
C1 A:PCP505 2.9 33.5 1.0
C3 A:PCP505 3.0 33.1 1.0
PB A:PCP505 3.3 37.5 1.0
OD1 A:ASP367 3.4 40.2 1.0
O3A A:PCP505 3.5 37.6 1.0
PA A:PCP505 3.5 35.5 1.0
OD1 A:ASP366 3.6 27.3 1.0
O A:HOH2411 3.7 39.1 1.0
C5 A:PCP505 3.8 32.3 1.0
O A:PRO302 4.0 29.1 1.0
C4 A:PCP505 4.0 33.3 1.0
O A:ILE301 4.2 25.7 1.0
O2B A:PCP505 4.2 34.9 1.0
O1A A:PCP505 4.3 33.8 1.0
OD2 A:ASP366 4.4 26.4 1.0
O3B A:PCP505 4.4 36.8 1.0
N A:GLU303 4.4 29.4 1.0
CG A:ASP366 4.4 28.2 1.0
CG A:ASP367 4.4 39.1 1.0
O2A A:PCP505 4.4 36.8 1.0
C A:PRO302 4.5 28.9 1.0
N A:THR304 4.5 31.2 1.0
CB A:THR304 4.6 27.6 1.0
CE1 A:TYR258 4.6 27.5 1.0
OG1 A:THR304 4.6 24.3 1.0
OD2 A:ASP367 4.7 37.7 1.0
CG2 A:ILE301 4.9 21.3 1.0

Manganese binding site 2 out of 5 in 1ecc

Go back to Manganese Binding Sites List in 1ecc
Manganese binding site 2 out of 5 in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2376

b:42.4
occ:0.40
 OE2 A:GLU449 2.6 44.4 1.0
CD A:GLU449 3.2 44.8 1.0
OE1 A:GLU449 3.3 45.0 1.0
O A:ALA448 4.1 36.8 1.0
ND2 A:ASN277 4.5 23.2 1.0
CG A:GLU449 4.6 42.4 1.0
C A:ALA448 4.7 37.4 1.0
OD1 A:ASN277 4.7 24.2 1.0
CB A:ALA448 4.8 37.5 1.0

Manganese binding site 3 out of 5 in 1ecc

Go back to Manganese Binding Sites List in 1ecc
Manganese binding site 3 out of 5 in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn506

b:32.7
occ:1.00
 O3 B:PCP505 2.2 29.8 1.0
O2 B:PCP505 2.2 30.4 1.0
O1B B:PCP505 2.2 32.8 1.0
O B:HOH2452 2.3 30.3 1.0
O1 B:PCP505 2.3 32.5 1.0
O B:HOH2451 2.4 29.2 1.0
C2 B:PCP505 2.9 31.7 1.0
C3 B:PCP505 3.0 30.9 1.0
C1 B:PCP505 3.1 30.6 1.0
PB B:PCP505 3.4 37.8 1.0
OD1 B:ASP367 3.4 27.4 1.0
PA B:PCP505 3.5 34.9 1.0
O3A B:PCP505 3.5 35.4 1.0
OD1 B:ASP366 3.5 22.0 1.0
O B:HOH2460 3.8 19.6 1.0
C5 B:PCP505 3.9 30.3 1.0
C4 B:PCP505 4.0 30.9 1.0
OD2 B:ASP366 4.0 15.3 1.0
O B:PRO302 4.1 26.3 1.0
OG1 B:THR304 4.1 26.1 1.0
O B:ILE301 4.2 26.9 1.0
CG B:ASP366 4.2 16.8 1.0
O1A B:PCP505 4.2 33.4 1.0
CB B:THR304 4.3 23.0 1.0
O2B B:PCP505 4.3 35.4 1.0
N B:GLU303 4.5 29.1 1.0
O3B B:PCP505 4.5 34.1 1.0
O2A B:PCP505 4.5 34.1 1.0
C B:PRO302 4.5 27.3 1.0
N B:THR304 4.6 24.4 1.0
CG B:ASP367 4.6 25.7 1.0
CE1 B:TYR258 4.7 18.8 1.0
CG2 B:ILE301 4.9 17.6 1.0
OD2 B:ASP367 4.9 24.8 1.0
CD1 B:TYR258 5.0 18.9 1.0
CA B:THR304 5.0 23.5 1.0

Manganese binding site 4 out of 5 in 1ecc

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Manganese binding site 4 out of 5 in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1449

b:76.5
occ:0.40
 O B:ILE428 2.8 41.1 1.0
OE2 B:GLU376 3.0 62.9 1.0
CD B:GLU376 3.9 64.5 1.0
C B:ILE428 4.0 37.8 1.0
CG B:GLU376 4.2 58.6 1.0
C B:ILE429 4.7 37.5 1.0
OE2 B:GLU380 4.7 44.8 1.0
CA B:ILE429 4.8 36.6 1.0
O B:ILE429 4.9 40.9 1.0
N B:ILE429 4.9 38.0 1.0

Manganese binding site 5 out of 5 in 1ecc

Go back to Manganese Binding Sites List in 1ecc
Manganese binding site 5 out of 5 in the Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Escherichia Coli Glutamine Phosphoribosylpyrophosphate (Prpp) Amidotransferase Complexed with Mn-Cprpp and 5-Oxo- Norleucine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2449

b:32.3
occ:1.00
 OE2 B:GLU449 2.2 31.4 1.0
O B:HOH2543 2.4 33.6 1.0
O B:HOH2597 2.4 33.5 1.0
O B:HOH2600 2.6 32.2 1.0
O B:HOH2598 2.7 33.3 1.0
O B:HOH2599 2.7 31.7 1.0
CD B:GLU449 3.2 32.5 1.0
OE1 B:GLU449 3.4 33.7 1.0
OD1 B:ASN277 3.8 19.4 1.0
ND2 B:ASN277 4.1 19.9 1.0
CG B:ASN277 4.4 22.2 1.0
CB B:SER273 4.4 21.8 1.0
CG B:GLU449 4.6 29.1 1.0
OG B:SER273 4.8 24.4 1.0
O B:HOH2497 5.0 22.0 1.0

Reference:

J.M.Krahn, J.H.Kim, M.R.Burns, R.J.Parry, H.Zalkin, J.L.Smith. Coupled Formation of An Amidotransferase Interdomain Ammonia Channel and A Phosphoribosyltransferase Active Site. Biochemistry V. 36 11061 1997.
ISSN: ISSN 0006-2960
PubMed: 9333323
DOI: 10.1021/BI9714114
Page generated: Sat Oct 5 10:09:42 2024

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