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Strontium in PDB 5m8h: Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus

Enzymatic activity of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus

All present enzymatic activity of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus:
2.4.2.17;

Protein crystallography data

The structure of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus, PDB code: 5m8h was solved by M.S.Alphey, Y.Ge, J.H.Naismith, R.G.Da Silva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.63 / 2.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.020, 146.730, 101.900, 90.00, 102.40, 90.00
R / Rfree (%) 22.7 / 26.9

Other elements in 5m8h:

The structure of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus also contains other interesting chemical elements:

Chlorine (Cl) 15 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus (pdb code 5m8h). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 10 binding sites of Strontium where determined in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus, PDB code: 5m8h:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 10 in 5m8h

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Strontium binding site 1 out of 10 in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr401

b:45.2
occ:0.50
 OG1 A:THR78 2.6 39.0 1.0
O A:HOH585 2.6 35.3 1.0
OD2 A:ASP76 2.8 38.8 1.0
OD1 A:ASP76 2.8 40.7 1.0
CG A:ASP76 3.2 36.8 1.0
CB A:THR78 3.5 41.1 1.0
O A:HOH595 3.6 29.1 1.0
OG A:SER308 3.9 35.2 1.0
O A:HOH590 3.9 38.3 1.0
NE2 A:GLN118 4.2 35.0 1.0
CG2 A:THR78 4.5 43.1 1.0
N A:THR78 4.5 35.8 1.0
CB A:SER308 4.6 31.3 1.0
OH A:TYR98 4.6 36.0 1.0
CA A:THR78 4.6 38.0 1.0
CB A:ASP76 4.7 35.1 1.0
CD A:GLN118 4.9 31.2 1.0
OE2 A:GLU122 4.9 45.8 1.0

Strontium binding site 2 out of 10 in 5m8h

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Strontium binding site 2 out of 10 in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr402

b:71.2
occ:0.50
 OD1 A:ASP147 2.8 87.2 1.0
O A:ASN144 3.0 35.4 1.0
ND2 A:ASN144 3.2 62.0 1.0
CG A:ASP147 3.7 78.5 1.0
CG A:ASN144 3.8 58.8 1.0
C A:ASN144 4.0 38.6 1.0
CA A:ASP147 4.1 54.7 1.0
OD1 A:ASN144 4.3 63.4 1.0
N A:ASP147 4.4 46.2 1.0
OD2 A:ASP147 4.4 88.7 1.0
CA A:ASN144 4.4 43.4 1.0
CB A:ASP147 4.5 65.1 1.0
CB A:ASN144 4.6 49.5 1.0

Strontium binding site 3 out of 10 in 5m8h

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Strontium binding site 3 out of 10 in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr401

b:65.0
occ:1.00
 OD1 B:ASP147 2.2 44.6 1.0
O B:ASN144 2.6 33.7 1.0
CG B:ASP147 3.5 39.4 1.0
C B:ASN144 3.6 30.0 1.0
O B:HOH508 4.0 35.6 1.0
CA B:ASP147 4.1 32.6 1.0
N B:ASP147 4.2 30.6 1.0
OD2 B:ASP147 4.3 44.5 1.0
CB B:ASP147 4.3 36.1 1.0
CA B:ASN144 4.4 30.6 1.0
N B:SER145 4.6 28.0 1.0
CB B:ASN144 4.6 34.0 1.0
CA B:SER145 4.7 26.6 1.0
C B:SER145 4.9 27.2 1.0

Strontium binding site 4 out of 10 in 5m8h

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Strontium binding site 4 out of 10 in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr402

b:55.6
occ:1.00
 OG1 B:THR78 2.4 30.6 1.0
O B:HOH558 2.9 40.3 1.0
OD2 B:ASP76 3.0 34.0 1.0
OD1 B:ASP76 3.1 30.7 1.0
O B:HOH647 3.1 35.1 1.0
O B:HOH634 3.1 37.8 1.0
O B:HOH650 3.3 33.8 1.0
CG B:ASP76 3.4 26.5 1.0
CB B:THR78 3.5 30.6 1.0
OG B:SER308 3.9 30.8 1.0
CG2 B:THR78 4.3 30.9 1.0
NE2 B:GLN118 4.3 29.6 1.0
OH B:TYR98 4.5 25.4 1.0
N B:THR78 4.5 28.7 1.0
CB B:SER308 4.6 28.4 1.0
CA B:THR78 4.6 28.5 1.0
OE2 B:GLU122 4.7 34.5 1.0
CB B:ASP76 5.0 25.3 1.0

Strontium binding site 5 out of 10 in 5m8h

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Strontium binding site 5 out of 10 in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr401

b:66.5
occ:1.00
 OE1 C:GLN381 2.7 62.2 1.0
CD C:GLN381 3.9 60.8 1.0
OE1 C:GLN347 4.3 46.0 1.0
NE2 C:GLN381 4.4 61.7 1.0
N C:TRP382 4.7 48.5 1.0
CA C:GLN381 4.8 56.9 1.0

Strontium binding site 6 out of 10 in 5m8h

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Strontium binding site 6 out of 10 in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr402

b:66.5
occ:1.00
 OD1 C:ASP147 2.3 42.9 1.0
O C:ASN144 2.7 32.5 1.0
O C:HOH585 2.7 31.4 1.0
CG C:ASP147 3.5 43.0 1.0
C C:ASN144 3.7 29.4 1.0
O C:HOH502 4.1 26.8 1.0
CA C:ASP147 4.1 36.9 1.0
N C:ASP147 4.2 34.3 1.0
CB C:ASP147 4.4 39.7 1.0
OD2 C:ASP147 4.4 47.6 1.0
CA C:ASN144 4.4 31.2 1.0
CB C:ASN144 4.6 36.3 1.0
N C:SER145 4.7 30.3 1.0
OD1 C:ASN144 4.7 57.0 1.0
O C:HOH503 4.8 3.0 0.5
CA C:SER145 4.8 30.3 1.0
C C:SER145 5.0 30.9 1.0

Strontium binding site 7 out of 10 in 5m8h

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Strontium binding site 7 out of 10 in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr403

b:59.3
occ:1.00
 OG1 C:THR78 2.4 32.2 1.0
OD2 C:ASP76 2.9 43.9 1.0
O C:HOH617 3.0 35.0 1.0
O C:HOH587 3.0 39.9 1.0
OD1 C:ASP76 3.0 42.1 1.0
O C:HOH622 3.2 28.7 1.0
O C:HOH625 3.4 37.6 1.0
CG C:ASP76 3.4 36.4 1.0
CB C:THR78 3.4 30.0 1.0
OG C:SER308 3.9 32.9 1.0
NE2 C:GLN118 4.2 25.5 1.0
CG2 C:THR78 4.3 31.0 1.0
OH C:TYR98 4.5 22.7 1.0
N C:THR78 4.5 27.9 1.0
CA C:THR78 4.6 30.2 1.0
CB C:SER308 4.6 27.6 1.0
OE2 C:GLU122 4.7 34.8 1.0
CB C:ASP76 4.9 33.8 1.0
CD C:GLN118 5.0 23.5 1.0

Strontium binding site 8 out of 10 in 5m8h

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Strontium binding site 8 out of 10 in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr401

b:58.6
occ:0.50
 OE1 D:GLN193 2.3 85.8 1.0
OE1 D:GLN196 2.9 69.6 1.0
CD D:GLN193 3.3 81.6 1.0
NE2 D:GLN193 3.8 81.5 1.0
CD D:GLN196 4.1 71.7 1.0
CG D:GLN193 4.5 76.0 1.0
CB D:GLN193 4.8 75.3 1.0
CA D:GLN193 4.8 76.7 1.0
NE2 D:GLN196 4.9 72.6 1.0
O D:GLN193 4.9 89.9 1.0

Strontium binding site 9 out of 10 in 5m8h

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Strontium binding site 9 out of 10 in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr402

b:49.5
occ:0.50
 OG1 D:THR78 2.6 39.0 1.0
O D:HOH530 2.9 29.8 1.0
OD2 D:ASP76 3.1 35.6 1.0
OD1 D:ASP76 3.1 34.7 1.0
O D:HOH612 3.2 37.5 1.0
CG D:ASP76 3.5 32.7 1.0
OG D:SER308 3.6 35.2 1.0
CB D:THR78 3.7 34.4 1.0
NE2 D:GLN118 4.2 33.5 1.0
CB D:SER308 4.4 32.6 1.0
OH D:TYR98 4.5 32.5 1.0
CG2 D:THR78 4.6 36.9 1.0
N D:THR78 4.6 29.8 1.0
CA D:THR78 4.8 30.6 1.0
OE2 D:GLU122 4.8 44.9 1.0
CD D:GLN118 5.0 29.5 1.0

Strontium binding site 10 out of 10 in 5m8h

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Strontium binding site 10 out of 10 in the Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Atp Phosphoribosyltransferase (Hiszg Atpprt) From Psychrobacter Arcticus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr403

b:88.5
occ:0.50
 O D:ASN144 3.1 45.1 1.0
O D:HOH540 3.3 43.2 1.0
OD1 D:ASP147 3.4 75.6 1.0
OD1 D:ASN144 3.5 71.5 1.0
C D:ASN144 4.0 45.6 1.0
CA D:ASN144 4.1 47.9 1.0
CG D:ASP147 4.2 70.4 1.0
CB D:ASN144 4.2 54.2 1.0
CG D:ASN144 4.3 61.4 1.0
CA D:ASP147 4.4 57.3 1.0
O D:HOH547 4.4 46.0 1.0
N D:ASP147 4.7 50.8 1.0
OD2 D:ASP147 4.8 78.1 1.0
CB D:ASP147 5.0 62.8 1.0

Reference:

R.Stroek, Y.Ge, P.D.Talbot, M.K.Glok, K.E.Bernas, C.M.Thomson, E.R.Gould, M.S.Alphey, H.Liu, G.J.Florence, J.H.Naismith, R.G.Da Silva. Kinetics and Structure of A Cold-Adapted Hetero-Octameric Atp Phosphoribosyltransferase. Biochemistry V. 56 793 2017.
ISSN: ISSN 1520-4995
PubMed: 28092443
DOI: 10.1021/ACS.BIOCHEM.6B01138
Page generated: Fri Oct 11 06:25:25 2024

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