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Magnesium in PDB 1zyk: Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium

Enzymatic activity of Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium

All present enzymatic activity of Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium:
2.4.2.18;

Protein crystallography data

The structure of Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium, PDB code: 1zyk was solved by M.Marino, M.Deuss, R.Sterner, O.Mayans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.556, 66.099, 117.069, 90.00, 107.76, 90.00
R / Rfree (%) 20.7 / 26.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium (pdb code 1zyk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium, PDB code: 1zyk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1zyk

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Magnesium binding site 1 out of 8 in the Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:70.0
occ:1.00
 O2B A:PRP601 1.5 29.7 1.0
O4 A:PRP601 1.9 58.7 1.0
O2 A:PRP601 1.9 56.1 1.0
PB A:PRP601 2.1 30.5 1.0
C4 A:PRP601 2.2 61.0 1.0
C1 A:PRP601 2.3 52.8 1.0
C2 A:PRP601 2.3 54.9 1.0
O3A A:PRP601 2.4 39.1 1.0
O1 A:PRP601 2.5 46.0 1.0
O1B A:PRP601 2.6 34.9 1.0
C3 A:PRP601 2.7 59.4 1.0
PA A:PRP601 3.1 36.6 1.0
O3 A:PRP601 3.2 57.8 1.0
N A:GLY79 3.4 24.2 1.0
O3B A:PRP601 3.5 39.2 1.0
C5 A:PRP601 3.6 66.9 1.0
O A:HOH957 3.8 56.2 1.0
CB A:SER91 3.9 25.3 1.0
OG A:SER91 4.0 30.2 1.0
CA A:GLY79 4.0 26.4 1.0
O2A A:PRP601 4.0 42.3 1.0
O1A A:PRP601 4.1 40.3 1.0
MG A:MG702 4.2 81.6 1.0
O A:GLY79 4.3 28.0 1.0
C A:ALA78 4.3 25.3 1.0
CA A:ALA78 4.4 26.6 1.0
C A:GLY79 4.5 28.8 1.0
O A:THR77 4.6 27.0 1.0
O5 A:PRP601 4.6 73.3 1.0
OD2 A:ASP223 4.6 28.7 1.0
O A:HOH862 4.7 13.7 1.0
O A:HOH813 4.8 25.3 1.0
OE1 A:GLU224 4.9 46.9 1.0
O3P A:PRP601 4.9 77.2 1.0

Magnesium binding site 2 out of 8 in 1zyk

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Magnesium binding site 2 out of 8 in the Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:81.6
occ:1.00
 OE1 A:GLU224 1.7 46.9 1.0
O5 A:PRP601 1.9 73.3 1.0
O3P A:PRP601 2.2 77.2 1.0
C3 A:PRP601 2.4 59.4 1.0
CD A:GLU224 2.4 44.0 1.0
P A:PRP601 2.4 79.9 1.0
C1 A:PRP601 2.6 52.8 1.0
C4 A:PRP601 2.7 61.0 1.0
C5 A:PRP601 2.7 66.9 1.0
O4 A:PRP601 2.8 58.7 1.0
C2 A:PRP601 2.8 54.9 1.0
O2P A:PRP601 3.0 79.3 1.0
CG A:GLU224 3.0 38.2 1.0
OE2 A:GLU224 3.3 44.0 1.0
OD1 A:ASP223 3.4 29.2 1.0
O3 A:PRP601 3.7 57.8 1.0
O1P A:PRP601 3.8 78.7 1.0
O1 A:PRP601 3.9 46.0 1.0
O A:ASP223 4.0 27.4 1.0
CG1 A:VAL90 4.2 19.4 1.0
O2 A:PRP601 4.2 56.1 1.0
CG A:ASP223 4.2 30.2 1.0
OG1 A:THR87 4.2 29.3 1.0
MG A:MG701 4.2 70.0 1.0
CB A:GLU224 4.4 34.1 1.0
OD2 A:ASP223 4.5 28.7 1.0
OD2 A:ASP83 4.5 57.5 1.0
C A:ASP223 4.6 29.1 1.0
O1A A:PRP601 4.8 40.3 1.0
O A:HOH957 4.9 56.2 1.0
PA A:PRP601 4.9 36.6 1.0

Magnesium binding site 3 out of 8 in 1zyk

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Magnesium binding site 3 out of 8 in the Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:71.7
occ:1.00
 O2B B:PRP602 1.5 44.7 1.0
O4 B:PRP602 1.9 69.7 1.0
O2 B:PRP602 2.0 69.6 1.0
PB B:PRP602 2.1 46.5 1.0
C4 B:PRP602 2.2 71.3 1.0
C1 B:PRP602 2.3 65.2 1.0
C2 B:PRP602 2.3 66.8 1.0
O3A B:PRP602 2.4 52.2 1.0
O1 B:PRP602 2.5 60.3 1.0
O1B B:PRP602 2.5 50.5 1.0
C3 B:PRP602 2.7 69.6 1.0
PA B:PRP602 3.1 51.3 1.0
O3 B:PRP602 3.2 68.6 1.0
N B:GLY79 3.3 26.3 1.0
O3B B:PRP602 3.5 51.6 1.0
C5 B:PRP602 3.6 74.8 1.0
CB B:SER91 3.9 28.5 1.0
O2A B:PRP602 4.0 57.4 1.0
CA B:GLY79 4.0 30.0 1.0
OG B:SER91 4.0 33.2 1.0
O1A B:PRP602 4.1 53.4 1.0
CA B:ALA78 4.2 27.6 1.0
C B:ALA78 4.2 27.1 1.0
O B:GLY79 4.3 31.6 1.0
MG B:MG704 4.3 53.7 1.0
O B:THR77 4.5 27.8 1.0
C B:GLY79 4.5 31.1 1.0
O5 B:PRP602 4.6 78.0 1.0
NZ B:LYS106 4.7 28.7 1.0
OD2 B:ASP223 4.7 29.6 1.0
OE2 B:GLU224 4.8 38.2 1.0
O B:HOH816 4.8 24.1 1.0
O3P B:PRP602 4.9 80.2 1.0
O B:HOH887 4.9 38.4 1.0
O B:HOH829 4.9 21.0 1.0
O B:HOH867 5.0 31.0 1.0

Magnesium binding site 4 out of 8 in 1zyk

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Magnesium binding site 4 out of 8 in the Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:53.7
occ:1.00
 OE2 B:GLU224 1.9 38.2 1.0
O5 B:PRP602 1.9 78.0 1.0
O3P B:PRP602 2.2 80.2 1.0
CD B:GLU224 2.3 35.2 1.0
C3 B:PRP602 2.4 69.6 1.0
P B:PRP602 2.4 82.5 1.0
C1 B:PRP602 2.6 65.2 1.0
CG B:GLU224 2.6 31.0 1.0
C4 B:PRP602 2.7 71.3 1.0
C5 B:PRP602 2.7 74.8 1.0
O4 B:PRP602 2.8 69.7 1.0
C2 B:PRP602 2.8 66.8 1.0
O2P B:PRP602 3.0 80.5 1.0
OE1 B:GLU224 3.2 37.7 1.0
OD1 B:ASP223 3.5 28.2 1.0
O B:ASP223 3.7 23.9 1.0
O3 B:PRP602 3.7 68.6 1.0
O1P B:PRP602 3.8 81.9 1.0
O1 B:PRP602 3.9 60.3 1.0
CB B:GLU224 4.1 26.3 1.0
CG1 B:VAL90 4.1 19.9 1.0
O2 B:PRP602 4.2 69.6 1.0
CG B:ASP223 4.2 29.3 1.0
MG B:MG703 4.3 71.7 1.0
C B:ASP223 4.3 26.0 1.0
OD2 B:ASP223 4.5 29.6 1.0
OG1 B:THR87 4.6 36.4 1.0
O1A B:PRP602 4.7 53.4 1.0
CA B:GLU224 4.8 24.9 1.0
N B:GLU224 4.8 25.5 1.0
OD2 B:ASP83 4.9 52.0 1.0
O B:HOH902 4.9 41.6 1.0
PA B:PRP602 4.9 51.3 1.0

Magnesium binding site 5 out of 8 in 1zyk

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Magnesium binding site 5 out of 8 in the Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg705

b:70.9
occ:1.00
 O2B C:PRP603 1.5 62.6 1.0
O4 C:PRP603 1.9 74.8 1.0
O2 C:PRP603 1.9 72.7 1.0
PB C:PRP603 2.1 62.6 1.0
C4 C:PRP603 2.2 75.9 1.0
C1 C:PRP603 2.3 71.5 1.0
C2 C:PRP603 2.3 72.5 1.0
O3A C:PRP603 2.4 65.6 1.0
O1 C:PRP603 2.5 69.7 1.0
O1B C:PRP603 2.6 64.4 1.0
C3 C:PRP603 2.7 74.4 1.0
PA C:PRP603 3.1 63.6 1.0
O3 C:PRP603 3.2 73.2 1.0
N C:GLY79 3.2 29.6 1.0
O3B C:PRP603 3.5 67.3 1.0
C5 C:PRP603 3.6 79.3 1.0
CB C:SER91 3.9 27.1 1.0
CA C:GLY79 3.9 30.6 1.0
O C:GLY79 4.0 33.4 1.0
O2A C:PRP603 4.0 66.4 1.0
OG C:SER91 4.0 37.2 1.0
C C:ALA78 4.1 29.3 1.0
O1A C:PRP603 4.1 66.4 1.0
CA C:ALA78 4.1 29.7 1.0
MG C:MG706 4.3 78.8 1.0
C C:GLY79 4.4 32.4 1.0
O C:THR77 4.4 27.1 1.0
O5 C:PRP603 4.6 84.4 1.0
O3P C:PRP603 4.9 87.1 1.0
OD2 C:ASP223 4.9 34.5 1.0
OE1 C:GLU224 4.9 45.9 1.0
O C:HOH828 5.0 26.2 1.0
CB C:ALA78 5.0 31.4 1.0
NZ C:LYS106 5.0 21.7 1.0

Magnesium binding site 6 out of 8 in 1zyk

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Magnesium binding site 6 out of 8 in the Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg706

b:78.8
occ:1.00
 OE1 C:GLU224 1.8 45.9 1.0
O5 C:PRP603 1.9 84.4 1.0
O3P C:PRP603 2.2 87.1 1.0
CD C:GLU224 2.2 39.9 1.0
C3 C:PRP603 2.4 74.4 1.0
P C:PRP603 2.4 88.2 1.0
C1 C:PRP603 2.6 71.5 1.0
CG C:GLU224 2.7 35.3 1.0
C4 C:PRP603 2.7 75.9 1.0
C5 C:PRP603 2.7 79.3 1.0
O4 C:PRP603 2.8 74.8 1.0
C2 C:PRP603 2.8 72.5 1.0
O2P C:PRP603 3.0 86.8 1.0
OE2 C:GLU224 3.1 40.9 1.0
OD1 C:ASP223 3.4 32.4 1.0
O C:ASP223 3.7 26.5 1.0
O3 C:PRP603 3.7 73.2 1.0
O1P C:PRP603 3.8 88.1 1.0
O1 C:PRP603 4.0 69.7 1.0
CG C:ASP223 4.0 32.3 1.0
CB C:GLU224 4.1 31.2 1.0
O2 C:PRP603 4.2 72.7 1.0
C C:ASP223 4.2 28.8 1.0
MG C:MG705 4.3 70.9 1.0
OD2 C:ASP223 4.3 34.5 1.0
CG1 C:VAL90 4.4 24.6 1.0
OD2 C:ASP83 4.7 49.3 1.0
N C:GLU224 4.7 29.6 1.0
OG1 C:THR87 4.7 34.9 1.0
CA C:GLU224 4.7 29.2 1.0
CG1 C:ILE222 4.7 28.3 1.0
O1A C:PRP603 4.8 66.4 1.0
PA C:PRP603 5.0 63.6 1.0
O C:HOH825 5.0 19.7 1.0

Magnesium binding site 7 out of 8 in 1zyk

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Magnesium binding site 7 out of 8 in the Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg707

b:43.8
occ:1.00
 O2B D:PRP604 1.5 41.7 1.0
O2 D:PRP604 1.9 55.6 1.0
O4 D:PRP604 1.9 59.8 1.0
PB D:PRP604 2.1 41.6 1.0
C4 D:PRP604 2.3 61.1 1.0
C1 D:PRP604 2.3 55.6 1.0
C2 D:PRP604 2.3 55.8 1.0
O3A D:PRP604 2.4 47.4 1.0
O1 D:PRP604 2.5 51.9 1.0
O1B D:PRP604 2.6 48.1 1.0
C3 D:PRP604 2.7 59.3 1.0
PA D:PRP604 3.1 44.5 1.0
N D:GLY79 3.1 27.9 1.0
O3 D:PRP604 3.2 58.3 1.0
O3B D:PRP604 3.5 50.3 1.0
C5 D:PRP604 3.6 64.0 1.0
CA D:GLY79 3.8 29.5 1.0
CB D:SER91 3.8 29.4 1.0
O2A D:PRP604 4.0 50.1 1.0
C D:ALA78 4.0 26.2 1.0
OG D:SER91 4.1 34.8 1.0
CA D:ALA78 4.1 28.3 1.0
O1A D:PRP604 4.1 47.1 1.0
MG D:MG708 4.3 89.3 1.0
O D:THR77 4.4 31.7 1.0
O D:GLY79 4.4 33.4 1.0
C D:GLY79 4.5 31.8 1.0
O D:HOH862 4.5 31.6 1.0
O5 D:PRP604 4.6 67.3 1.0
O3P D:PRP604 4.9 70.5 1.0
NZ D:LYS106 4.9 24.1 1.0
CB D:ALA78 4.9 25.8 1.0
OE1 D:GLU224 4.9 40.4 1.0
O D:HOH933 5.0 56.7 1.0
OD2 D:ASP223 5.0 47.8 1.0

Magnesium binding site 8 out of 8 in 1zyk

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Magnesium binding site 8 out of 8 in the Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Anthranilate Phosphoribosyltransferase in Complex with Prpp, Anthranilate and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg708

b:89.3
occ:1.00
 OE1 D:GLU224 1.7 40.4 1.0
O5 D:PRP604 1.9 67.3 1.0
O3P D:PRP604 2.2 70.5 1.0
CD D:GLU224 2.3 40.0 1.0
C3 D:PRP604 2.4 59.3 1.0
P D:PRP604 2.4 72.2 1.0
C1 D:PRP604 2.6 55.6 1.0
C4 D:PRP604 2.7 61.1 1.0
C5 D:PRP604 2.7 64.0 1.0
O4 D:PRP604 2.8 59.8 1.0
C2 D:PRP604 2.8 55.8 1.0
CG D:GLU224 3.0 40.1 1.0
O2P D:PRP604 3.0 71.1 1.0
OE2 D:GLU224 3.1 37.7 1.0
OD1 D:ASP223 3.6 52.2 1.0
O D:ASP223 3.7 40.9 1.0
O3 D:PRP604 3.7 58.3 1.0
O1P D:PRP604 3.8 71.6 1.0
O1 D:PRP604 4.0 51.9 1.0
CG D:ASP223 4.1 48.1 1.0
O2 D:PRP604 4.2 55.6 1.0
C D:ASP223 4.2 42.4 1.0
OD2 D:ASP223 4.3 47.8 1.0
MG D:MG707 4.3 43.8 1.0
CG1 D:VAL90 4.3 24.2 1.0
CB D:GLU224 4.4 40.4 1.0
OG1 D:THR87 4.5 35.4 1.0
OD2 D:ASP83 4.6 51.6 1.0
N D:GLU224 4.8 42.0 1.0
O1A D:PRP604 4.8 47.1 1.0
N D:ASP223 4.8 41.9 1.0
CA D:GLU224 4.9 41.1 1.0
CA D:ASP223 4.9 43.5 1.0
PA D:PRP604 5.0 44.5 1.0

Reference:

M.Marino, M.Deuss, D.I.Svergun, P.V.Konarev, R.Sterner, O.Mayans. Structural and Mutational Analysis of Substrate Complexation By Anthranilate Phosphoribosyltransferase From Sulfolobus Solfataricus. J.Biol.Chem. V. 281 21410 2006.
ISSN: ISSN 0021-9258
PubMed: 16714288
DOI: 10.1074/JBC.M601403200
Page generated: Tue Aug 13 20:16:16 2024

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