Magnesium in PDB 5c1r: Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd)

Enzymatic activity of Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd)

All present enzymatic activity of Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd):
2.4.2.18;

Protein crystallography data

The structure of Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd), PDB code: 5c1r was solved by G.L.Evans, E.N.Baker, J.S.Lott, Tb Structural Genomics Consortium(Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.09 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.301, 78.490, 100.485, 90.00, 110.41, 90.00
R / Rfree (%) 17.2 / 20.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd) (pdb code 5c1r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd), PDB code: 5c1r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5c1r

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Magnesium binding site 1 out of 4 in the Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:19.1
occ:1.00
 O A:HOH524 2.1 21.2 1.0
O19 A:51N403 2.1 16.8 0.8
O21 A:51N403 2.2 10.3 0.8
O A:HOH594 2.2 18.4 1.0
OE1 A:GLU252 2.2 19.8 1.0
OG A:SER119 2.2 15.5 1.0
CB A:SER119 3.0 15.0 1.0
CD A:GLU252 3.2 19.8 1.0
P20 A:51N403 3.2 13.4 0.8
P17 A:51N403 3.3 13.9 0.8
OE2 A:GLU252 3.5 19.9 1.0
O16 A:51N403 3.5 13.8 0.8
O14 A:51N403 3.8 14.6 0.8
O A:HOH510 3.9 30.8 1.0
N A:GLY107 4.0 15.2 1.0
N A:SER119 4.0 15.9 1.0
CA A:SER119 4.1 16.5 1.0
O15 A:51N403 4.1 17.5 0.8
OD2 A:ASP251 4.1 16.3 1.0
O A:HOH589 4.2 29.8 1.0
O A:ASP251 4.3 17.6 1.0
O18 A:51N403 4.3 14.7 0.8
O A:HOH675 4.3 17.9 1.0
CA A:GLY107 4.4 16.8 1.0
O22 A:51N403 4.4 18.6 0.8
O A:HOH557 4.4 24.4 1.0
CG A:GLU252 4.4 18.6 1.0
C06 A:51N403 4.5 14.3 0.8
C A:VAL106 4.7 16.7 1.0
CG A:ASP251 4.7 17.2 1.0
OD1 A:ASP251 4.7 20.0 1.0
CA A:VAL106 4.9 15.9 1.0

Magnesium binding site 2 out of 4 in 5c1r

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Magnesium binding site 2 out of 4 in the Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:33.0
occ:0.75
 O A:VAL113 2.1 31.1 1.0
O A:HOH505 2.1 28.5 1.0
OD1 A:ASP111 2.1 27.3 1.0
O A:HOH639 2.2 25.6 1.0
O A:HOH511 2.2 28.5 1.0
O A:HOH601 2.2 33.9 1.0
CG A:ASP111 3.0 27.3 1.0
OD2 A:ASP111 3.3 23.7 1.0
C A:VAL113 3.3 32.4 1.0
N A:VAL113 3.9 25.1 1.0
CA A:VAL113 4.0 25.9 1.0
O11 A:51N403 4.1 25.5 0.8
O A:HOH557 4.2 24.4 1.0
N A:ASP111 4.3 26.9 1.0
CB A:VAL113 4.3 24.1 1.0
CB A:ASP111 4.3 26.2 1.0
N A:ASN114 4.3 31.2 1.0
OG1 A:THR115 4.4 25.1 1.0
N A:THR115 4.4 29.4 1.0
O A:HOH510 4.5 30.8 1.0
OD1 A:ASP251 4.5 20.0 1.0
O A:HOH562 4.5 29.8 1.0
CA A:ASN114 4.6 31.8 1.0
N A:GLY112 4.7 24.4 1.0
CA A:ASP111 4.7 24.3 1.0
O A:HOH589 4.8 29.8 1.0
C A:ASP111 4.9 28.6 1.0
N A:GLY110 4.9 19.5 1.0
CG2 A:THR115 5.0 23.3 1.0

Magnesium binding site 3 out of 4 in 5c1r

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Magnesium binding site 3 out of 4 in the Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:14.1
occ:1.00
 OE2 B:GLU252 2.0 15.9 1.0
O19 B:51N403 2.1 12.3 1.0
O B:HOH600 2.1 12.0 1.0
OG B:SER119 2.1 11.3 1.0
O21 B:51N403 2.1 12.1 1.0
O B:HOH534 2.2 16.2 1.0
CD B:GLU252 3.0 16.1 1.0
CB B:SER119 3.0 12.2 1.0
P20 B:51N403 3.3 15.0 1.0
P17 B:51N403 3.3 17.4 1.0
OE1 B:GLU252 3.4 13.4 1.0
O16 B:51N403 3.6 16.5 1.0
O B:HOH505 3.7 26.8 1.0
O14 B:51N403 3.8 15.3 1.0
N B:GLY107 3.9 13.4 1.0
N B:SER119 4.0 10.8 1.0
CA B:SER119 4.1 10.2 1.0
OD2 B:ASP251 4.1 15.2 1.0
O B:ASP251 4.2 14.5 1.0
O15 B:51N403 4.2 17.2 1.0
CG B:GLU252 4.3 17.2 1.0
CA B:GLY107 4.3 11.4 1.0
O18 B:51N403 4.3 15.2 1.0
O B:HOH703 4.3 14.4 1.0
O B:HOH585 4.4 21.8 1.0
C06 B:51N403 4.5 16.8 1.0
O22 B:51N403 4.5 16.3 1.0
O B:HOH579 4.5 23.5 1.0
CG B:ASP251 4.6 17.6 1.0
OD1 B:ASP251 4.6 18.6 1.0
C B:VAL106 4.7 11.4 1.0
CA B:VAL106 4.9 10.1 1.0

Magnesium binding site 4 out of 4 in 5c1r

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Magnesium binding site 4 out of 4 in the Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Stereoisomer of Prpp Bound in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyl (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:35.0
occ:1.00
 OD1 B:ASP111 2.0 24.9 1.0
O B:HOH636 2.2 24.9 1.0
O B:HOH515 2.2 29.0 1.0
O B:HOH709 2.2 30.8 1.0
O B:HOH559 2.3 33.3 1.0
O B:VAL113 2.3 28.4 1.0
CG B:ASP111 2.8 27.4 1.0
OD2 B:ASP111 3.1 30.1 1.0
C B:VAL113 3.5 28.4 1.0
O11 B:51N403 3.9 26.6 1.0
O B:HOH585 3.9 21.8 1.0
N B:VAL113 4.1 23.2 1.0
N B:ASP111 4.1 21.4 1.0
CB B:ASP111 4.1 23.8 1.0
CA B:VAL113 4.3 26.4 1.0
O B:HOH579 4.4 23.5 1.0
OG1 B:THR115 4.4 20.4 1.0
CA B:ASP111 4.5 20.0 1.0
OD1 B:ASP251 4.6 18.6 1.0
N B:GLY112 4.6 24.7 1.0
N B:ASN114 4.6 30.8 1.0
O B:HOH505 4.6 26.8 1.0
N B:THR115 4.6 30.6 1.0
O B:HOH562 4.6 27.0 1.0
CB B:VAL113 4.7 24.4 1.0
CA B:ASN114 4.7 37.3 1.0
N B:GLY110 4.8 15.9 1.0
C B:ASP111 4.8 23.7 1.0

Reference:

G.L.Evans, E.N.Baker, J.S.Lott. Binding and Mimicking of the Phosphate-Rich Substrate, Prpp. To Be Published.
Page generated: Mon Dec 14 20:05:05 2020

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