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Manganese in PDB 5c7s: Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd)

Enzymatic activity of Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd)

All present enzymatic activity of Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd):
2.4.2.18;

Protein crystallography data

The structure of Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd), PDB code: 5c7s 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) 24.56 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.178, 78.481, 100.446, 90.00, 109.90, 90.00
R / Rfree (%) 20.2 / 25.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd) (pdb code 5c7s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd), PDB code: 5c7s:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5c7s

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Manganese binding site 1 out of 4 in the Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:24.9
occ:1.00
 OE2 A:GLU252 2.4 28.7 1.0
O2A A:PRP403 2.5 21.6 1.0
O2B A:PRP403 2.5 20.7 1.0
OG A:SER119 2.5 21.6 1.0
O A:HOH507 2.6 20.4 1.0
O A:HOH530 2.6 19.7 1.0
CB A:SER119 3.2 17.6 1.0
CD A:GLU252 3.2 21.0 1.0
O3A A:PRP403 3.3 36.8 1.0
PB A:PRP403 3.4 23.2 1.0
PA A:PRP403 3.4 25.2 1.0
MN A:MN402 3.4 40.6 1.0
OE1 A:GLU252 3.5 22.7 1.0
N A:GLY107 3.7 20.6 1.0
O A:HOH520 3.8 29.2 1.0
OD2 A:ASP251 3.9 18.1 1.0
CA A:GLY107 4.0 19.8 1.0
O A:HOH546 4.1 21.5 1.0
N A:SER119 4.2 20.5 1.0
O4 A:PRP403 4.3 30.2 1.0
O A:ASP251 4.3 17.2 1.0
CA A:SER119 4.3 22.6 1.0
O3B A:PRP403 4.3 24.2 1.0
O1A A:PRP403 4.3 27.3 1.0
C A:VAL106 4.4 18.8 1.0
O1B A:PRP403 4.5 29.2 1.0
CG A:ASP251 4.5 25.8 1.0
CG A:GLU252 4.5 20.0 1.0
OD1 A:ASP251 4.5 26.9 1.0
O1 A:PRP403 4.6 29.1 1.0
C1 A:PRP403 4.7 31.0 1.0
CA A:VAL106 4.8 18.9 1.0
O A:HOH515 4.9 25.2 1.0
C A:GLY107 5.0 20.3 1.0

Manganese binding site 2 out of 4 in 5c7s

Go back to Manganese Binding Sites List in 5c7s
Manganese binding site 2 out of 4 in the Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:40.6
occ:1.00
 O A:HOH520 2.5 29.2 1.0
OD1 A:ASP251 2.5 26.9 1.0
O A:HOH529 2.6 29.9 1.0
OE2 A:GLU252 2.6 28.7 1.0
O A:HOH507 2.7 20.4 1.0
O A:HOH602 3.1 33.9 1.0
CG A:ASP251 3.4 25.8 1.0
O A:HOH580 3.4 33.5 1.0
CD A:GLU252 3.4 21.0 1.0
MN A:MN401 3.4 24.9 1.0
CG A:GLU252 3.5 20.0 1.0
OD2 A:ASP251 3.5 18.1 1.0
OD2 A:ASP111 3.7 26.0 1.0
O2B A:PRP403 3.8 20.7 1.0
OG1 A:THR115 4.3 26.4 1.0
O A:HOH505 4.5 31.1 1.0
O A:ASP251 4.5 17.2 1.0
OE1 A:GLU252 4.6 22.7 1.0
O1B A:PRP403 4.6 29.2 1.0
PB A:PRP403 4.6 23.2 1.0
O4 A:PRP403 4.7 30.2 1.0
O A:HOH556 4.7 38.6 1.0
CG A:ASP111 4.7 27.3 1.0
O3A A:PRP403 4.7 36.8 1.0
CB A:ASP251 4.8 21.5 1.0
C A:ASP251 4.8 20.1 1.0
O A:HOH530 4.8 19.7 1.0
N A:ASP251 4.9 17.1 1.0
CB A:GLU252 5.0 23.2 1.0

Manganese binding site 3 out of 4 in 5c7s

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Manganese binding site 3 out of 4 in the Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:47.2
occ:1.00
 O B:HOH509 2.4 38.3 1.0
OD1 B:ASP251 2.5 31.5 1.0
O B:HOH546 2.5 30.6 1.0
OE2 B:GLU252 2.7 28.2 1.0
O B:HOH502 2.7 23.1 1.0
O B:HOH594 2.8 38.8 1.0
O B:HOH584 3.1 34.4 1.0
CG B:ASP251 3.3 26.4 1.0
OD2 B:ASP251 3.4 22.1 1.0
MN B:MN402 3.5 26.6 1.0
CD B:GLU252 3.5 25.8 1.0
CG B:GLU252 3.7 23.6 1.0
OD2 B:ASP111 3.8 32.1 1.0
O3B B:PRP403 3.9 28.6 1.0
OG1 B:THR115 4.5 32.5 1.0
O3A B:PRP403 4.5 37.0 1.0
O B:ASP251 4.5 22.9 1.0
PB B:PRP403 4.6 28.5 1.0
O2B B:PRP403 4.6 30.7 1.0
OE1 B:GLU252 4.7 32.8 1.0
CG B:ASP111 4.7 30.5 1.0
CB B:ASP251 4.7 26.2 1.0
O B:HOH537 4.8 23.8 1.0
O4 B:PRP403 4.8 25.4 1.0
C B:ASP251 4.8 28.0 1.0
N B:ASP251 5.0 26.5 1.0

Manganese binding site 4 out of 4 in 5c7s

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Manganese binding site 4 out of 4 in the Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Prpp Complexed with Two MN2+ in the Active Site of Mycobacterium Tuberculosis Anthranilate Phosphoribosyltransferase (Anprt; Trpd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:26.6
occ:1.00
 OE2 B:GLU252 2.5 28.2 1.0
O2A B:PRP403 2.6 21.6 1.0
O B:HOH502 2.6 23.1 1.0
O3B B:PRP403 2.6 28.6 1.0
OG B:SER119 2.6 20.7 1.0
O B:HOH537 2.6 23.8 1.0
O3A B:PRP403 2.9 37.0 1.0
CB B:SER119 3.2 21.2 1.0
PB B:PRP403 3.2 28.5 1.0
PA B:PRP403 3.3 23.9 1.0
CD B:GLU252 3.3 25.8 1.0
MN B:MN401 3.5 47.2 1.0
OE1 B:GLU252 3.6 32.8 1.0
N B:GLY107 3.7 20.5 1.0
OD2 B:ASP251 4.0 22.1 1.0
O1A B:PRP403 4.1 32.3 1.0
O B:HOH546 4.1 30.6 1.0
O B:HOH520 4.1 20.6 1.0
CA B:GLY107 4.1 24.6 1.0
N B:SER119 4.2 19.9 1.0
O1B B:PRP403 4.2 25.8 1.0
CA B:SER119 4.3 25.8 1.0
O B:ASP251 4.4 22.9 1.0
O2B B:PRP403 4.4 30.7 1.0
C B:VAL106 4.4 27.5 1.0
O4 B:PRP403 4.4 25.4 1.0
O1 B:PRP403 4.6 25.4 1.0
CG B:ASP251 4.6 26.4 1.0
CG B:GLU252 4.6 23.6 1.0
OD1 B:ASP251 4.7 31.5 1.0
CA B:VAL106 4.7 22.8 1.0
C1 B:PRP403 4.8 29.3 1.0
O B:HOH594 4.8 38.8 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: Sat Oct 5 23:43:56 2024

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