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Manganese in PDB 1i0b: High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta

Enzymatic activity of High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta

All present enzymatic activity of High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta:
3.1.8.1;

Protein crystallography data

The structure of High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1i0b was solved by H.M.Holden, M.M.Benning, F.M.Raushel, H.Shim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.444, 90.034, 68.385, 90.00, 91.72, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1i0b:

The structure of High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta (pdb code 1i0b). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1i0b:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1i0b

Go back to Manganese Binding Sites List in 1i0b
Manganese binding site 1 out of 4 in the High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:16.3
occ:1.00
 O A:HOH1010 2.1 14.8 1.0
O1 A:FMT369 2.1 15.7 1.0
NE2 A:HIS55 2.1 15.7 1.0
OD2 A:ASP301 2.1 18.7 1.0
NE2 A:HIS57 2.2 16.9 1.0
C A:FMT369 2.9 11.9 1.0
O2 A:EDO408 3.0 25.7 0.5
CD2 A:HIS55 3.1 16.3 1.0
CE1 A:HIS57 3.1 13.8 1.0
CG A:ASP301 3.1 26.9 1.0
CE1 A:HIS55 3.2 17.1 1.0
CD2 A:HIS57 3.2 25.5 1.0
O2 A:FMT369 3.3 19.4 1.0
OD1 A:ASP301 3.4 19.6 1.0
O2 A:EDO408 3.5 17.1 0.5
MN A:MN402 3.7 17.8 1.0
C2 A:EDO408 3.7 24.0 1.0
NZ A:LYS169 4.0 14.6 1.0
CG2 A:VAL101 4.2 14.0 1.0
CG A:HIS55 4.3 24.1 1.0
ND1 A:HIS57 4.3 15.7 1.0
CE1 A:HIS230 4.3 23.9 1.0
CG A:HIS57 4.3 20.5 1.0
ND1 A:HIS55 4.3 12.6 1.0
O A:HOH1012 4.4 18.4 1.0
CB A:ASP301 4.4 17.7 1.0
NE2 A:HIS230 4.4 21.5 1.0
O A:HOH854 4.5 62.0 1.0
O A:HOH853 4.9 28.4 1.0
CA A:ASP301 4.9 20.2 1.0

Manganese binding site 2 out of 4 in 1i0b

Go back to Manganese Binding Sites List in 1i0b
Manganese binding site 2 out of 4 in the High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:17.8
occ:1.00
 O A:HOH1012 2.0 18.4 1.0
O A:HOH1010 2.0 14.8 1.0
O2 A:FMT369 2.1 19.4 1.0
ND1 A:HIS201 2.2 19.8 1.0
NE2 A:HIS230 2.2 21.5 1.0
O A:HOH853 2.5 28.4 1.0
CE1 A:HIS201 3.0 18.9 1.0
CD2 A:HIS230 3.2 22.3 1.0
C A:FMT369 3.2 11.9 1.0
CE1 A:HIS230 3.2 23.9 1.0
CG A:HIS201 3.3 22.5 1.0
O1 A:FMT369 3.5 15.7 1.0
MN A:MN401 3.7 16.3 1.0
O2 A:EDO408 3.7 17.1 0.5
CB A:HIS201 3.7 17.9 1.0
O A:HOH947 4.1 69.3 1.0
NE2 A:HIS201 4.1 30.7 1.0
NE1 A:TRP131 4.2 13.8 1.0
OD1 A:ASP301 4.2 19.6 1.0
CD2 A:HIS201 4.3 35.5 1.0
NE2 A:HIS55 4.3 15.7 1.0
CG A:HIS230 4.3 30.1 1.0
ND1 A:HIS230 4.3 17.8 1.0
CE1 A:HIS55 4.3 17.1 1.0
NZ A:LYS169 4.4 14.6 1.0
O2 A:EDO408 4.6 25.7 0.5
CA A:HIS201 4.6 14.9 1.0
C2 A:EDO408 4.8 24.0 1.0
CE A:LYS169 4.9 11.9 1.0
NE2 A:HIS254 4.9 23.8 1.0
CD1 A:TRP131 4.9 12.1 1.0
OD2 A:ASP301 4.9 18.7 1.0
O A:HOH1103 5.0 40.9 1.0
CG A:ASP301 5.0 26.9 1.0

Manganese binding site 3 out of 4 in 1i0b

Go back to Manganese Binding Sites List in 1i0b
Manganese binding site 3 out of 4 in the High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:13.7
occ:1.00
 O1 B:FMT369 2.0 15.4 1.0
O B:HOH1009 2.0 12.5 1.0
NE2 B:HIS55 2.1 11.5 1.0
NE2 B:HIS57 2.1 16.1 1.0
OD2 B:ASP301 2.2 14.8 1.0
C B:FMT369 2.9 13.4 1.0
CE1 B:HIS55 3.1 16.6 1.0
CD2 B:HIS57 3.1 12.8 1.0
CG B:ASP301 3.1 14.1 1.0
CD2 B:HIS55 3.1 10.8 1.0
CE1 B:HIS57 3.2 11.2 1.0
O2 B:FMT369 3.3 16.1 1.0
OD1 B:ASP301 3.4 14.3 1.0
O1 B:EDO407 3.4 11.0 0.5
C1 B:EDO407 3.5 21.7 1.0
MN B:MN402 3.7 13.8 1.0
O B:HOH1127 3.7 35.9 1.0
NZ B:LYS169 4.1 13.8 1.0
CG2 B:VAL101 4.1 13.1 1.0
ND1 B:HIS55 4.2 13.0 1.0
CG B:HIS57 4.2 16.9 1.0
ND1 B:HIS57 4.3 13.5 1.0
CG B:HIS55 4.3 11.2 1.0
CE1 B:HIS230 4.3 9.5 1.0
CB B:ASP301 4.4 12.9 1.0
NE2 B:HIS230 4.4 10.5 1.0
O B:HOH1011 4.5 16.9 1.0
O B:HOH1015 4.9 16.6 1.0
C2 B:EDO407 4.9 26.2 1.0
CA B:ASP301 4.9 13.5 1.0

Manganese binding site 4 out of 4 in 1i0b

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Manganese binding site 4 out of 4 in the High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of High Resolution Structure of the Manganese-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:13.8
occ:1.00
 O B:HOH1009 2.1 12.5 1.0
O B:HOH1015 2.1 16.6 1.0
O2 B:FMT369 2.2 16.1 1.0
NE2 B:HIS230 2.2 10.5 1.0
ND1 B:HIS201 2.2 15.3 1.0
O B:HOH1011 2.3 16.9 1.0
CE1 B:HIS201 3.1 14.9 1.0
CD2 B:HIS230 3.1 16.1 1.0
C B:FMT369 3.2 13.4 1.0
CE1 B:HIS230 3.2 9.5 1.0
CG B:HIS201 3.4 17.5 1.0
O1 B:FMT369 3.5 15.4 1.0
MN B:MN401 3.7 13.7 1.0
O1 B:EDO407 3.8 11.0 0.5
CB B:HIS201 3.8 14.2 1.0
NE1 B:TRP131 4.2 13.3 1.0
OD1 B:ASP301 4.2 14.3 1.0
O B:HOH1017 4.3 26.3 1.0
CG B:HIS230 4.3 14.4 1.0
NE2 B:HIS201 4.3 17.4 1.0
ND1 B:HIS230 4.3 16.0 1.0
NZ B:LYS169 4.4 13.8 1.0
CE1 B:HIS55 4.4 16.6 1.0
CD2 B:HIS201 4.5 15.3 1.0
NE2 B:HIS55 4.5 11.5 1.0
O B:HOH1127 4.5 35.9 1.0
O B:HOH1020 4.6 30.8 1.0
CA B:HIS201 4.6 23.3 1.0
C1 B:EDO407 4.9 21.7 1.0
NE2 B:HIS254 4.9 12.9 1.0
CE B:LYS169 4.9 10.8 1.0
CD1 B:TRP131 5.0 14.3 1.0
CG B:ASP301 5.0 14.1 1.0

Reference:

M.M.Benning, H.Shim, F.M.Raushel, H.M.Holden. High Resolution X-Ray Structures of Different Metal-Substituted Forms of Phosphotriesterase From Pseudomonas Diminuta. Biochemistry V. 40 2712 2001.
ISSN: ISSN 0006-2960
PubMed: 11258882
DOI: 10.1021/BI002661E
Page generated: Sat Oct 5 10:58:19 2024

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