Atomistry » Manganese » PDB 1ho5-1j53 » 1i0b
Atomistry »
  Manganese »
    PDB 1ho5-1j53 »
      1i0b »

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

Go back to Manganese Binding Sites List in 1i0b
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy