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Manganese in PDB 2xmo: The Crystal Structure of LMO2642

Protein crystallography data

The structure of The Crystal Structure of LMO2642, PDB code: 2xmo was solved by J.H.Jeong, Y.G.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.963, 103.267, 73.765, 90.00, 102.80, 90.00
R / Rfree (%) 21.18 / 24.25

Other elements in 2xmo:

The structure of The Crystal Structure of LMO2642 also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Calcium (Ca) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of LMO2642 (pdb code 2xmo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The Crystal Structure of LMO2642, PDB code: 2xmo:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 2xmo

Go back to Manganese Binding Sites List in 2xmo
Manganese binding site 1 out of 2 in the The Crystal Structure of LMO2642


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of LMO2642 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn555

b:13.1
occ:1.00
O A:HOH2284 2.1 13.8 1.0
O2 A:PO41444 2.2 16.5 1.0
NE2 A:HIS49 2.2 12.3 1.0
NE2 A:HIS283 2.3 13.2 1.0
OD2 A:ASP47 2.3 13.9 1.0
OD2 A:ASP101 2.3 9.3 1.0
CE1 A:HIS49 3.0 15.5 1.0
CE1 A:HIS283 3.1 14.8 1.0
CG A:ASP47 3.3 12.8 1.0
FE A:FE556 3.3 13.6 1.0
CG A:ASP101 3.3 12.9 1.0
CD2 A:HIS283 3.3 12.6 1.0
P A:PO41444 3.3 16.5 1.0
CD2 A:HIS49 3.4 14.2 1.0
O1 A:PO41444 3.6 18.1 1.0
CB A:ASP101 3.7 10.2 1.0
CB A:ASP47 3.8 12.4 1.0
O4 A:PO41444 3.9 19.1 1.0
ND1 A:HIS49 4.2 14.7 1.0
O A:HOH2287 4.2 25.2 1.0
O A:HIS281 4.2 12.5 1.0
OD1 A:ASP47 4.3 12.6 1.0
ND1 A:HIS283 4.3 13.7 1.0
CG A:HIS49 4.4 14.3 1.0
CE1 A:HIS243 4.4 13.6 1.0
CG A:HIS283 4.4 12.8 1.0
OD1 A:ASP101 4.4 10.7 1.0
NE2 A:HIS243 4.5 12.4 1.0
O3 A:PO41444 4.6 16.2 1.0
CA A:ASP47 4.6 9.6 1.0
CD2 A:HIS135 4.6 15.5 1.0
CA A:HIS281 4.7 11.9 1.0
C A:HIS281 4.9 13.0 1.0
ND1 A:HIS281 5.0 13.1 1.0
O A:HOH2285 5.0 30.2 1.0

Manganese binding site 2 out of 2 in 2xmo

Go back to Manganese Binding Sites List in 2xmo
Manganese binding site 2 out of 2 in the The Crystal Structure of LMO2642


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of LMO2642 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn555

b:14.9
occ:1.00
O B:HOH2240 2.1 13.7 1.0
OD2 B:ASP47 2.1 15.3 1.0
NE2 B:HIS49 2.2 15.6 1.0
O4 B:PO41444 2.3 14.8 1.0
NE2 B:HIS283 2.3 17.6 1.0
OD2 B:ASP101 2.3 11.8 1.0
CE1 B:HIS49 2.9 19.0 1.0
CE1 B:HIS283 3.1 18.3 1.0
CG B:ASP47 3.2 15.0 1.0
FE B:FE556 3.3 14.9 1.0
CD2 B:HIS283 3.3 16.2 1.0
CG B:ASP101 3.3 12.5 1.0
P B:PO41444 3.4 18.1 1.0
CD2 B:HIS49 3.4 16.1 1.0
O1 B:PO41444 3.6 17.4 1.0
CB B:ASP101 3.7 11.8 1.0
CB B:ASP47 3.8 15.2 1.0
O3 B:PO41444 3.8 18.7 1.0
ND1 B:HIS49 4.1 19.0 1.0
OD1 B:ASP47 4.2 14.2 1.0
O B:HIS281 4.2 15.3 1.0
O B:HOH2242 4.3 20.6 1.0
ND1 B:HIS283 4.3 18.1 1.0
CE1 B:HIS243 4.4 12.5 1.0
CG B:HIS283 4.4 14.8 1.0
CG B:HIS49 4.4 16.4 1.0
OD1 B:ASP101 4.5 12.7 1.0
NE2 B:HIS243 4.5 12.8 1.0
CD2 B:HIS135 4.5 15.0 1.0
CA B:ASP47 4.6 13.5 1.0
O2 B:PO41444 4.6 18.5 1.0
CA B:HIS281 4.8 13.8 1.0
C B:HIS281 4.9 14.6 1.0
ND1 B:HIS281 5.0 11.9 1.0

Reference:

Y.G.Kim, J.H.Jeong, N.C.Ha, K.J.Kim. Structural and Functional Analysis of the LMO2642 Cyclic Nucleotide Phosphodiesterase From Listeria Monocytogenes. Proteins V. 79 1205 2011.
ISSN: ISSN 0887-3585
PubMed: 21246635
DOI: 10.1002/PROT.22954
Page generated: Sat Oct 5 15:28:07 2024

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