Manganese in PDB 3gg0: Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex

The structure of Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex, PDB code: 3gg0 was solved by T.Barends, E.Hartmann, J.Griese, T.Beitlich, N.Kirienko, D.Ryjenkov, J.Reinstein, R.Shoeman, M.Gomelsky, I.Schlichting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.45 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.020, 96.890, 126.870, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 29.5

The binding sites of Manganese atom in the Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex (pdb code 3gg0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex, PDB code: 3gg0:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:16.9 occ:1.00 OE2 A:GLU272 2.0 31.2 1.0 OE2 A:GLU188 2.1 19.7 1.0 OD1 A:ASN239 2.1 29.8 1.0 OD2 A:ASP302 2.2 29.3 1.0 O2P A:C2E501 2.3 19.8 1.0 O A:HOH409 2.4 12.5 1.0 CG A:ASP302 3.1 29.6 1.0 CG A:ASN239 3.1 30.0 1.0 CD A:GLU188 3.1 20.8 1.0 CD A:GLU272 3.2 32.3 1.0 P1 A:C2E501 3.3 19.9 1.0 O1P A:C2E501 3.4 20.8 1.0 ND2 A:ASN239 3.4 30.2 1.0 OD1 A:ASP302 3.5 28.7 1.0 OE1 A:GLU188 3.6 20.4 1.0 NZ A:LYS323 3.8 20.9 1.0 MN A:MN503 3.8 17.0 1.0 OE1 A:GLU272 3.8 32.8 1.0 O5' A:C2E501 4.0 20.3 1.0 CB A:GLU272 4.2 33.5 1.0 CB A:ASP302 4.2 29.5 1.0 CG A:GLU272 4.3 33.0 1.0 CG A:GLU188 4.3 20.7 1.0 O A:HOH408 4.4 10.3 1.0 O A:HOH420 4.4 15.8 1.0 CB A:ASN239 4.5 29.9 1.0 C2A A:C2E501 4.6 20.7 1.0 C5' A:C2E501 4.7 19.5 1.0 O3A A:C2E501 4.7 20.7 1.0 OE1 A:GLU359 4.8 21.2 1.0 O2A A:C2E501 4.8 19.7 1.0 CD A:LYS323 4.9 22.2 1.0 CD2 A:LEU190 4.9 17.2 1.0 CE A:LYS323 4.9 21.6 1.0

Manganese binding site 2 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:17.0 occ:1.00 OE1 A:GLU359 2.0 21.2 1.0 OD1 A:ASP303 2.2 33.0 1.0 O1P A:C2E501 2.4 20.8 1.0 OD1 A:ASP302 2.4 28.7 1.0 O A:HOH409 2.4 12.5 1.0 CD A:GLU359 2.7 19.8 1.0 OE2 A:GLU359 2.7 19.6 1.0 CG A:ASP302 3.1 29.6 1.0 OD2 A:ASP302 3.2 29.3 1.0 O5' A:C2E501 3.2 20.3 1.0 CG A:ASP303 3.2 33.7 1.0 P1 A:C2E501 3.3 19.9 1.0 OD2 A:ASP303 3.7 34.6 1.0 MN A:MN502 3.8 16.9 1.0 O2P A:C2E501 4.0 19.8 1.0 N A:ASP303 4.0 31.8 1.0 CG A:GLU359 4.1 20.1 1.0 CB A:ASP303 4.4 33.1 1.0 CA A:ASP303 4.5 33.1 1.0 CB A:ASP302 4.5 29.5 1.0 C5' A:C2E501 4.5 19.5 1.0 NZ A:LYS323 4.5 20.9 1.0 O3A A:C2E501 4.6 20.7 1.0 O A:HOH410 4.7 28.8 1.0 O A:HOH408 4.7 10.3 1.0 C A:ASP302 4.8 30.6 1.0 OE2 A:GLU272 4.8 31.2 1.0 CA A:ASP302 4.9 29.9 1.0 CB A:GLU359 5.0 19.5 1.0 CD A:LYS323 5.0 22.2 1.0

Manganese binding site 3 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:23.1 occ:1.00 OD1 B:ASP302 2.0 29.4 1.0 OE2 B:GLU188 2.1 22.4 1.0 OE2 B:GLU272 2.1 34.2 1.0 OD1 B:ASN239 2.2 25.3 1.0 O B:HOH407 2.3 15.1 1.0 O2P B:C2E501 2.3 25.0 1.0 CG B:ASP302 3.0 29.9 1.0 CG B:ASN239 3.1 26.2 1.0 O1P B:C2E501 3.2 27.1 1.0 CD B:GLU188 3.2 23.6 1.0 ND2 B:ASN239 3.3 25.7 1.0 CD B:GLU272 3.3 34.1 1.0 P1 B:C2E501 3.3 25.6 1.0 OD2 B:ASP302 3.4 29.9 1.0 MN B:MN503 3.7 29.4 1.0 OE1 B:GLU188 3.9 24.5 1.0 OE1 B:GLU272 4.0 34.6 1.0 O B:HOH461 4.0 28.5 1.0 NZ B:LYS323 4.0 23.1 1.0 CB B:ASP302 4.1 30.3 1.0 CB B:GLU272 4.1 34.1 1.0 O5' B:C2E501 4.3 26.8 1.0 CG B:GLU272 4.3 33.9 1.0 CG B:GLU188 4.4 23.5 1.0 CB B:ASN239 4.5 26.5 1.0 C2A B:C2E501 4.5 23.7 1.0 O2A B:C2E501 4.6 23.8 1.0 O3A B:C2E501 4.6 25.9 1.0 CD B:LYS323 4.7 23.8 1.0 C5' B:C2E501 4.9 26.4 1.0 C3A B:C2E501 5.0 24.3 1.0 CE B:LYS323 5.0 23.4 1.0

Manganese binding site 4 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Klebsiella Pneumoniae BLRP1 pH 9.0 Manganese/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:29.4 occ:1.00 O1P B:C2E501 1.9 27.1 1.0 OE1 B:GLU359 2.1 25.4 1.0 OD2 B:ASP302 2.1 29.9 1.0 O B:HOH407 2.3 15.1 1.0 OD1 B:ASP303 2.3 33.9 1.0 OE2 B:GLU359 2.5 24.0 1.0 CD B:GLU359 2.6 24.2 1.0 O B:HOH430 3.0 29.5 1.0 CG B:ASP302 3.1 29.9 1.0 P1 B:C2E501 3.1 25.6 1.0 OD1 B:ASP302 3.3 29.4 1.0 CG B:ASP303 3.3 33.7 1.0 O5' B:C2E501 3.4 26.8 1.0 O B:HOH406 3.7 29.5 1.0 MN B:MN502 3.7 23.1 1.0 OD2 B:ASP303 3.8 33.9 1.0 O2P B:C2E501 3.9 25.0 1.0 N B:ASP303 4.0 32.2 1.0 CG B:GLU359 4.1 22.3 1.0 O3A B:C2E501 4.4 25.9 1.0 CA B:ASP303 4.5 33.4 1.0 CB B:ASP302 4.5 30.3 1.0 CB B:ASP303 4.5 33.3 1.0 C5' B:C2E501 4.7 26.4 1.0 C B:ASP302 4.8 31.2 1.0 NZ B:LYS323 4.8 23.1 1.0 OE2 B:GLU272 4.8 34.2 1.0 CD B:LYS323 4.8 23.8 1.0 CA B:ASP302 4.8 30.4 1.0 OE2 B:GLU188 5.0 22.4 1.0 CB B:GLU359 5.0 21.1 1.0

T.R.Barends, E.Hartmann, J.J.Griese, T.Beitlich, N.V.Kirienko, D.A.Ryjenkov, J.Reinstein, R.L.Shoeman, M.Gomelsky, I.Schlichting. Structure and Mechanism of A Bacterial Light-Regulated Cyclic Nucleotide Phosphodiesterase. Nature V. 459 1015 2009.
ISSN: ISSN 0028-0836
PubMed: 19536266
DOI: 10.1038/NATURE07966