Manganese in PDB 3gfz: Klebsiella Pneumoniae BLRP1 pH 6 Manganese/Cy-Digmp Complex

The structure of Klebsiella Pneumoniae BLRP1 pH 6 Manganese/Cy-Digmp Complex, PDB code: 3gfz 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)	48.54 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.450, 97.090, 127.170, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 27.2

The binding sites of Manganese atom in the Klebsiella Pneumoniae BLRP1 pH 6 Manganese/Cy-Digmp Complex (pdb code 3gfz). 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 6 Manganese/Cy-Digmp Complex, PDB code: 3gfz:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 6 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 6 Manganese/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:43.1 occ:1.00 OE2 A:GLU272 1.9 46.4 1.0 O2P A:C2E501 2.1 44.2 1.0 OD2 A:ASP302 2.1 40.5 1.0 OD1 A:ASN239 2.2 36.4 1.0 OE2 A:GLU188 2.2 41.6 1.0 O A:HOH752 2.3 28.7 1.0 CG A:ASP302 3.0 41.2 1.0 CD A:GLU272 3.1 43.5 1.0 CG A:ASN239 3.1 38.6 1.0 CD A:GLU188 3.2 41.8 1.0 P1 A:C2E501 3.3 43.0 1.0 OD1 A:ASP302 3.4 42.0 1.0 ND2 A:ASN239 3.4 37.7 1.0 OE1 A:GLU188 3.6 41.9 1.0 O1P A:C2E501 3.7 46.8 1.0 OE1 A:GLU272 3.9 46.2 1.0 O A:HOH419 4.0 42.2 1.0 CB A:GLU272 4.0 42.0 1.0 O5' A:C2E501 4.1 47.6 1.0 CG A:GLU272 4.1 42.9 1.0 CB A:ASP302 4.2 40.1 1.0 MN A:MN503 4.2 49.4 1.0 CG A:GLU188 4.5 41.8 1.0 CB A:ASN239 4.5 39.3 1.0 O3A A:C2E501 4.6 41.2 1.0 NZ A:LYS323 4.6 41.5 1.0 C2A A:C2E501 4.7 39.3 1.0 C5' A:C2E501 4.9 45.5 1.0 C3A A:C2E501 5.0 37.9 1.0 OE1 A:GLU359 5.0 41.0 1.0 CD A:LYS323 5.0 41.4 1.0

Manganese binding site 2 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 6 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 6 Manganese/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:49.4 occ:1.00 O1P A:C2E501 2.0 46.8 1.0 OD1 A:ASP303 2.1 44.8 1.0 OE1 A:GLU359 2.2 41.0 1.0 OD1 A:ASP302 2.4 42.0 1.0 OE2 A:GLU359 2.4 45.2 1.0 CD A:GLU359 2.6 40.8 1.0 O A:HOH752 3.0 28.7 1.0 CG A:ASP302 3.1 41.2 1.0 CG A:ASP303 3.1 42.0 1.0 P1 A:C2E501 3.3 43.0 1.0 OD2 A:ASP302 3.4 40.5 1.0 O5' A:C2E501 3.6 47.6 1.0 OD2 A:ASP303 3.7 44.5 1.0 N A:ASP303 3.8 40.8 1.0 O A:HOH789 3.9 42.9 1.0 O2P A:C2E501 4.0 44.2 1.0 O A:HOH419 4.1 42.2 1.0 CG A:GLU359 4.1 40.6 1.0 MN A:MN502 4.2 43.1 1.0 CA A:ASP303 4.3 41.1 1.0 CB A:ASP303 4.3 41.4 1.0 CB A:ASP302 4.4 40.1 1.0 O3A A:C2E501 4.5 41.2 1.0 C A:ASP302 4.6 40.4 1.0 CA A:ASP302 4.8 40.1 1.0 CB A:GLU359 4.8 39.7 1.0 C5' A:C2E501 5.0 45.5 1.0

Manganese binding site 3 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 6 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 6 Manganese/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:41.6 occ:1.00 OD1 B:ASP302 2.0 43.5 1.0 O2P B:C2E501 2.1 43.8 1.0 OE2 B:GLU188 2.1 43.8 1.0 OE2 B:GLU272 2.2 44.9 1.0 O B:HOH798 2.2 35.0 1.0 OD1 B:ASN239 2.3 36.3 1.0 CG B:ASP302 3.1 43.5 1.0 CD B:GLU188 3.1 42.1 1.0 CG B:ASN239 3.2 38.0 1.0 P1 B:C2E501 3.3 43.0 1.0 CD B:GLU272 3.3 42.8 1.0 ND2 B:ASN239 3.4 37.8 1.0 OD2 B:ASP302 3.5 46.3 1.0 OE1 B:GLU188 3.6 44.3 1.0 O1P B:C2E501 3.9 46.0 1.0 CB B:GLU272 4.0 41.1 1.0 O5' B:C2E501 4.0 46.4 1.0 O B:HOH751 4.1 51.0 1.0 CG B:GLU272 4.2 42.5 1.0 OE1 B:GLU272 4.2 45.9 1.0 O A:HOH563 4.2 42.4 1.0 CB B:ASP302 4.2 42.1 1.0 MN B:MN503 4.3 53.3 1.0 NZ B:LYS323 4.3 42.3 1.0 CG B:GLU188 4.4 41.4 1.0 O3A B:C2E501 4.5 41.2 1.0 CB B:ASN239 4.6 38.6 1.0 C2A B:C2E501 4.6 40.4 1.0 O2A B:C2E501 4.8 39.2 1.0 C5' B:C2E501 4.9 45.0 1.0 C3A B:C2E501 4.9 40.1 1.0 OE2 B:GLU359 5.0 43.2 1.0

Manganese binding site 4 out of 4 in the Klebsiella Pneumoniae BLRP1 pH 6 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 6 Manganese/Cy-Digmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn503 b:53.3 occ:1.00 O1P B:C2E501 1.9 46.0 1.0 OD1 B:ASP303 2.0 46.8 1.0 OD2 B:ASP302 2.2 46.3 1.0 OE2 B:GLU359 2.4 43.2 1.0 OE1 B:GLU359 2.5 43.4 1.0 CD B:GLU359 2.7 41.6 1.0 O B:HOH800 2.9 56.3 1.0 CG B:ASP302 3.1 43.5 1.0 P1 B:C2E501 3.1 43.0 1.0 O A:HOH559 3.3 44.4 1.0 CG B:ASP303 3.3 44.5 1.0 O B:HOH798 3.4 35.0 1.0 OD1 B:ASP302 3.5 43.5 1.0 O5' B:C2E501 3.5 46.4 1.0 N B:ASP303 3.7 42.4 1.0 O2P B:C2E501 3.9 43.8 1.0 O B:HOH751 3.9 51.0 1.0 OD2 B:ASP303 3.9 48.0 1.0 CG B:GLU359 4.1 41.5 1.0 CA B:ASP303 4.2 42.8 1.0 MN B:MN502 4.3 41.6 1.0 O3A B:C2E501 4.3 41.2 1.0 CB B:ASP302 4.3 42.1 1.0 CB B:ASP303 4.3 42.7 1.0 C B:ASP302 4.5 42.1 1.0 CA B:ASP302 4.7 41.8 1.0 OD1 B:ASP325 4.7 48.9 1.0 C5' B:C2E501 4.9 45.0 1.0 CB B:GLU359 5.0 40.0 1.0 O B:HOH713 5.0 42.5 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