Cobalt in PDB 1jn1: Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671)

The structure of Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671), PDB code: 1jn1 was solved by C.Lehmann, K.Lim, J.Toedt, W.Krajewski, A.Howard, E.Eisenstein, O.Herzberg, Structure 2 Function Project (S2F), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.90
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	112.300, 112.300, 187.600, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 29

The binding sites of Cobalt atom in the Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671) (pdb code 1jn1). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671), PDB code: 1jn1:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co201 b:46.4 occ:1.00 OD1 A:ASP9 2.0 45.1 1.0 ND1 A:HIS43 2.1 35.0 1.0 ND1 A:HIS35 2.2 41.9 1.0 NE2 A:HIS11 2.2 46.2 1.0 CD2 A:HIS11 2.9 41.6 1.0 CG A:ASP9 3.0 48.0 1.0 CE1 A:HIS35 3.1 45.3 1.0 CE1 A:HIS43 3.1 34.8 1.0 CG A:HIS43 3.1 36.4 1.0 CG A:HIS35 3.2 51.3 1.0 CE1 A:HIS11 3.3 44.1 1.0 OD2 A:ASP9 3.3 51.1 1.0 CB A:HIS43 3.4 35.2 1.0 CB A:HIS35 3.6 51.4 1.0 CA A:HIS35 4.0 43.1 1.0 CG A:HIS11 4.1 49.5 1.0 NE2 A:HIS43 4.2 36.1 1.0 NE2 A:HIS35 4.2 45.9 1.0 CD2 A:HIS43 4.2 35.4 1.0 O A:HIS35 4.2 39.3 1.0 ND1 A:HIS11 4.3 48.7 1.0 CD2 A:HIS35 4.3 50.1 1.0 CB A:ASP9 4.3 46.6 1.0 C A:HIS35 4.6 41.2 1.0 CA A:VAL40 4.8 34.3 1.0 CA A:GLY38 4.8 46.0 1.0 O A:ASP39 4.8 38.2 1.0 N A:VAL40 4.9 39.4 1.0 N A:ASP39 4.9 40.0 1.0 C A:ASP39 4.9 35.3 1.0 CA A:HIS43 5.0 32.4 1.0

Cobalt binding site 2 out of 4 in the Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:55.1 occ:1.00 ND1 B:HIS43 2.0 44.9 1.0 OD1 B:ASP9 2.0 52.5 1.0 NE2 B:HIS11 2.1 34.2 1.0 ND1 B:HIS35 2.1 39.9 1.0 CE1 B:HIS43 2.8 36.2 1.0 CG B:ASP9 2.8 58.2 1.0 CE1 B:HIS35 3.0 45.7 1.0 CE1 B:HIS11 3.0 43.9 1.0 CD2 B:HIS11 3.0 47.4 1.0 OD2 B:ASP9 3.1 63.3 1.0 CG B:HIS43 3.1 46.8 1.0 CG B:HIS35 3.2 42.8 1.0 CB B:HIS35 3.5 40.4 1.0 CB B:HIS43 3.6 42.9 1.0 NE2 B:HIS43 4.0 31.6 1.0 ND1 B:HIS11 4.1 48.7 1.0 CG B:HIS11 4.1 47.3 1.0 NE2 B:HIS35 4.1 44.1 1.0 CD2 B:HIS43 4.1 37.5 1.0 CA B:HIS35 4.2 43.5 1.0 CB B:ASP9 4.2 44.3 1.0 CD2 B:HIS35 4.2 44.5 1.0 O B:HIS35 4.3 44.9 1.0 O B:ASP39 4.5 34.7 1.0 C B:HIS35 4.8 43.9 1.0 CA B:VAL40 4.8 45.6 1.0 C B:ASP39 4.8 45.4 1.0 O B:VAL10 4.9 41.9 1.0 N B:VAL40 4.9 47.6 1.0 C B:GLY38 5.0 43.6 1.0

Cobalt binding site 3 out of 4 in the Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co203 b:44.6 occ:1.00 ND1 C:HIS35 2.1 68.2 1.0 OD1 C:ASP9 2.2 72.8 1.0 NE2 C:HIS11 2.2 55.8 1.0 ND1 C:HIS43 2.3 49.5 1.0 CE1 C:HIS11 2.4 61.4 1.0 CG C:ASP9 2.9 64.4 1.0 OD2 C:ASP9 2.9 60.8 1.0 CG C:HIS35 2.9 70.5 1.0 CE1 C:HIS35 3.1 67.8 1.0 CB C:HIS35 3.2 69.6 1.0 CE1 C:HIS43 3.3 52.9 1.0 CG C:HIS43 3.3 53.4 1.0 CD2 C:HIS11 3.5 56.3 1.0 CB C:HIS43 3.5 46.8 1.0 CA C:HIS35 3.6 66.0 1.0 ND1 C:HIS11 3.6 61.0 1.0 CD2 C:HIS35 4.1 71.0 1.0 CG C:HIS11 4.2 60.9 1.0 NE2 C:HIS35 4.2 71.9 1.0 O C:HIS35 4.2 66.5 1.0 CB C:ASP9 4.3 52.2 1.0 NE2 C:HIS43 4.4 52.6 1.0 C C:HIS35 4.4 71.8 1.0 CD2 C:HIS43 4.4 55.3 1.0 N C:HIS35 4.7 67.8 1.0 O C:VAL10 5.0 60.8 1.0

Cobalt binding site 4 out of 4 in the Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae (HI0671) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co204 b:76.6 occ:1.00 OE1 B:GLU150 2.1 48.6 1.0 OE1 C:GLU150 2.2 54.6 1.0 OE2 C:GLU150 2.4 56.8 1.0 OE2 B:GLU150 2.4 63.2 1.0 CD B:GLU150 2.5 57.7 1.0 CD C:GLU150 2.6 53.7 1.0 OE1 A:GLU150 2.7 37.3 1.0 OE2 A:GLU150 2.9 33.8 1.0 NE2 C:HIS6 2.9 55.7 1.0 CD A:GLU150 3.1 41.9 1.0 CE1 C:HIS6 3.7 55.7 1.0 NE2 A:HIS6 3.8 51.5 1.0 CD2 C:HIS6 3.8 56.0 1.0 NE2 B:HIS6 3.9 52.8 1.0 CG B:GLU150 3.9 60.2 1.0 CG C:GLU150 4.0 56.1 1.0 CB B:GLU150 4.4 48.8 1.0 CD2 A:HIS6 4.4 54.6 1.0 CG A:GLU150 4.6 42.2 1.0 CB C:GLU150 4.7 43.9 1.0 CE1 A:HIS6 4.7 58.8 1.0 CD2 B:HIS6 4.7 52.8 1.0 ND1 C:HIS6 4.8 50.3 1.0 CE1 B:HIS6 4.8 55.2 1.0 CG C:HIS6 4.9 53.4 1.0

C.Lehmann, K.Lim, J.Toedt, W.Krajewski, A.Howard, E.Eisenstein, O.Herzberg. Structure of 2C-Methyl-D-Erythrol-2,4-Cyclodiphosphate Synthase From Haemophilus Influenzae: Activation By Conformational Transition. Proteins V. 49 135 2002.
ISSN: ISSN 0887-3585
PubMed: 12211023
DOI: 10.1002/PROT.10182