Nickel in PDB 2jk8: Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety

The structure of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety, PDB code: 2jk8 was solved by D.V.Palanivelu, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.948, 82.877, 126.729, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 27.5

The structure of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Nickel atom in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety (pdb code 2jk8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety, PDB code: 2jk8:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:68.2 occ:1.00 O A:HOH2001 1.9 57.1 1.0 NE2 A:HIS18 2.0 64.4 1.0 NE2 A:HIS17 2.1 72.2 1.0 O A:HOH2002 2.8 53.7 1.0 CE1 A:HIS17 2.8 70.3 1.0 CE1 A:HIS18 2.9 62.9 1.0 CD2 A:HIS18 3.1 61.6 1.0 CD2 A:HIS17 3.2 71.2 1.0 ND1 A:HIS17 4.0 68.9 1.0 O A:GLU12 4.0 74.9 1.0 ND1 A:HIS18 4.0 59.0 1.0 CG A:HIS18 4.1 59.4 1.0 CG A:HIS17 4.2 66.2 1.0 CB A:SER15 4.8 60.6 1.0

Nickel binding site 2 out of 4 in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:60.0 occ:1.00 NZ A:LYS49 2.0 53.9 1.0 NE2 B:HIS231 2.0 56.7 1.0 NE2 A:HIS45 2.1 65.8 1.0 O B:HOH2003 2.1 35.8 1.0 O A:HOH2003 2.4 41.8 1.0 CE1 A:HIS45 2.8 62.5 1.0 CE A:LYS49 2.8 56.1 1.0 CE1 B:HIS231 2.9 54.5 1.0 CD2 B:HIS231 3.1 59.0 1.0 CD2 A:HIS45 3.3 63.6 1.0 ND1 B:HIS231 4.0 51.1 1.0 ND1 A:HIS45 4.0 56.0 1.0 CG B:HIS231 4.1 55.9 1.0 CD A:LYS49 4.3 57.1 1.0 CG A:HIS45 4.3 57.7 1.0

Nickel binding site 3 out of 4 in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:75.3 occ:1.00 NE2 B:HIS17 2.0 71.7 1.0 NE2 B:HIS18 2.1 65.8 1.0 O B:HOH2002 2.2 57.2 1.0 CE1 B:HIS17 2.4 70.8 1.0 CE1 B:HIS18 2.9 62.2 1.0 CD2 B:HIS18 3.0 60.9 1.0 CD2 B:HIS17 3.3 69.9 1.0 O B:HOH2001 3.3 53.0 1.0 ND1 B:HIS17 3.6 69.0 1.0 ND1 B:HIS18 4.0 59.6 1.0 CG B:HIS18 4.1 58.0 1.0 CG B:HIS17 4.1 65.3 1.0 O B:GLU12 4.1 71.5 1.0 CB B:SER15 4.8 61.7 1.0

Nickel binding site 4 out of 4 in the Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Type IV Secretion System Effector Protein Bepa Complexed with A Pyrophosphate Moiety within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni502 b:64.6 occ:1.00 NZ B:LYS49 2.0 55.3 1.0 NE2 A:HIS231 2.0 57.7 1.0 NE2 B:HIS45 2.1 65.2 1.0 O A:HOH2004 2.1 38.5 1.0 CE1 A:HIS231 2.7 54.8 1.0 CE B:LYS49 2.7 57.2 1.0 CE1 B:HIS45 2.9 62.8 1.0 CD2 A:HIS231 3.1 58.9 1.0 CD2 B:HIS45 3.1 63.3 1.0 ND1 A:HIS231 3.9 51.5 1.0 CG A:HIS231 4.1 56.1 1.0 ND1 B:HIS45 4.1 58.3 1.0 CD B:LYS49 4.2 57.6 1.0 CG B:HIS45 4.2 58.9 1.0 OD2 B:ASP46 4.5 66.5 1.0

D.V.Palanivelu, A.Goepfert, M.Meury, P.Guye, C.Dehio, T.Schirmer. Fic Domain Catalyzed Adenylylation: Insight Provided By the Structural Analysis of the Type IV Secretion System Effector Bepa. Protein Sci. V. 20 492 2011.
ISSN: ISSN 0961-8368
PubMed: 21213248
DOI: 10.1002/PRO.581