Nickel in PDB 2vy3: Type IV Secretion System Effector Protein Bepa

The structure of Type IV Secretion System Effector Protein Bepa, PDB code: 2vy3 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 / 2.8
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.336, 84.610, 126.680, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 27.6

The structure of Type IV Secretion System Effector Protein Bepa also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Nickel atom in the Type IV Secretion System Effector Protein Bepa (pdb code 2vy3). 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, PDB code: 2vy3:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:71.8 occ:1.00 O A:HOH2002 2.0 57.1 1.0 NE2 A:HIS18 2.0 64.8 1.0 NE2 A:HIS17 2.0 67.3 1.0 O A:HOH2001 2.2 55.7 1.0 CE1 A:HIS17 2.7 65.9 1.0 CE1 A:HIS18 2.7 62.5 1.0 CD2 A:HIS18 3.1 60.6 1.0 CD2 A:HIS17 3.2 66.5 1.0 ND1 A:HIS18 3.8 56.0 1.0 ND1 A:HIS17 3.9 66.6 1.0 CG A:HIS18 4.0 58.4 1.0 CG A:HIS17 4.1 63.2 1.0 O A:GLU12 4.2 75.2 1.0 CB A:SER15 4.9 59.5 1.0

Nickel binding site 2 out of 4 in the Type IV Secretion System Effector Protein Bepa


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:51.2 occ:1.00 NZ A:LYS49 2.0 51.9 1.0 NE2 B:HIS231 2.0 54.6 1.0 NE2 A:HIS45 2.1 63.3 1.0 O A:HOH2003 2.2 25.5 1.0 O A:HOH2004 2.4 21.1 1.0 CE1 A:HIS45 2.9 61.8 1.0 CE1 B:HIS231 2.9 52.2 1.0 CE A:LYS49 2.9 53.0 1.0 CD2 B:HIS231 3.0 54.9 1.0 CD2 A:HIS45 3.2 63.4 1.0 ND1 B:HIS231 4.0 49.0 1.0 ND1 A:HIS45 4.1 57.8 1.0 CG B:HIS231 4.1 53.5 1.0 CG A:HIS45 4.2 57.1 1.0 CD A:LYS49 4.4 56.7 1.0 NZ A:LYS42 4.5 64.7 1.0 OD2 A:ASP46 4.7 60.4 1.0

Nickel binding site 3 out of 4 in the Type IV Secretion System Effector Protein Bepa


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:80.3 occ:1.00 NE2 B:HIS17 2.0 69.0 1.0 NE2 B:HIS18 2.1 64.4 1.0 O B:HOH2002 2.3 55.2 1.0 O B:HOH2001 2.4 59.1 1.0 CE1 B:HIS17 2.4 66.8 1.0 CE1 B:HIS18 2.8 61.7 1.0 CD2 B:HIS18 3.1 59.6 1.0 CD2 B:HIS17 3.3 66.7 1.0 ND1 B:HIS17 3.6 67.6 1.0 ND1 B:HIS18 3.8 55.8 1.0 CG B:HIS18 4.0 59.0 1.0 CG B:HIS17 4.1 64.2 1.0 O B:GLU12 4.1 75.8 1.0 CB B:SER15 4.9 60.3 1.0

Nickel binding site 4 out of 4 in the Type IV Secretion System Effector Protein Bepa


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni502 b:54.4 occ:1.00 NZ B:LYS49 2.0 52.6 1.0 NE2 A:HIS231 2.0 54.6 1.0 NE2 B:HIS45 2.1 62.9 1.0 O B:HOH2003 2.2 20.6 1.0 CE B:LYS49 2.7 53.6 1.0 CE1 B:HIS45 2.9 61.5 1.0 CE1 A:HIS231 3.0 52.2 1.0 CD2 A:HIS231 3.0 54.3 1.0 CD2 B:HIS45 3.2 62.2 1.0 ND1 A:HIS231 4.0 49.2 1.0 CD B:LYS49 4.0 57.1 1.0 CG A:HIS231 4.1 52.8 1.0 ND1 B:HIS45 4.1 57.3 1.0 CG B:HIS45 4.3 57.9 1.0 OD2 B:ASP46 4.4 59.8 1.0 O A:HIS231 4.8 54.0 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