Nickel in PDB 4kk7: Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis.

The structure of Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis., PDB code: 4kk7 was solved by K.V.Korotkov, T.J.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.48 / 1.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.700, 110.630, 110.510, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.4

The binding sites of Nickel atom in the Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis. (pdb code 4kk7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis., PDB code: 4kk7:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:18.1 occ:1.00 O A:HOH915 2.0 20.3 1.0 O3 A:TRS505 2.1 20.0 1.0 NE2 A:HIS366 2.1 20.4 1.0 N A:TRS505 2.1 22.5 1.0 OG A:SER177 2.1 19.8 1.0 C3 A:TRS505 2.8 22.5 1.0 C A:TRS505 2.9 23.4 1.0 CB A:SER177 3.1 19.9 1.0 CD2 A:HIS366 3.1 20.2 1.0 CE1 A:HIS366 3.1 20.2 1.0 C1 A:TRS505 3.5 24.0 1.0 OD1 A:ASP175 4.2 18.5 1.0 ND1 A:HIS366 4.2 19.3 1.0 C2 A:TRS505 4.2 24.4 1.0 OD2 A:ASP175 4.2 20.4 1.0 CG A:HIS366 4.2 19.4 1.0 O2 A:TRS505 4.3 23.7 1.0 O A:HOH633 4.4 22.4 1.0 CA A:SER177 4.5 18.7 1.0 O A:HOH918 4.6 39.5 1.0 CG A:ASP175 4.6 18.9 1.0 O1 A:TRS505 4.7 28.5 1.0 C A:SER177 4.9 18.1 1.0 CB A:ARG365 5.0 23.5 1.0

Nickel binding site 2 out of 4 in the Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni502 b:20.6 occ:0.88 OD1 A:ASP179 1.9 20.0 1.0 O A:HOH942 2.0 22.0 1.0 CG A:ASP179 2.9 19.6 1.0 OD2 A:ASP179 3.2 21.4 1.0 OE1 A:GLU185 4.0 24.1 1.0 O A:PRO180 4.1 16.9 1.0 O A:HOH712 4.1 33.3 1.0 O A:SER363 4.1 18.4 1.0 O A:ASP179 4.3 16.2 1.0 CB A:ASP179 4.3 18.5 1.0 OE2 A:GLU185 4.3 29.4 1.0 O A:ALA176 4.4 19.8 1.0 NE2 A:GLN182 4.5 37.9 1.0 C A:ASP179 4.6 17.1 1.0 CD A:GLU185 4.6 26.1 1.0 N A:ASP179 4.6 17.0 1.0 CA A:ASP179 4.7 17.3 1.0 C A:PRO180 4.8 17.5 1.0 O A:HOH730 4.9 29.8 1.0

Nickel binding site 3 out of 4 in the Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni503 b:38.5 occ:0.50 NE2 A:HIS93 2.1 39.6 1.0 CE1 A:HIS93 3.1 37.1 1.0 CD2 A:HIS93 3.1 36.2 1.0 OE1 A:GLN91 3.7 52.0 1.0 ND1 A:HIS93 4.2 35.7 1.0 CG A:HIS93 4.3 34.0 1.0 N A:GLN126 4.8 39.2 1.0 CD A:GLN91 4.9 50.5 1.0

Nickel binding site 4 out of 4 in the Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of ECCB1 From the Type VII (Esx-1) Secretion System of Mycobacterium Tuberculosis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni504 b:41.8 occ:0.40 CE1 A:HIS184 1.9 39.1 1.0 NE2 A:HIS184 2.1 40.2 1.0 ND1 A:HIS184 3.2 36.9 1.0 OE1 A:GLN182 3.4 40.1 1.0 CD2 A:HIS184 3.5 38.2 1.0 CG A:HIS184 4.0 35.7 1.0 OE2 A:GLU331 4.1 49.1 1.0 CD A:GLN182 4.2 35.1 1.0 OE1 A:GLU331 4.5 48.5 1.0 CD A:GLU331 4.7 47.0 1.0 NE2 A:GLN182 4.7 37.9 1.0 CB A:GLN182 4.8 28.5 1.0 O A:HOH796 4.9 39.7 1.0

J.M.Wagner, S.Chan, T.J.Evans, S.Kahng, J.Kim, M.A.Arbing, D.Eisenberg, K.V.Korotkov. Structures of ECCB1 and ECCD1 From the Core Complex of the Mycobacterial Esx-1 Type VII Secretion System. Bmc Struct.Biol. V. 16 5 2016.
ISSN: ESSN 1472-6807
PubMed: 26922638
DOI: 10.1186/S12900-016-0056-6