Zinc in PDB 2byo: Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C)

The structure of Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C), PDB code: 2byo was solved by G.Sulzenbacher, S.Canaan, V.Roig-Zamboni, D.Maurin, B.Gicquel, Y.Bourne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.14 / 2.15
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	54.257, 54.257, 269.983, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 22.4

The binding sites of Zinc atom in the Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C) (pdb code 2byo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C), PDB code: 2byo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1208 b:31.2 occ:1.00 OD1 A:ASP21 1.8 31.8 1.0 O A:HOH2118 2.3 20.3 1.0 CG A:ASP21 2.6 36.0 1.0 OD2 A:ASP21 2.8 35.2 1.0 CB A:ASP21 4.0 36.2 1.0 CB A:ALA23 4.2 30.4 1.0 N A:ALA23 4.9 31.6 1.0 CA A:ASP21 4.9 39.2 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1209 b:39.2 occ:1.00 NE2 A:HIS42 2.0 28.0 1.0 OD2 A:ASP61 2.1 31.2 1.0 O A:HOH2119 2.3 26.8 1.0 O A:HOH2120 2.4 20.4 1.0 CE1 A:HIS42 2.8 26.2 1.0 CG A:ASP61 3.0 30.9 1.0 CD2 A:HIS42 3.0 24.7 1.0 CB A:ASP61 3.3 28.6 1.0 ND1 A:HIS42 3.9 27.3 1.0 CG A:HIS42 4.1 26.8 1.0 OD1 A:ASP61 4.1 33.5 1.0 CA A:ASP61 4.3 27.5 1.0 CB A:ALA44 4.6 28.4 1.0 O A:HOH2111 4.6 39.2 1.0 C A:ASP61 4.9 27.6 1.0 O A:HOH2110 4.9 26.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1210 b:34.2 occ:1.00 OD1 A:ASP98 1.9 34.3 1.0 OD2 A:ASP99 1.9 38.4 1.0 CG A:ASP99 2.7 37.1 1.0 OD1 A:ASP99 2.9 38.8 1.0 CG A:ASP98 2.9 34.9 1.0 OD2 A:ASP98 3.3 36.7 1.0 CB A:ASP99 4.1 36.8 1.0 O A:HOH2057 4.1 27.1 1.0 O A:HOH2059 4.2 44.5 1.0 CB A:ASP98 4.3 34.4 1.0 N A:ASP98 4.3 32.9 1.0 O A:HOH2058 4.4 30.1 1.0 CD2 A:PHE97 4.4 33.0 1.0 N A:ASP99 4.5 33.7 1.0 C A:ASP98 4.6 34.2 1.0 CA A:ASP98 4.6 33.0 1.0 CB A:PHE97 4.8 32.7 1.0 CA A:ASP99 4.9 35.9 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1211 b:58.9 occ:0.70 OD1 A:ASP160 2.0 60.1 1.0 O A:HOH2121 2.2 48.7 1.0 O A:HOH2122 2.7 51.7 1.0 CG A:ASP160 3.2 59.0 1.0 OD2 A:ASP160 3.8 60.3 1.0 CB A:SER53 4.1 52.6 1.0 N A:GLY162 4.2 66.0 1.0 CB A:ASP160 4.4 55.7 1.0 CA A:GLY162 4.5 67.8 1.0 N A:SER53 4.6 52.6 1.0 CA A:ASP160 4.6 58.0 1.0 C A:ASP160 4.6 60.6 1.0 CD A:PRO161 4.7 62.9 1.0 CA A:SER53 4.7 52.2 1.0 N A:PRO161 4.7 62.8 1.0 CB A:ASP52 4.7 59.9 1.0 OG A:SER53 4.8 50.6 1.0 C A:ASP52 4.8 54.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1212 b:51.5 occ:0.40 NE2 A:HIS180 2.1 27.0 1.0 O A:HOH2123 2.5 33.1 1.0 O A:HOH2124 2.7 45.6 1.0 CE1 A:HIS180 2.9 28.4 1.0 CD2 A:HIS180 3.3 25.7 1.0 CB A:TRP200 3.8 27.3 1.0 O A:HOH2096 4.0 40.8 1.0 ND1 A:HIS180 4.1 27.2 1.0 ND2 A:ASN201 4.3 32.6 1.0 CG A:HIS180 4.3 26.5 1.0 CG A:TRP200 4.4 26.8 1.0 CD2 A:LEU38 4.5 29.0 1.0 CB A:SER178 4.6 28.7 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Mycobacterium Tuberculosis Lipoprotein Lppx (RV2945C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1213 b:52.5 occ:0.40 OD1 A:ASP63 1.9 29.4 1.0 ND1 A:HIS42 1.9 27.3 1.0 CE1 A:HIS42 2.6 26.2 1.0 O A:HOH2035 2.6 43.5 1.0 CG A:ASP63 2.8 30.9 1.0 OD2 A:ASP63 3.0 36.9 1.0 CG A:HIS42 3.1 26.8 1.0 O A:HOH2033 3.6 42.2 1.0 CB A:HIS42 3.7 27.1 1.0 NE2 A:HIS42 3.8 28.0 1.0 CD2 A:HIS42 4.0 24.7 1.0 CD A:LYS199 4.1 29.3 1.0 CB A:ASP63 4.1 30.3 1.0 CA A:ASP63 4.5 29.1 1.0 O A:HOH2034 4.5 48.4 1.0 N A:ASP63 4.5 28.3 1.0 CA A:HIS42 4.7 26.7 1.0 CE A:LYS199 4.7 31.1 1.0 C A:VAL62 4.8 28.3 1.0 O A:VAL62 4.9 28.4 1.0

G.Sulzenbacher, S.Canaan, Y.Bordat, O.Neyrolles, G.Stadthagen, V.Roig-Zamboni, J.Rauzier, D.Maurin, F.Laval, M.Daffe, C.Cambillau, B.Gicquel, Y.Bourne, M.Jackson. Lppx Is A Lipoprotein Required For the Translocation of Phthiocerol Dimycocerosates to the Surface of Mycobacterium Tuberculosis. Embo J. V. 25 1436 2006.
ISSN: ISSN 0261-4189
PubMed: 16541102
DOI: 10.1038/SJ.EMBOJ.7601048