Zinc in PDB 7a9a: Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis

The structure of Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis, PDB code: 7a9a was solved by D.Vakhrameev, A.Kavaleuski, S.Bukhdruker, E.Marin, T.Sushko, I.P.Grabovec, A.Gilep, N.Strushkevich, V.Borshchevskiy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.95 / 1.17
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	21.035, 61.322, 76.91, 90.15, 90.32, 93.75
R / Rfree (%)	15.4 / 18.7

The structure of Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Iron	(Fe)	8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 43;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis (pdb code 7a9a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 43 binding sites of Zinc where determined in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis, PDB code: 7a9a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 43 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis


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 Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:10.7 occ:1.00 OD2 A:ASP34 2.0 8.1 1.0 O A:HOH224 2.0 13.2 1.0 OD1 A:ASP35 2.1 8.1 1.0 O A:HOH205 2.2 9.6 1.0 CG A:ASP34 2.9 7.2 1.0 CG A:ASP35 3.0 8.3 1.0 OD2 A:ASP35 3.2 8.6 1.0 OD1 A:ASP34 3.2 7.6 1.0 O A:HOH240 4.1 24.4 1.0 CB A:ASP34 4.2 7.4 1.0 HB2 A:ASP34 4.3 8.9 1.0 CB A:ASP35 4.4 7.8 1.0 HA A:ASP35 4.5 8.7 1.0 N A:ASP35 4.5 6.5 1.0 HB2 A:ARG32 4.6 7.7 1.0 C A:ASP34 4.6 7.2 1.0 H A:ASP35 4.7 7.8 1.0 CA A:ASP35 4.7 7.3 1.0 O A:ASP34 4.8 8.6 1.0 HB3 A:ASP34 4.9 8.9 1.0 HB3 A:ASP35 4.9 9.3 1.0 HB2 A:ASP35 4.9 9.3 1.0

Zinc binding site 2 out of 43 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis


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 Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:10.6 occ:1.00 OD2 A:ASP39 2.1 8.2 1.0 O A:HOH253 2.1 12.4 1.0 CG A:ASP39 3.0 8.8 1.0 OD1 A:ASP39 3.2 9.1 1.0 O A:HOH226 3.9 13.5 1.0 O A:HOH261 4.1 14.2 0.4 HG3 A:PRO37 4.1 10.3 0.6 O A:HOH284 4.1 17.4 1.0 O A:HOH261 4.2 15.8 0.6 HG2 A:PRO37 4.3 10.3 0.6 HB2 A:PRO37 4.4 10.8 0.5 CB A:ASP39 4.4 9.0 1.0 HG2 A:PRO37 4.4 10.6 0.5 HB2 A:PRO37 4.6 10.7 0.6 HB2 A:ASP39 4.6 10.8 1.0 CG A:PRO37 4.6 8.6 0.6 HB3 A:ASP39 4.7 10.8 1.0

Zinc binding site 3 out of 43 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis


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 Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:29.7 occ:1.00 H2 A:MET1 1.8 20.4 1.0 H3 A:MET1 1.8 20.4 1.0 O A:HOH245 2.0 22.1 1.0 O A:MET1 2.1 15.9 1.0 N A:MET1 2.1 17.0 1.0 O A:HOH267 2.6 27.6 1.0 H1 A:MET1 2.9 20.4 1.0 C A:MET1 2.9 15.5 1.0 CA A:MET1 3.1 17.4 1.0 O A:HOH232 3.6 17.2 0.6 HA A:MET1 3.8 20.8 1.0 HB3 A:MET1 3.9 23.3 1.0 H A:ASP3 4.0 13.8 1.0 CB A:MET1 4.0 19.4 1.0 OD1 A:ASP3 4.1 16.5 1.0 N A:ASN2 4.2 13.1 1.0 HB2 A:MET1 4.3 23.3 1.0 OD2 A:ASP3 4.4 17.5 1.0 CG A:ASP3 4.4 16.0 1.0 HA A:ASN2 4.5 14.1 1.0 O A:HOH206 4.6 19.0 1.0 N A:ASP3 4.7 11.5 1.0 H A:ASN2 4.8 15.7 1.0 O A:HOH232 4.8 11.1 0.4 CA A:ASN2 4.9 11.7 1.0

Zinc binding site 4 out of 43 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis


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 Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:32.7 occ:1.00 OD2 A:ASP51 1.9 14.5 0.8 O A:HOH251 2.3 24.1 1.0 O A:HOH242 2.4 36.2 1.0 O A:HOH279 2.6 22.1 1.0 CG A:ASP51 2.7 14.0 0.8 OD1 A:ASP51 2.9 14.4 0.8 H A:ALA48 3.6 10.8 1.0 HB3 A:ALA48 3.9 11.4 1.0 CB A:ASP51 4.1 12.8 1.0 HB2 A:ASP51 4.3 15.4 0.8 HB1 A:ALA47 4.4 11.5 1.0 O A:HOH257 4.4 37.9 1.0 HA A:ALA47 4.5 10.8 1.0 N A:ALA48 4.5 9.0 1.0 HB3 A:ASP51 4.5 15.4 0.8 HB2 A:ALA48 4.6 11.4 1.0 CB A:ALA48 4.7 9.5 1.0 OG A:SER50 4.8 15.2 1.0 HG A:SER50 4.9 18.3 1.0

Zinc binding site 5 out of 43 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis


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 Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:12.2 occ:1.00 OD2 B:ASP34 2.0 11.6 1.0 O B:HOH218 2.1 18.3 1.0 OD1 B:ASP35 2.1 11.1 1.0 O B:HOH205 2.2 10.8 1.0 CG B:ASP34 2.9 10.8 1.0 CG B:ASP35 3.0 11.2 1.0 OD2 B:ASP35 3.2 11.5 1.0 OD1 B:ASP34 3.3 11.2 1.0 O B:HOH251 4.0 26.5 1.0 CB B:ASP34 4.3 10.2 1.0 HB2 B:ASP34 4.3 12.2 1.0 CB B:ASP35 4.4 10.9 1.0 HA B:ASP35 4.4 11.6 1.0 N B:ASP35 4.5 9.2 1.0 C B:ASP34 4.5 9.6 1.0 HB2 B:ARG32 4.7 9.9 1.0 CA B:ASP35 4.7 9.7 1.0 O B:ASP34 4.7 10.2 1.0 H B:ASP35 4.7 11.0 1.0 HB3 B:ASP35 4.9 13.0 1.0 HB2 B:ASP35 4.9 13.0 1.0 HB3 B:ASP34 4.9 12.2 1.0

Zinc binding site 6 out of 43 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis


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 Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:10.6 occ:0.53 OD2 B:ASP17 1.8 13.0 1.0 O1 B:EDO107 1.9 36.4 1.0 O B:HOH242 2.1 15.4 0.6 HO1 B:EDO107 2.2 43.7 1.0 O B:HOH242 2.3 8.1 0.4 CG B:ASP17 2.8 12.1 1.0 OD1 B:ASP17 3.2 12.8 1.0 C1 B:EDO107 3.2 36.8 1.0 H21 B:EDO107 3.3 43.9 1.0 HD21 B:LEU6 3.6 16.1 1.0 H12 B:EDO107 3.7 44.2 1.0 C2 B:EDO107 3.7 36.6 1.0 HD11 B:LEU20 3.8 16.2 1.0 HB3 B:ALA19 3.9 11.9 1.0 H11 B:EDO107 4.0 44.2 1.0 O2 B:EDO107 4.1 36.3 1.0 HG B:LEU20 4.1 15.2 1.0 CB B:ASP17 4.1 10.2 1.0 HB2 B:ASP17 4.2 12.2 1.0 HD23 B:LEU6 4.3 16.1 1.0 CD2 B:LEU6 4.4 13.4 1.0 HB3 B:ASP17 4.5 12.2 1.0 CD1 B:LEU20 4.6 13.5 1.0 HD12 B:LEU20 4.6 16.2 1.0 HO2 B:EDO107 4.7 43.5 1.0 H22 B:EDO107 4.7 43.9 1.0 CB B:ALA19 4.7 9.9 1.0 CG B:LEU20 4.8 12.7 1.0 HB2 B:ALA19 4.8 11.9 1.0 HD21 B:LEU20 4.9 16.2 1.0

Zinc binding site 7 out of 43 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:58.7 occ:1.00 H3 B:MET1 1.8 20.1 1.0 H2 B:MET1 1.8 20.1 1.0 O B:MET1 2.0 20.3 1.0 N B:MET1 2.1 16.7 1.0 C B:MET1 2.7 19.5 1.0 CA B:MET1 2.8 19.4 1.0 H1 B:MET1 2.9 20.1 1.0 HA B:MET1 3.0 23.2 1.0 N B:ASN2 4.0 18.4 1.0 CB B:MET1 4.2 20.8 1.0 H B:ASP3 4.3 17.2 1.0 HA B:ASN2 4.5 19.6 1.0 OD2 B:ASP3 4.6 20.9 1.0 OD1 B:ASP3 4.6 19.8 1.0 H B:ASN2 4.6 22.1 1.0 CG B:ASP3 4.7 19.4 1.0 CA B:ASN2 4.8 16.3 1.0 N B:ASP3 4.9 14.4 1.0

Zinc binding site 8 out of 43 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:29.6 occ:0.63 ZN B:ZN105 0.0 29.6 0.6 ZN B:ZN105 1.3 24.8 0.4 OE2 B:GLU53 2.0 19.6 1.0 O B:HOH258 2.5 32.2 1.0 CD B:GLU53 2.7 18.2 1.0 OE1 B:GLU53 2.8 18.2 1.0 HB3 H:ASP39 3.4 24.0 1.0 O B:HOH245 4.0 11.3 0.4 HB2 H:ASP39 4.0 24.0 1.0 CB H:ASP39 4.1 20.0 1.0 CG B:GLU53 4.2 16.6 1.0 O B:HOH211 4.3 32.9 1.0 HA H:ASP39 4.4 22.8 1.0 O B:HOH203 4.4 20.5 1.0 O B:HOH245 4.5 26.2 0.6 HG3 B:GLU53 4.5 19.9 1.0 HG2 B:GLU53 4.5 19.9 1.0 CA H:ASP39 4.8 19.0 1.0

Zinc binding site 9 out of 43 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn105 b:24.8 occ:0.37 ZN B:ZN105 0.0 24.8 0.4 ZN B:ZN105 1.3 29.6 0.6 O B:HOH258 2.3 32.2 1.0 OE1 B:GLU53 2.8 18.2 1.0 OE2 B:GLU53 3.0 19.6 1.0 CD B:GLU53 3.3 18.2 1.0 HB3 H:ASP39 4.1 24.0 1.0 O B:HOH245 4.5 26.2 0.6 O B:HOH245 4.5 11.3 0.4 CG B:GLU53 4.8 16.6 1.0 HA H:ASP39 5.0 22.8 1.0 CB H:ASP39 5.0 20.0 1.0

Zinc binding site 10 out of 43 in the Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Rubredoxin B (RV3250C) From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn106 b:62.9 occ:1.00 OD2 B:ASP38 2.2 21.0 1.0 O B:HOH265 2.3 14.9 1.0 O H:HOH207 2.3 22.7 1.0 OD1 B:ASP38 2.4 19.4 1.0 CG B:ASP38 2.6 19.8 1.0 O B:HOH209 3.1 39.7 1.0 HZ3 B:LYS49 3.5 10.9 0.2 OD2 H:ASP51 3.5 20.9 1.0 OD1 H:ASP51 3.5 21.0 1.0 CG H:ASP51 3.9 20.2 1.0 O B:HOH250 4.0 15.2 0.5 HZ3 B:LYS49 4.1 12.2 0.8 O B:ASP34 4.1 10.2 1.0 CB B:ASP38 4.1 18.7 1.0 NZ B:LYS49 4.3 9.1 0.2 O B:HOH250 4.4 20.3 0.5 O B:HOH251 4.4 26.5 1.0 HB2 B:ASP38 4.5 22.4 1.0 HB3 B:ASP38 4.5 22.4 1.0 HZ1 B:LYS49 4.6 10.9 0.2 ZN H:ZN101 4.6 80.6 1.0 HZ2 B:LYS49 4.7 10.9 0.2 HA B:ASP38 4.7 21.0 1.0 NZ B:LYS49 4.8 10.2 0.8 HA B:ASP34 4.9 12.2 1.0 HZ2 B:LYS49 4.9 12.2 0.8 CA B:ASP38 5.0 17.5 1.0 HZ1 B:LYS49 5.0 12.2 0.8 O B:HOH241 5.0 15.6 0.5

T.Sushko, A.Kavaleuski, I.Grabovec, A.Kavaleuskaya, D.Vakhrameev, S.Bukhdruker, E.Marin, A.Kuzikov, R.Masamrekh, V.Shumyantseva, K.Tsumoto, V.Borshchevskiy, A.Gilep, N.Strushkevich. A New Twist of Rubredoxin Function in M. Tuberculosis. Bioorg.Chem. V. 109 04721 2021.
ISSN: ISSN 0045-2068
PubMed: 33618255
DOI: 10.1016/J.BIOORG.2021.104721