Zinc in PDB 7x0r: Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum

The structure of Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum, PDB code: 7x0r was solved by S.Dong, X.Yao, Y.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.05 / 1.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.83, 62.09, 81.3, 90, 101.7, 90
R / Rfree (%)	15.7 / 17.4

The binding sites of Zinc atom in the Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum (pdb code 7x0r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum, PDB code: 7x0r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum


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 Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:20.6 occ:1.00 OD2 A:ASP355 2.0 28.1 1.0 O A:HOH620 2.0 23.9 1.0 OD1 A:ASP354 2.0 19.8 1.0 O A:HOH511 2.1 24.1 1.0 O A:TYR351 2.1 18.4 1.0 OD1 A:ASP355 2.3 30.6 1.0 CG A:ASP355 2.4 31.8 1.0 CG A:ASP354 3.1 21.7 1.0 C A:TYR351 3.3 15.7 1.0 OD2 A:ASP354 3.4 21.2 1.0 HA A:GLU352 3.5 24.3 1.0 H A:ASP354 3.7 24.7 1.0 HE3 A:LYS340 3.8 44.8 1.0 HB3 A:TYR351 3.8 18.7 1.0 O A:HOH594 3.9 20.2 1.0 CB A:ASP355 3.9 35.0 1.0 OE2 A:GLU344 3.9 26.7 1.0 N A:GLU352 4.1 17.0 1.0 CA A:GLU352 4.2 20.2 1.0 HB2 A:ASP355 4.3 41.9 1.0 HD2 A:TYR351 4.3 22.5 1.0 CA A:TYR351 4.3 14.0 1.0 N A:ASP355 4.3 26.2 1.0 H A:TYR351 4.4 20.6 1.0 CB A:ASP354 4.4 21.9 1.0 C A:ASP354 4.4 30.0 1.0 N A:ASP354 4.4 20.6 1.0 O A:ASN349 4.4 27.7 1.0 HA A:ASN349 4.4 30.7 1.0 HB3 A:ASP355 4.4 41.9 1.0 H A:ASP355 4.5 31.4 1.0 CB A:TYR351 4.5 15.6 1.0 C A:GLU352 4.5 20.8 1.0 N A:TYR351 4.6 17.1 1.0 CA A:ASP355 4.6 36.2 1.0 CA A:ASP354 4.6 24.0 1.0 CE A:LYS340 4.7 37.4 1.0 HZ2 A:LYS340 4.7 54.3 1.0 HZ1 A:LYS340 4.7 54.3 1.0 HA A:ASP355 4.8 43.4 1.0 H A:LEU353 4.8 21.2 1.0 O A:ASP354 4.8 31.6 1.0 O A:HOH525 4.8 39.9 1.0 N A:LEU353 4.9 17.6 1.0 CD2 A:TYR351 4.9 18.7 1.0 HB2 A:ASP354 4.9 26.3 1.0 HB3 A:ASP354 4.9 26.3 1.0 C A:ASN349 4.9 23.7 1.0 H A:GLU352 5.0 20.4 1.0 NZ A:LYS340 5.0 45.3 1.0 HG3 A:LYS340 5.0 23.2 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum


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 Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:21.5 occ:1.00 O A:HOH672 2.0 25.6 1.0 OE2 A:GLU213 2.1 27.1 1.0 O A:HOH681 2.2 29.1 1.0 CD A:GLU213 2.9 25.0 1.0 OE1 A:GLU213 2.9 27.3 1.0 HG A:SER217 3.1 27.7 1.0 HB2 A:SER217 3.6 21.5 1.0 OG A:SER217 3.8 23.1 1.0 HB3 A:SER217 3.9 21.5 1.0 CB A:SER217 4.0 17.9 1.0 CG A:GLU213 4.3 23.0 1.0 O A:HOH708 4.4 37.0 1.0 HA A:THR214 4.4 17.5 1.0 HG2 A:GLU213 4.6 27.6 1.0 HG3 A:GLU213 4.6 27.6 1.0 O A:GLU213 4.8 16.9 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum


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 Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:18.7 occ:1.00 OE2 A:GLU76 2.0 27.5 1.0 O A:HOH657 2.1 24.7 1.0 CD A:GLU76 2.7 26.6 1.0 OE1 A:GLU76 2.8 34.5 1.0 HH12 A:ARG72 2.8 66.1 1.0 HH22 A:ARG72 3.5 70.5 1.0 NH1 A:ARG72 3.7 55.1 1.0 HE2 A:LYS75 3.7 49.1 1.0 HD3 A:LYS75 3.8 35.5 1.0 HG2 A:LYS75 3.9 25.6 1.0 HZ3 A:LYS75 4.1 57.4 1.0 CG A:GLU76 4.2 17.8 1.0 NH2 A:ARG72 4.2 58.7 1.0 HH11 A:ARG72 4.2 66.1 1.0 HG2 A:GLU76 4.4 21.3 1.0 CE A:LYS75 4.4 40.9 1.0 CD A:LYS75 4.4 29.6 1.0 CZ A:ARG72 4.4 55.6 1.0 HG3 A:GLU76 4.6 21.3 1.0 HA A:GLU76 4.6 19.5 1.0 CG A:LYS75 4.6 21.4 1.0 NZ A:LYS75 4.7 47.8 1.0 HZ1 A:LYS75 4.9 57.4 1.0 HH21 A:ARG72 5.0 70.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum


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 Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:25.2 occ:1.00 OD2 A:ASP276 2.0 15.6 1.0 OE1 A:GLU68 2.0 31.1 1.0 O A:HOH700 2.1 29.1 1.0 O A:HOH687 2.1 23.1 1.0 O A:HOH682 2.5 31.3 1.0 HB2 A:ASP276 2.8 14.1 1.0 CD A:GLU68 2.8 35.4 1.0 OE2 A:GLU68 2.9 30.8 1.0 CG A:ASP276 3.0 16.2 1.0 HH21 A:ARG274 3.1 27.9 1.0 CB A:ASP276 3.3 11.8 1.0 HB3 A:ASP276 3.5 14.1 1.0 O A:HOH719 3.6 37.2 1.0 O A:HOH624 3.7 22.8 1.0 NH2 A:ARG274 3.9 23.2 1.0 HG3 A:ARG72 4.0 42.1 1.0 HH22 A:ARG274 4.0 27.9 1.0 OD1 A:ASP276 4.1 14.0 1.0 HA2 A:GLY69 4.2 17.5 1.0 CG A:GLU68 4.3 29.1 1.0 HB3 A:GLU68 4.3 20.7 1.0 O A:HOH705 4.5 24.3 1.0 OD1 A:ASN277 4.6 21.8 1.0 HG3 A:GLU68 4.6 35.0 1.0 CA A:ASP276 4.7 10.9 1.0 HE A:ARG274 4.8 19.0 1.0 O A:HOH723 4.8 35.9 1.0 HG2 A:GLU68 4.9 35.0 1.0 CG A:ARG72 4.9 35.1 1.0 N A:GLY69 4.9 13.1 1.0 CB A:GLU68 4.9 17.2 1.0 CA A:GLY69 4.9 14.6 1.0 HG2 A:ARG72 5.0 42.1 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum


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 Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:33.4 occ:1.00 O A:HOH506 2.0 31.9 1.0 OE1 B:GLU85 2.0 42.6 1.0 O B:HOH527 2.0 35.2 1.0 OE1 A:GLU85 2.1 39.2 1.0 CD B:GLU85 2.8 41.9 1.0 CD A:GLU85 3.0 38.8 1.0 OE2 B:GLU85 3.1 31.7 1.0 OE2 A:GLU85 3.4 32.3 1.0 O A:HOH715 3.6 36.8 1.0 HE1 B:TYR83 3.7 16.7 1.0 O A:HOH645 4.0 41.2 1.0 O A:HOH505 4.1 36.1 1.0 HB2 A:GLU85 4.2 31.2 1.0 CG A:GLU85 4.2 32.0 1.0 O B:HOH736 4.2 50.8 1.0 CG B:GLU85 4.3 28.9 1.0 HG22 B:VAL57 4.3 32.4 1.0 HB2 B:GLU85 4.3 29.2 1.0 O B:HOH660 4.4 44.5 1.0 HG3 A:GLU85 4.4 38.4 1.0 HE1 A:TYR83 4.5 22.4 1.0 HG3 B:GLU85 4.6 34.7 1.0 CB A:GLU85 4.6 26.0 1.0 HB3 A:GLU85 4.6 31.2 1.0 CE1 B:TYR83 4.6 13.9 1.0 OH B:TYR83 4.6 18.7 1.0 CB B:GLU85 4.8 24.3 1.0 HG2 B:GLU85 4.9 34.7 1.0 HG22 A:VAL57 4.9 25.0 1.0 HG23 B:VAL57 4.9 32.4 1.0 HG2 A:GLU85 4.9 38.4 1.0 H B:VAL57 5.0 22.2 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum


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 Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:19.0 occ:1.00 O B:HOH644 2.0 19.4 1.0 OD2 B:ASP355 2.0 22.8 1.0 OD1 B:ASP354 2.0 18.2 1.0 O B:HOH513 2.1 18.1 1.0 O B:TYR351 2.1 15.8 1.0 OD1 B:ASP355 2.2 24.4 1.0 CG B:ASP355 2.4 29.8 1.0 CG B:ASP354 3.1 16.4 1.0 C B:TYR351 3.3 14.0 1.0 HA B:GLU352 3.4 19.2 1.0 OD2 B:ASP354 3.5 17.0 1.0 H B:ASP354 3.6 21.0 1.0 HE3 B:LYS340 3.8 36.0 1.0 HB3 B:TYR351 3.8 16.3 1.0 CB B:ASP355 3.9 32.0 1.0 O B:HOH583 3.9 14.4 1.0 OE2 B:GLU344 4.0 23.7 1.0 CA B:GLU352 4.1 16.0 1.0 N B:GLU352 4.1 14.0 1.0 HD2 B:TYR351 4.2 14.8 1.0 HB2 B:ASP355 4.3 38.5 1.0 O B:ASN349 4.3 18.0 1.0 C B:ASP354 4.3 23.2 1.0 N B:ASP355 4.4 24.6 1.0 N B:ASP354 4.4 17.5 1.0 HB3 B:ASP355 4.4 38.5 1.0 CA B:TYR351 4.4 13.8 1.0 CB B:ASP354 4.4 17.3 1.0 H B:TYR351 4.4 16.5 1.0 C B:GLU352 4.5 19.6 1.0 HA B:ASN349 4.5 22.6 1.0 CB B:TYR351 4.5 13.6 1.0 H B:ASP355 4.6 29.5 1.0 CA B:ASP355 4.6 34.3 1.0 CA B:ASP354 4.6 17.1 1.0 N B:TYR351 4.6 13.7 1.0 O B:ASP354 4.7 26.6 1.0 HA B:ASP355 4.7 41.2 1.0 H B:LEU353 4.7 18.7 1.0 CE B:LYS340 4.7 30.0 1.0 HZ2 B:LYS340 4.7 43.6 1.0 N B:LEU353 4.8 15.6 1.0 HB2 B:ASN349 4.8 28.7 1.0 HZ3 B:LYS340 4.8 43.6 1.0 O B:HOH602 4.8 50.3 1.0 C B:ASN349 4.9 18.6 1.0 CD2 B:TYR351 4.9 12.4 1.0 H B:GLU352 4.9 16.8 1.0 HB3 B:ASP354 5.0 20.8 1.0 HB2 B:ASP354 5.0 20.8 1.0 HG3 B:LYS340 5.0 23.3 1.0 O B:GLU352 5.0 20.3 1.0 NZ B:LYS340 5.0 36.3 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum


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 Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:18.4 occ:1.00 OE1 B:GLU97 1.9 24.1 1.0 OD2 B:ASP101 2.0 21.7 1.0 CG B:ASP101 2.7 23.3 1.0 OD1 B:ASP101 2.8 23.3 1.0 CD B:GLU97 2.9 24.8 1.0 HG3 B:GLU97 2.9 19.5 1.0 CG B:GLU97 3.2 16.2 1.0 HG2 B:GLU97 3.3 19.5 1.0 OE2 B:GLU97 4.0 24.6 1.0 CB B:ASP101 4.2 17.3 1.0 HB2 B:ASP101 4.4 20.7 1.0 HB3 B:ASP101 4.5 20.7 1.0 O B:GLU97 4.6 15.2 1.0 CB B:GLU97 4.7 15.6 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum


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 Substrate Binding Protein Lbp Complexed Wtih Guanosine From Clostridium Thermocellum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:24.2 occ:1.00 OE1 B:GLU68 2.0 27.7 1.0 O B:HOH732 2.2 24.8 1.0 OD2 B:ASP276 2.4 15.5 1.0 CD B:GLU68 2.7 29.3 1.0 HB2 B:ASP276 2.8 13.2 1.0 OE2 B:GLU68 2.9 31.1 1.0 CG B:ASP276 3.1 14.3 1.0 HH21 B:ARG274 3.2 24.2 1.0 CB B:ASP276 3.3 11.0 1.0 HB3 B:ASP276 3.4 13.2 1.0 O B:HOH652 3.7 19.6 1.0 HG3 B:ARG72 3.9 30.4 1.0 NH2 B:ARG274 3.9 20.2 1.0 HH22 B:ARG274 4.1 24.2 1.0 OD1 B:ASP276 4.2 12.5 1.0 CG B:GLU68 4.2 19.9 1.0 HB3 B:GLU68 4.2 16.5 1.0 HA2 B:GLY69 4.3 12.2 1.0 OD1 B:ASN277 4.4 18.0 1.0 HG3 B:GLU68 4.5 23.9 1.0 O B:HOH717 4.6 22.4 1.0 CA B:ASP276 4.7 10.5 1.0 O B:HOH516 4.7 37.9 1.0 HG2 B:GLU68 4.7 23.9 1.0 CB B:GLU68 4.7 13.8 1.0 CG B:ARG72 4.8 25.3 1.0 HE B:ARG274 4.8 17.5 1.0 O B:HOH774 4.8 26.7 1.0 N B:GLY69 4.9 12.6 1.0 HG2 B:ARG72 4.9 30.4 1.0 C B:GLU68 5.0 13.0 1.0

F.Yan, S.Dong, Y.J.Liu, X.Yao, C.Chen, Y.Xiao, E.A.Bayer, Y.Shoham, C.You, Q.Cui, Y.Feng. Deciphering Cellodextrin and Glucose Uptake in Clostridium Thermocellum. Mbio V. 13 47622 2022.
ISSN: ESSN 2150-7511
PubMed: 36069444
DOI: 10.1128/MBIO.01476-22