Zinc in PDB 3wgh: Crystal Structure of Rsp in Complex with Beta-Nadh

The structure of Crystal Structure of Rsp in Complex with Beta-Nadh, PDB code: 3wgh was solved by Y.Zheng, T.-P.Ko, R.-T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.61 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.793, 75.123, 59.208, 90.00, 94.37, 90.00
R / Rfree (%)	17.7 / 23.7

The structure of Crystal Structure of Rsp in Complex with Beta-Nadh also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Rsp in Complex with Beta-Nadh (pdb code 3wgh). 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 Rsp in Complex with Beta-Nadh, PDB code: 3wgh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Rsp in Complex with Beta-Nadh


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 Rsp in Complex with Beta-Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:59.9 occ:1.00 NE2 A:HIS194 2.1 43.8 1.0 O A:HOH570 2.5 53.1 1.0 CE1 A:HIS194 2.9 33.6 1.0 O A:HOH608 3.1 55.0 1.0 CD2 A:HIS194 3.2 41.1 1.0 O2 B:CAC302 3.4 0.2 1.0 O B:HOH403 3.7 47.2 1.0 OD1 A:ASP181 3.9 72.4 1.0 ZN A:ZN304 4.0 0.1 1.0 ND1 A:HIS194 4.0 40.1 1.0 CG A:HIS194 4.2 39.2 1.0 NH1 B:ARG20 4.3 44.0 1.0 O A:HOH571 4.5 37.3 1.0 O A:ILE180 4.5 56.3 1.0 CD B:ARG20 4.7 41.1 1.0 CB A:ASN192 4.8 40.6 1.0 C A:PRO179 5.0 58.3 1.0 ND2 A:ASN192 5.0 46.2 1.0 CG A:ASN192 5.0 45.5 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Rsp in Complex with Beta-Nadh


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 Rsp in Complex with Beta-Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:0.1 occ:1.00 O B:HOH592 1.8 98.3 1.0 O B:HOH403 1.9 47.2 1.0 OE1 B:GLU24 2.2 68.3 1.0 OD1 A:ASP181 2.8 72.4 1.0 OD2 A:ASP181 3.1 73.8 1.0 CG A:ASP181 3.4 67.4 1.0 O A:HOH608 3.4 55.0 1.0 CD B:GLU24 3.4 69.0 1.0 O2 B:CAC302 3.6 0.2 1.0 ZN A:ZN303 4.0 59.9 1.0 OE2 B:GLU24 4.3 71.1 1.0 CG B:GLU24 4.4 63.8 1.0 O B:HOH500 4.8 62.6 1.0 CB A:ASP181 4.9 63.9 1.0 CB B:GLU24 4.9 58.4 1.0 AS B:CAC302 4.9 0.3 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Rsp in Complex with Beta-Nadh


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 Rsp in Complex with Beta-Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:69.2 occ:1.00 OE2 A:GLU24 2.0 66.3 1.0 OD1 B:ASP181 2.3 55.1 1.0 CD A:GLU24 2.6 65.8 1.0 OE1 A:GLU24 2.7 69.5 1.0 O A:HOH527 2.8 38.6 1.0 OD2 B:ASP181 2.9 65.2 1.0 CG B:ASP181 2.9 54.5 1.0 O A:HOH585 3.0 62.5 1.0 O A:HOH584 3.1 55.8 1.0 CG A:GLU24 4.1 60.9 1.0 CB B:ASP181 4.3 51.4 1.0 ZN B:ZN303 4.8 51.9 1.0 CB A:GLU24 4.8 56.1 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Rsp in Complex with Beta-Nadh


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 Rsp in Complex with Beta-Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:1.0 occ:1.00 O A:HOH657 1.9 63.9 1.0 O A:HOH557 2.4 66.7 1.0 O A:HOH503 2.5 73.7 1.0 OD2 A:ASP187 2.9 65.1 1.0 OD1 A:ASP187 3.5 64.8 1.0 CG A:ASP187 3.6 60.1 1.0 O A:HOH545 3.8 38.9 1.0 O A:HOH601 4.4 65.0 1.0 CG A:PRO185 4.7 57.3 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Rsp in Complex with Beta-Nadh


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 Rsp in Complex with Beta-Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:51.9 occ:1.00 O B:HOH491 2.1 49.1 1.0 NE2 B:HIS194 2.2 35.3 1.0 O B:HOH492 2.3 44.8 1.0 O A:HOH527 3.0 38.6 1.0 CD2 B:HIS194 3.1 28.9 1.0 CE1 B:HIS194 3.2 30.2 1.0 O2 A:CAC302 3.8 97.6 1.0 O B:HOH579 4.0 62.2 1.0 NH1 A:ARG20 4.2 35.3 1.0 CG B:HIS194 4.3 32.8 1.0 ND1 B:HIS194 4.3 35.5 1.0 O B:HOH472 4.4 36.2 1.0 O A:HOH584 4.5 55.8 1.0 O B:ILE180 4.6 47.6 1.0 CD A:ARG20 4.6 37.9 1.0 OD1 B:ASP181 4.7 55.1 1.0 ZN A:ZN305 4.8 69.2 1.0 CB B:ASN192 4.9 29.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Rsp in Complex with Beta-Nadh


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 Rsp in Complex with Beta-Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:0.3 occ:1.00 O B:HOH452 2.4 64.7 1.0 OE2 B:GLU136 2.5 76.2 1.0 O B:HOH541 2.8 65.2 1.0 O B:HOH435 3.1 55.1 1.0 O B:HOH453 3.1 74.6 1.0 CD B:GLU136 3.1 73.5 1.0 OE1 B:GLU136 3.2 76.2 1.0 CG B:GLU136 4.5 62.2 1.0 OH B:TYR161 4.9 65.9 1.0 O B:HOH528 5.0 63.5 1.0

Y.Zheng, T.-P.Ko, R.-T.Guo. Redox Level Sensing By Rsp Binding to Nad and Dna To Be Published.