Zinc in PDB 3s2e: Crystal Structure of Furx Nadh Complex 1

The structure of Crystal Structure of Furx Nadh Complex 1, PDB code: 3s2e was solved by R.Hayes, E.J.Sanchez, B.N.Webb, T.Hooper, M.S.Nissen, Q.Li, L.Xun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.04 / 1.76
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	68.187, 92.744, 117.684, 106.11, 89.95, 90.13
R / Rfree (%)	16.5 / 19.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Furx Nadh Complex 1 (pdb code 3s2e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Furx Nadh Complex 1, PDB code: 3s2e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of Furx Nadh Complex 1


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 Furx Nadh Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:16.9 occ:1.00 NE2 A:HIS65 2.0 15.1 1.0 OE2 A:GLU66 2.1 17.2 1.0 SG A:CYS42 2.3 15.3 1.0 SG A:CYS152 2.3 17.0 1.0 CD2 A:HIS65 3.0 14.7 1.0 CE1 A:HIS65 3.0 14.3 1.0 CB A:CYS152 3.1 16.1 1.0 CD A:GLU66 3.2 15.3 1.0 CB A:CYS42 3.3 14.8 1.0 CG A:GLU66 3.6 13.6 1.0 NH2 A:ARG335 4.1 18.9 1.0 ND1 A:HIS65 4.1 16.5 1.0 CG A:HIS65 4.1 16.6 1.0 NH1 A:ARG335 4.2 20.2 1.0 O1 A:GOL600 4.2 20.5 1.0 OE1 A:GLU66 4.2 17.8 1.0 O2 A:GOL600 4.3 20.9 1.0 O A:HOH345 4.3 15.1 1.0 O A:HOH377 4.4 22.7 1.0 CZ A:ARG335 4.5 24.4 1.0 C1 A:GOL600 4.5 19.1 1.0 CA A:CYS42 4.5 13.7 1.0 CA A:CYS152 4.6 14.8 1.0 N A:CYS42 4.6 14.4 1.0 CB A:THR44 4.7 15.8 1.0 OG1 A:THR44 5.0 16.1 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of Furx Nadh Complex 1


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 Furx Nadh Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:17.9 occ:1.00 SG A:CYS96 2.3 18.8 1.0 SG A:CYS110 2.4 16.4 1.0 SG A:CYS102 2.4 16.3 1.0 SG A:CYS99 2.4 15.4 1.0 CB A:CYS110 3.3 12.3 1.0 CB A:CYS99 3.4 17.0 1.0 CB A:CYS96 3.4 21.7 1.0 CB A:CYS102 3.5 17.4 1.0 N A:CYS96 3.6 17.9 1.0 N A:GLY97 3.8 16.3 1.0 N A:CYS99 3.9 18.9 1.0 CA A:CYS96 3.9 20.2 1.0 CA A:CYS110 4.0 12.6 1.0 CA A:CYS99 4.2 19.9 1.0 C A:CYS96 4.2 23.2 1.0 O A:HOH361 4.2 19.7 1.0 N A:CYS102 4.3 16.9 1.0 N A:TYR98 4.3 18.8 1.0 CA A:CYS102 4.4 16.0 1.0 CB A:ALA95 4.5 12.4 1.0 C A:ALA95 4.6 17.7 1.0 CA A:GLY97 4.7 18.6 1.0 C A:CYS99 4.9 16.4 1.0 C A:CYS110 4.9 15.3 1.0 C A:GLY97 4.9 17.0 1.0 O A:CYS99 5.0 17.7 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of Furx Nadh Complex 1


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 Furx Nadh Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:16.3 occ:1.00 NE2 B:HIS65 2.0 17.1 1.0 OE2 B:GLU66 2.1 18.4 1.0 SG B:CYS42 2.3 15.4 1.0 SG B:CYS152 2.4 15.7 1.0 CD2 B:HIS65 3.0 14.4 1.0 CE1 B:HIS65 3.0 14.2 1.0 CB B:CYS152 3.1 18.4 1.0 CD B:GLU66 3.1 16.4 1.0 CB B:CYS42 3.3 13.0 1.0 CG B:GLU66 3.7 12.8 1.0 NH2 B:ARG335 4.1 18.3 1.0 ND1 B:HIS65 4.1 15.6 1.0 CG B:HIS65 4.1 16.7 1.0 O3 B:GOL600 4.1 21.8 1.0 OE1 B:GLU66 4.2 17.4 1.0 NH1 B:ARG335 4.2 18.9 1.0 O B:HOH345 4.2 16.7 1.0 O2 B:GOL600 4.3 21.8 1.0 O B:HOH374 4.4 22.1 1.0 CZ B:ARG335 4.5 22.3 1.0 CA B:CYS42 4.5 12.1 1.0 C3 B:GOL600 4.5 24.6 1.0 N B:CYS42 4.6 13.6 1.0 CA B:CYS152 4.6 13.5 1.0 CB B:THR44 4.7 15.2 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of Furx Nadh Complex 1


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 Furx Nadh Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:17.8 occ:1.00 SG B:CYS110 2.3 15.6 1.0 SG B:CYS96 2.4 18.9 1.0 SG B:CYS102 2.4 16.0 1.0 SG B:CYS99 2.4 17.6 1.0 CB B:CYS110 3.3 12.7 1.0 CB B:CYS99 3.4 17.1 1.0 CB B:CYS102 3.4 15.3 1.0 CB B:CYS96 3.4 22.8 1.0 N B:CYS96 3.6 17.5 1.0 N B:GLY97 3.8 16.2 1.0 N B:CYS99 3.8 20.0 1.0 CA B:CYS96 3.9 17.9 1.0 CA B:CYS110 4.0 13.9 1.0 CA B:CYS99 4.2 20.5 1.0 C B:CYS96 4.2 23.2 1.0 N B:CYS102 4.3 15.8 1.0 O B:HOH393 4.3 20.9 1.0 N B:TYR98 4.3 18.8 1.0 CA B:CYS102 4.4 15.1 1.0 CB B:ALA95 4.6 13.5 1.0 C B:ALA95 4.6 19.2 1.0 CA B:GLY97 4.7 17.9 1.0 C B:CYS99 4.9 14.6 1.0 C B:GLY97 4.9 15.8 1.0 C B:CYS110 4.9 14.4 1.0 O B:HOH2163 4.9 34.6 1.0 O B:HOH1477 5.0 42.5 1.0 C B:TYR98 5.0 19.3 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of Furx Nadh Complex 1


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 Furx Nadh Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn500 b:16.1 occ:1.00 OE2 C:GLU66 2.0 15.6 1.0 NE2 C:HIS65 2.1 14.3 1.0 SG C:CYS42 2.3 16.6 1.0 SG C:CYS152 2.3 16.6 1.0 CE1 C:HIS65 3.0 14.5 1.0 CD2 C:HIS65 3.0 12.9 1.0 CD C:GLU66 3.1 16.9 1.0 CB C:CYS152 3.1 14.2 1.0 CB C:CYS42 3.3 13.5 1.0 CG C:GLU66 3.6 11.5 1.0 O3 C:GOL600 4.0 22.5 1.0 NH2 C:ARG335 4.1 18.0 1.0 ND1 C:HIS65 4.1 14.9 1.0 CG C:HIS65 4.2 14.4 1.0 OE1 C:GLU66 4.2 14.1 1.0 O2 C:GOL600 4.2 21.4 1.0 NH1 C:ARG335 4.2 18.0 1.0 O C:HOH353 4.2 16.7 1.0 O C:HOH374 4.4 24.3 1.0 CZ C:ARG335 4.5 20.9 1.0 CA C:CYS42 4.5 14.8 1.0 C3 C:GOL600 4.6 20.4 1.0 CA C:CYS152 4.6 13.4 1.0 N C:CYS42 4.7 16.0 1.0 CB C:THR44 4.7 17.0 1.0 OG1 C:THR44 4.9 15.4 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of Furx Nadh Complex 1


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 Furx Nadh Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:17.6 occ:1.00 SG C:CYS110 2.3 16.3 1.0 SG C:CYS96 2.3 18.0 1.0 SG C:CYS99 2.4 17.1 1.0 SG C:CYS102 2.4 15.2 1.0 CB C:CYS110 3.3 12.0 1.0 CB C:CYS99 3.4 20.7 1.0 CB C:CYS102 3.4 15.9 1.0 CB C:CYS96 3.5 23.4 1.0 N C:CYS96 3.6 19.5 1.0 N C:GLY97 3.9 17.2 1.0 N C:CYS99 3.9 19.0 1.0 CA C:CYS96 4.0 19.3 1.0 CA C:CYS110 4.0 16.5 1.0 CA C:CYS99 4.2 19.6 1.0 N C:CYS102 4.2 14.3 1.0 O C:HOH352 4.3 20.7 1.0 C C:CYS96 4.3 18.1 1.0 CA C:CYS102 4.4 16.0 1.0 N C:TYR98 4.4 17.1 1.0 CB C:ALA95 4.6 14.4 1.0 C C:ALA95 4.7 17.8 1.0 CA C:GLY97 4.9 17.4 1.0 C C:CYS99 4.9 18.5 1.0 C C:CYS110 4.9 17.1 1.0 C C:GLY97 5.0 16.2 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of Furx Nadh Complex 1


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 Furx Nadh Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn500 b:16.9 occ:1.00 OE2 D:GLU66 2.0 18.1 1.0 NE2 D:HIS65 2.0 15.3 1.0 SG D:CYS152 2.3 17.4 1.0 SG D:CYS42 2.4 17.1 1.0 CE1 D:HIS65 3.0 15.5 1.0 CD2 D:HIS65 3.0 12.9 1.0 CD D:GLU66 3.1 17.8 1.0 CB D:CYS152 3.1 14.5 1.0 CB D:CYS42 3.3 14.9 1.0 CG D:GLU66 3.6 12.1 1.0 NH2 D:ARG335 4.1 18.1 1.0 ND1 D:HIS65 4.1 15.8 1.0 O1 D:GOL600 4.1 22.1 1.0 CG D:HIS65 4.1 15.2 1.0 OE1 D:GLU66 4.2 14.0 1.0 O D:HOH349 4.2 17.4 1.0 NH1 D:ARG335 4.2 18.0 1.0 O2 D:GOL600 4.3 21.8 1.0 O D:HOH361 4.5 24.8 1.0 CA D:CYS42 4.5 16.4 1.0 CZ D:ARG335 4.5 23.7 1.0 C1 D:GOL600 4.6 24.6 1.0 N D:CYS42 4.6 18.2 1.0 CA D:CYS152 4.6 15.6 1.0 CB D:THR44 4.7 17.4 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of Furx Nadh Complex 1


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 Furx Nadh Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:18.0 occ:1.00 SG D:CYS110 2.3 16.9 1.0 SG D:CYS96 2.3 18.1 1.0 SG D:CYS99 2.4 16.6 1.0 SG D:CYS102 2.4 15.3 1.0 CB D:CYS110 3.2 12.3 1.0 CB D:CYS99 3.4 20.0 1.0 CB D:CYS96 3.4 23.8 1.0 CB D:CYS102 3.5 14.8 1.0 N D:CYS96 3.6 18.4 1.0 N D:GLY97 3.8 17.8 1.0 N D:CYS99 3.9 19.3 1.0 CA D:CYS96 3.9 18.8 1.0 CA D:CYS110 4.0 14.7 1.0 CA D:CYS99 4.2 21.8 1.0 C D:CYS96 4.3 20.3 1.0 N D:CYS102 4.3 14.8 1.0 O D:HOH350 4.3 21.1 1.0 N D:TYR98 4.4 19.1 1.0 CA D:CYS102 4.4 14.2 1.0 CB D:ALA95 4.6 14.2 1.0 C D:ALA95 4.7 17.6 1.0 CA D:GLY97 4.9 19.5 1.0 O D:HOH1157 4.9 35.9 1.0 C D:CYS110 4.9 16.9 1.0 C D:CYS99 4.9 18.5 1.0 C D:GLY97 5.0 20.5 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of Furx Nadh Complex 1


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 Furx Nadh Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn500 b:26.5 occ:1.00 NE2 E:HIS65 2.2 18.0 1.0 SG E:CYS42 2.3 19.5 0.7 O E:HOH1664 2.3 22.4 1.0 O E:HOH2130 2.4 34.8 1.0 SG E:CYS152 2.4 23.6 1.0 SG E:CYS42 2.5 6.7 0.3 CD2 E:HIS65 3.1 16.4 1.0 C5N E:NAD1250 3.2 31.2 1.0 CB E:CYS42 3.2 14.4 1.0 CE1 E:HIS65 3.3 20.1 1.0 CB E:CYS152 3.4 24.9 1.0 OG1 E:THR44 4.0 24.1 1.0 CB E:THR44 4.0 18.5 1.0 C6N E:NAD1250 4.0 23.4 1.0 C4N E:NAD1250 4.2 32.5 1.0 CG E:HIS65 4.3 13.9 1.0 ND1 E:HIS65 4.3 15.4 1.0 O E:HOH1665 4.4 33.3 1.0 NH1 E:ARG335 4.6 23.2 1.0 CA E:CYS42 4.7 26.9 1.0 CG2 E:THR44 4.7 20.2 1.0 CA E:CYS152 4.7 21.6 1.0 N1N E:NAD1250 5.0 36.2 1.0 OE2 E:GLU66 5.0 25.8 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of Furx Nadh Complex 1


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 Furx Nadh Complex 1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:16.8 occ:1.00 SG E:CYS99 2.3 14.6 1.0 SG E:CYS102 2.4 15.4 1.0 SG E:CYS96 2.4 16.3 1.0 SG E:CYS110 2.4 15.4 1.0 CB E:CYS110 3.3 14.4 1.0 CB E:CYS102 3.4 15.2 1.0 CB E:CYS99 3.4 19.2 1.0 CB E:CYS96 3.5 14.4 1.0 N E:CYS96 3.5 15.7 1.0 N E:GLY97 3.7 15.0 1.0 N E:CYS99 3.8 16.5 1.0 CA E:CYS96 3.9 15.8 1.0 CA E:CYS110 4.0 15.0 1.0 CA E:CYS99 4.2 13.9 1.0 C E:CYS96 4.2 21.6 1.0 N E:CYS102 4.3 15.6 1.0 O E:HOH367 4.3 19.0 1.0 N E:TYR98 4.4 17.0 1.0 CA E:CYS102 4.4 14.1 1.0 C E:ALA95 4.6 17.8 1.0 CB E:ALA95 4.6 12.7 1.0 CA E:GLY97 4.8 19.3 1.0 O E:HOH369 4.8 19.5 1.0 C E:CYS99 4.9 19.1 1.0 C E:CYS110 4.9 17.9 1.0 C E:TYR98 5.0 16.6 1.0 O E:CYS99 5.0 15.6 1.0 C E:GLY97 5.0 20.9 1.0

R.Hayes, E.J.Sanchez, B.N.Webb, T.Hooper, M.S.Nissen, Q.Li, L.Xun. Crystal Structures and Furfural Reduction Mechanism of A Bacterial Zinc-Dependent Alcohol Dehydrogenase To Be Published.