Zinc in PDB 3s2f: Crystal Structure of Furx Nadh:Furfural

The structure of Crystal Structure of Furx Nadh:Furfural, PDB code: 3s2f 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)	45.98 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	68.271, 92.854, 117.690, 106.08, 89.97, 89.98
R / Rfree (%)	18.2 / 21.4

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Furx Nadh:Furfural (pdb code 3s2f). 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:Furfural, PDB code: 3s2f:
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:Furfural


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:Furfural within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:22.9 occ:1.00 OE2 A:GLU66 2.1 21.8 1.0 NE2 A:HIS65 2.2 20.4 1.0 SG A:CYS42 2.5 24.0 1.0 SG A:CYS152 2.5 24.1 1.0 CD2 A:HIS65 3.1 22.0 1.0 CE1 A:HIS65 3.1 22.4 1.0 CD A:GLU66 3.2 19.3 1.0 CB A:CYS152 3.2 19.3 1.0 CB A:CYS42 3.3 23.1 1.0 CG A:GLU66 3.6 14.4 1.0 ND1 A:HIS65 4.1 15.8 1.0 CG A:HIS65 4.2 23.2 1.0 NH2 A:ARG335 4.2 22.6 1.0 OE1 A:GLU66 4.3 20.7 1.0 NH1 A:ARG335 4.3 31.3 1.0 O A:HOH355 4.4 16.8 1.0 O A:HOH1577 4.4 28.1 1.0 CZ A:ARG335 4.5 25.2 1.0 CA A:CYS42 4.6 24.3 1.0 O1P A:ISP600 4.6 29.8 1.0 C1 A:ISP600 4.6 27.7 1.0 CA A:CYS152 4.6 16.0 1.0 CB A:THR44 4.7 22.0 1.0 N A:CYS42 4.8 21.8 1.0 OG1 A:THR44 4.9 21.6 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of Furx Nadh:Furfural


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:Furfural within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:22.9 occ:1.00 SG A:CYS102 2.5 20.2 1.0 SG A:CYS96 2.5 22.5 1.0 SG A:CYS99 2.5 20.0 1.0 SG A:CYS110 2.5 20.1 1.0 CB A:CYS110 3.2 17.4 1.0 CB A:CYS99 3.4 21.9 1.0 CB A:CYS102 3.4 18.8 1.0 CB A:CYS96 3.5 26.4 1.0 N A:CYS96 3.5 20.2 1.0 N A:GLY97 3.7 17.1 1.0 N A:CYS99 3.8 20.6 1.0 CA A:CYS96 3.9 22.7 1.0 CA A:CYS110 4.0 20.7 1.0 C A:CYS96 4.2 24.6 1.0 CA A:CYS99 4.2 20.2 1.0 O A:HOH573 4.2 22.9 1.0 N A:CYS102 4.2 18.8 1.0 N A:TYR98 4.4 22.1 1.0 CA A:CYS102 4.4 20.7 1.0 CB A:ALA95 4.5 20.0 1.0 C A:ALA95 4.6 24.9 1.0 CA A:GLY97 4.7 24.0 1.0 C A:CYS110 4.9 19.9 1.0 C A:CYS99 4.9 21.7 1.0 C A:GLY97 4.9 21.2 1.0 CA A:ALA95 5.0 22.8 1.0 C A:TYR98 5.0 23.5 1.0 O A:CYS99 5.0 19.7 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of Furx Nadh:Furfural


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:Furfural within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:22.1 occ:1.00 OE2 B:GLU66 2.1 18.9 1.0 NE2 B:HIS65 2.1 16.4 1.0 SG B:CYS42 2.5 20.6 1.0 SG B:CYS152 2.5 25.2 1.0 CD2 B:HIS65 3.1 17.7 1.0 CE1 B:HIS65 3.1 15.8 1.0 CD B:GLU66 3.2 16.3 1.0 CB B:CYS152 3.2 16.2 1.0 CB B:CYS42 3.3 23.3 1.0 CG B:GLU66 3.6 13.5 1.0 ND1 B:HIS65 4.1 12.8 1.0 CG B:HIS65 4.2 17.9 1.0 NH2 B:ARG335 4.2 21.4 1.0 OE1 B:GLU66 4.3 21.3 1.0 NH1 B:ARG335 4.3 30.8 1.0 O B:HOH345 4.4 19.9 1.0 O1P B:ISP600 4.4 29.3 1.0 O B:HOH622 4.5 30.0 1.0 C1 B:ISP600 4.5 24.3 1.0 CA B:CYS42 4.6 21.8 1.0 CZ B:ARG335 4.6 23.7 1.0 CA B:CYS152 4.7 14.9 1.0 CB B:THR44 4.7 18.4 1.0 N B:CYS42 4.7 20.9 1.0 C2 B:ISP600 4.9 26.1 1.0 OG1 B:THR44 4.9 18.2 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of Furx Nadh:Furfural


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:Furfural within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:23.7 occ:1.00 SG B:CYS102 2.5 21.4 1.0 SG B:CYS99 2.5 18.3 1.0 SG B:CYS96 2.5 20.6 1.0 SG B:CYS110 2.6 22.8 1.0 CB B:CYS110 3.3 15.8 1.0 CB B:CYS99 3.3 23.1 1.0 CB B:CYS96 3.4 24.7 1.0 CB B:CYS102 3.5 18.9 1.0 N B:CYS96 3.5 17.3 1.0 N B:GLY97 3.7 20.3 1.0 N B:CYS99 3.8 21.4 1.0 CA B:CYS96 3.9 20.9 1.0 CA B:CYS110 4.0 19.8 1.0 O B:HOH493 4.1 19.8 1.0 CA B:CYS99 4.2 24.3 1.0 C B:CYS96 4.2 21.1 1.0 N B:CYS102 4.3 16.0 1.0 N B:TYR98 4.4 21.4 1.0 CA B:CYS102 4.5 19.8 1.0 CB B:ALA95 4.5 15.6 1.0 C B:ALA95 4.6 22.9 1.0 CA B:GLY97 4.7 21.7 1.0 C B:CYS99 4.9 21.7 1.0 C B:CYS110 4.9 18.0 1.0 C B:GLY97 5.0 20.6 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of Furx Nadh:Furfural


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:Furfural within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn500 b:20.8 occ:1.00 OE2 C:GLU66 2.1 15.4 1.0 NE2 C:HIS65 2.1 21.1 1.0 SG C:CYS42 2.5 22.7 1.0 SG C:CYS152 2.5 20.1 1.0 CE1 C:HIS65 3.0 18.8 1.0 CD2 C:HIS65 3.0 14.7 1.0 CB C:CYS152 3.2 13.7 1.0 CD C:GLU66 3.2 19.4 1.0 CB C:CYS42 3.3 21.0 1.0 CG C:GLU66 3.7 15.0 1.0 NH2 C:ARG335 4.0 20.2 1.0 ND1 C:HIS65 4.0 16.1 1.0 CG C:HIS65 4.1 17.0 1.0 OE1 C:GLU66 4.3 19.4 1.0 O C:HOH350 4.3 20.9 1.0 NH1 C:ARG335 4.3 31.1 1.0 CZ C:ARG335 4.6 23.0 1.0 CA C:CYS42 4.6 21.7 1.0 O C:HOH583 4.6 27.5 1.0 CA C:CYS152 4.6 16.4 1.0 C1 C:ISP600 4.7 18.7 1.0 N C:CYS42 4.7 24.1 1.0 O1P C:ISP600 4.7 25.5 1.0 CB C:THR44 4.8 22.4 1.0 OG1 C:THR44 4.9 22.9 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of Furx Nadh:Furfural


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:Furfural within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:21.4 occ:1.00 SG C:CYS99 2.5 18.5 1.0 SG C:CYS96 2.5 21.5 1.0 SG C:CYS102 2.5 20.3 1.0 SG C:CYS110 2.6 18.9 1.0 CB C:CYS110 3.2 16.3 1.0 CB C:CYS99 3.4 22.7 1.0 CB C:CYS102 3.4 20.0 1.0 CB C:CYS96 3.6 19.9 1.0 N C:CYS96 3.7 22.2 1.0 N C:GLY97 3.7 23.6 1.0 N C:CYS99 3.8 26.6 1.0 CA C:CYS110 4.0 22.1 1.0 CA C:CYS96 4.0 25.7 1.0 CA C:CYS99 4.2 23.3 1.0 N C:CYS102 4.2 21.0 1.0 C C:CYS96 4.3 25.1 1.0 O C:HOH363 4.3 25.8 1.0 CA C:CYS102 4.4 21.1 1.0 N C:TYR98 4.4 23.0 1.0 CB C:ALA95 4.6 20.3 1.0 CA C:GLY97 4.7 23.4 1.0 C C:ALA95 4.7 23.5 1.0 C C:CYS110 4.8 20.0 1.0 O C:HOH1760 4.9 42.3 1.0 C C:CYS99 4.9 19.3 1.0 C C:GLY97 4.9 24.9 1.0 N C:GLU111 5.0 18.5 1.0 C C:TYR98 5.0 23.2 1.0

Zinc binding site 7 out of 16 in the Crystal Structure of Furx Nadh:Furfural


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:Furfural within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn500 b:23.0 occ:1.00 OE2 D:GLU66 2.1 18.3 1.0 NE2 D:HIS65 2.1 20.1 1.0 SG D:CYS42 2.5 21.0 1.0 SG D:CYS152 2.5 22.5 1.0 CE1 D:HIS65 3.0 21.7 1.0 CD2 D:HIS65 3.1 20.8 1.0 CB D:CYS152 3.2 14.6 1.0 CD D:GLU66 3.2 17.4 1.0 CB D:CYS42 3.2 19.7 1.0 CG D:GLU66 3.7 17.6 1.0 NH2 D:ARG335 4.0 18.8 1.0 ND1 D:HIS65 4.1 17.8 1.0 CG D:HIS65 4.1 19.0 1.0 O D:HOH370 4.2 20.9 1.0 OE1 D:GLU66 4.3 16.0 1.0 NH1 D:ARG335 4.4 25.4 1.0 CA D:CYS42 4.5 21.6 1.0 C1 D:ISP600 4.5 22.6 1.0 O D:HOH2045 4.6 33.8 1.0 CZ D:ARG335 4.6 24.8 1.0 O1P D:ISP600 4.6 31.5 1.0 CA D:CYS152 4.6 16.4 1.0 N D:CYS42 4.6 27.1 1.0 CB D:THR44 4.7 24.3 1.0

Zinc binding site 8 out of 16 in the Crystal Structure of Furx Nadh:Furfural


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:Furfural within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:24.6 occ:1.00 SG D:CYS96 2.5 21.9 1.0 SG D:CYS99 2.5 22.3 1.0 SG D:CYS102 2.5 21.5 1.0 SG D:CYS110 2.5 24.7 1.0 CB D:CYS110 3.2 16.4 1.0 CB D:CYS99 3.3 16.4 1.0 CB D:CYS96 3.5 22.4 1.0 CB D:CYS102 3.5 19.4 1.0 N D:CYS96 3.5 23.1 1.0 N D:GLY97 3.7 20.2 1.0 N D:CYS99 3.8 22.2 1.0 CA D:CYS96 3.9 25.2 1.0 CA D:CYS110 3.9 19.8 1.0 CA D:CYS99 4.2 25.1 1.0 C D:CYS96 4.2 26.7 1.0 O D:HOH366 4.3 25.6 1.0 N D:CYS102 4.3 18.4 1.0 N D:TYR98 4.4 24.8 1.0 CA D:CYS102 4.4 21.1 1.0 CB D:ALA95 4.5 16.7 1.0 C D:ALA95 4.6 25.7 1.0 CA D:GLY97 4.7 25.2 1.0 C D:CYS110 4.8 20.4 1.0 C D:CYS99 4.9 19.7 1.0 N D:GLU111 4.9 20.3 1.0 C D:GLY97 5.0 27.2 1.0

Zinc binding site 9 out of 16 in the Crystal Structure of Furx Nadh:Furfural


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:Furfural within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn500 b:23.4 occ:1.00 NE2 E:HIS65 2.1 16.9 1.0 OXT E:FU2600 2.2 26.3 1.0 SG E:CYS42 2.4 18.3 1.0 SG E:CYS152 2.4 17.8 1.0 C1 E:FU2600 2.9 23.7 1.0 CD2 E:HIS65 3.0 18.3 1.0 CB E:CYS42 3.1 16.8 1.0 CE1 E:HIS65 3.2 15.6 1.0 C5N E:NAD1250 3.3 18.5 1.0 CB E:CYS152 3.4 14.9 1.0 C6N E:NAD1250 4.0 19.4 1.0 C4N E:NAD1250 4.1 20.0 1.0 OG1 E:THR44 4.1 21.6 1.0 CB E:THR44 4.2 21.6 1.0 CG E:HIS65 4.2 17.1 1.0 ND1 E:HIS65 4.3 16.4 1.0 C2 E:FU2600 4.4 24.7 1.0 NH1 E:ARG335 4.5 16.7 1.0 CA E:CYS42 4.6 16.2 1.0 CA E:CYS152 4.8 16.1 1.0 CG2 E:THR44 4.9 23.7 1.0 OE2 E:GLU66 4.9 21.1 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of Furx Nadh:Furfural


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:Furfural within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:21.0 occ:1.00 SG E:CYS96 2.5 21.6 1.0 SG E:CYS102 2.5 19.1 1.0 SG E:CYS99 2.5 17.1 1.0 SG E:CYS110 2.5 21.2 1.0 CB E:CYS110 3.2 20.4 1.0 CB E:CYS99 3.3 17.0 1.0 CB E:CYS102 3.4 17.6 1.0 CB E:CYS96 3.5 20.6 1.0 N E:CYS96 3.6 23.7 1.0 N E:GLY97 3.7 20.1 1.0 N E:CYS99 3.8 17.9 1.0 CA E:CYS96 3.9 21.5 1.0 CA E:CYS110 4.0 17.9 1.0 CA E:CYS99 4.1 19.7 1.0 C E:CYS96 4.2 24.1 1.0 O E:HOH348 4.3 20.7 1.0 N E:CYS102 4.3 16.4 1.0 N E:TYR98 4.4 19.7 1.0 CA E:CYS102 4.5 18.7 1.0 CB E:ALA95 4.6 20.1 1.0 C E:ALA95 4.6 16.6 1.0 CA E:GLY97 4.7 23.6 1.0 O E:HOH612 4.8 26.0 1.0 C E:CYS99 4.8 18.0 1.0 C E:CYS110 4.9 18.4 1.0 C E:GLY97 5.0 22.5 1.0 C E:TYR98 5.0 18.8 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.