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Zinc in PDB 3s1l: Crystal Structure of Apo-Form Furx

Protein crystallography data

The structure of Crystal Structure of Apo-Form Furx, PDB code: 3s1l 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) 35.49 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.461, 67.880, 84.686, 76.49, 76.96, 86.30
R / Rfree (%) 18.3 / 22.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Apo-Form Furx (pdb code 3s1l). 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 Apo-Form Furx, PDB code: 3s1l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3s1l

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Zinc binding site 1 out of 8 in the Crystal Structure of Apo-Form Furx


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Apo-Form Furx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:26.7
occ:1.00
 SG A:CYS102 2.4 22.2 1.0
SG A:CYS99 2.4 24.2 1.0
SG A:CYS110 2.4 27.3 1.0
SG A:CYS96 2.5 28.5 1.0
CB A:CYS99 3.2 26.9 1.0
CB A:CYS110 3.3 23.7 1.0
CB A:CYS102 3.4 24.8 1.0
CB A:CYS96 3.6 32.5 1.0
N A:CYS96 3.6 24.2 1.0
N A:GLY97 3.7 27.4 1.0
N A:CYS99 3.8 26.7 1.0
CA A:CYS96 4.0 30.9 1.0
CA A:CYS99 4.1 22.6 1.0
CA A:CYS110 4.1 24.8 1.0
N A:CYS102 4.3 21.7 1.0
C A:CYS96 4.3 34.6 1.0
O A:HOH384 4.4 31.2 1.0
CA A:CYS102 4.4 24.7 1.0
N A:TYR98 4.5 25.4 1.0
CB A:ALA95 4.5 22.7 1.0
C A:ALA95 4.7 26.7 1.0
CA A:GLY97 4.7 28.1 1.0
C A:CYS99 4.8 26.8 1.0
O A:HOH460 4.8 41.6 1.0
O A:CYS99 4.9 23.6 1.0
C A:CYS110 5.0 28.6 1.0

Zinc binding site 2 out of 8 in 3s1l

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Zinc binding site 2 out of 8 in the Crystal Structure of Apo-Form Furx


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Apo-Form Furx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:28.7
occ:1.00
 OE2 A:GLU66 2.0 24.6 1.0
NE2 A:HIS65 2.1 29.4 1.0
SG A:CYS42 2.3 28.9 1.0
SG A:CYS152 2.4 25.7 1.0
CD2 A:HIS65 3.0 25.9 1.0
CE1 A:HIS65 3.1 28.8 1.0
CD A:GLU66 3.1 22.2 1.0
CB A:CYS152 3.2 21.4 1.0
CB A:CYS42 3.3 26.5 1.0
NH2 A:ARG335 3.6 30.0 1.0
CG A:GLU66 3.6 22.7 1.0
CG A:HIS65 4.1 24.7 1.0
ND1 A:HIS65 4.1 27.8 1.0
OE1 A:GLU66 4.2 24.1 1.0
O A:HOH355 4.2 26.2 1.0
O A:HOH453 4.4 37.5 1.0
CA A:CYS42 4.4 26.8 1.0
N A:CYS42 4.5 25.3 1.0
C6 A:P6G600 4.6 40.9 1.0
CB A:THR44 4.6 31.2 1.0
CA A:CYS152 4.7 20.0 1.0
OG1 A:THR44 4.7 34.1 1.0
CZ A:ARG335 4.8 25.6 1.0
O A:HOH753 4.8 38.4 1.0
O7 A:P6G600 5.0 38.5 1.0

Zinc binding site 3 out of 8 in 3s1l

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Zinc binding site 3 out of 8 in the Crystal Structure of Apo-Form Furx


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 Apo-Form Furx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:27.1
occ:1.00
 SG B:CYS110 2.4 26.9 1.0
SG B:CYS102 2.4 25.8 1.0
SG B:CYS96 2.4 27.7 1.0
SG B:CYS99 2.4 25.0 1.0
CB B:CYS110 3.2 25.0 1.0
CB B:CYS99 3.4 27.1 1.0
CB B:CYS102 3.5 27.5 1.0
CB B:CYS96 3.5 31.3 1.0
N B:CYS96 3.6 25.1 1.0
N B:GLY97 3.7 30.2 1.0
N B:CYS99 3.8 25.9 1.0
CA B:CYS96 3.9 28.6 1.0
CA B:CYS110 4.1 26.2 1.0
O B:HOH377 4.1 24.7 1.0
CA B:CYS99 4.2 25.7 1.0
C B:CYS96 4.2 32.1 1.0
N B:CYS102 4.4 23.8 1.0
N B:TYR98 4.4 25.2 1.0
CA B:CYS102 4.5 25.4 1.0
CB B:ALA95 4.6 27.7 1.0
C B:ALA95 4.7 29.1 1.0
CA B:GLY97 4.7 28.2 1.0
O B:HOH418 4.8 35.1 1.0
C B:CYS99 4.9 27.8 1.0
O B:CYS99 4.9 25.4 1.0
C B:GLY97 4.9 33.9 1.0
C B:TYR98 5.0 30.5 1.0
C B:CYS110 5.0 24.7 1.0

Zinc binding site 4 out of 8 in 3s1l

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Zinc binding site 4 out of 8 in the Crystal Structure of Apo-Form Furx


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 Apo-Form Furx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:25.9
occ:1.00
 OE2 B:GLU66 2.0 24.5 1.0
NE2 B:HIS65 2.1 25.4 1.0
SG B:CYS152 2.4 25.6 1.0
SG B:CYS42 2.4 24.7 1.0
CD2 B:HIS65 3.0 26.4 1.0
CE1 B:HIS65 3.1 25.5 1.0
CD B:GLU66 3.1 23.4 1.0
CB B:CYS152 3.2 22.1 1.0
CB B:CYS42 3.4 25.4 1.0
CG B:GLU66 3.6 21.4 1.0
NH2 B:ARG335 3.6 24.0 1.0
CG B:HIS65 4.1 22.3 1.0
ND1 B:HIS65 4.1 23.8 1.0
OE1 B:GLU66 4.2 25.1 1.0
O B:HOH440 4.2 38.0 1.0
O B:HOH371 4.3 25.1 1.0
CA B:CYS42 4.5 24.5 1.0
N B:CYS42 4.6 26.5 1.0
CA B:CYS152 4.6 19.9 1.0
CZ B:ARG335 4.8 29.4 1.0
CB B:THR44 4.8 28.7 1.0
O7 B:P6G600 4.8 44.2 1.0
C6 B:P6G600 4.9 40.7 1.0
OG1 B:THR44 5.0 28.6 1.0

Zinc binding site 5 out of 8 in 3s1l

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Zinc binding site 5 out of 8 in the Crystal Structure of Apo-Form Furx


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 Apo-Form Furx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:23.9
occ:1.00
 SG C:CYS110 2.4 21.0 1.0
SG C:CYS96 2.4 27.4 1.0
SG C:CYS99 2.4 20.4 1.0
SG C:CYS102 2.4 21.7 1.0
CB C:CYS110 3.2 19.6 1.0
CB C:CYS99 3.3 21.4 1.0
CB C:CYS102 3.4 21.4 1.0
CB C:CYS96 3.5 24.9 1.0
N C:CYS96 3.6 21.9 1.0
N C:GLY97 3.7 22.9 1.0
N C:CYS99 3.9 23.6 1.0
CA C:CYS96 3.9 24.8 1.0
CA C:CYS110 4.0 20.2 1.0
O C:HOH348 4.2 24.1 1.0
CA C:CYS99 4.2 26.5 1.0
C C:CYS96 4.3 27.7 1.0
N C:CYS102 4.3 21.8 1.0
CA C:CYS102 4.5 26.9 1.0
N C:TYR98 4.5 25.5 1.0
CB C:ALA95 4.6 20.9 1.0
C C:ALA95 4.7 25.0 1.0
O C:HOH447 4.7 29.9 1.0
CA C:GLY97 4.7 24.8 1.0
O C:HOH611 4.8 41.0 1.0
C C:CYS110 4.9 24.7 1.0
C C:CYS99 4.9 23.5 1.0

Zinc binding site 6 out of 8 in 3s1l

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Zinc binding site 6 out of 8 in the Crystal Structure of Apo-Form Furx


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 Apo-Form Furx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:30.4
occ:1.00
 OE2 C:GLU66 2.1 27.2 1.0
NE2 C:HIS65 2.2 31.1 1.0
SG C:CYS42 2.3 28.4 1.0
SG C:CYS152 2.4 26.8 1.0
CE1 C:HIS65 3.1 29.9 1.0
CD2 C:HIS65 3.1 22.8 1.0
CD C:GLU66 3.2 31.4 1.0
CB C:CYS152 3.2 24.3 1.0
CB C:CYS42 3.3 31.9 1.0
NH2 C:ARG335 3.7 33.0 1.0
O1 C:P6G600 3.7 56.2 1.0
CG C:GLU66 3.7 31.0 1.0
ND1 C:HIS65 4.1 27.8 1.0
CG C:HIS65 4.2 23.0 1.0
OE1 C:GLU66 4.2 28.9 1.0
O C:HOH363 4.3 25.8 1.0
O C:HOH395 4.4 44.2 1.0
CA C:CYS42 4.5 31.2 1.0
N C:CYS42 4.5 28.5 1.0
CA C:CYS152 4.7 25.8 1.0
CB C:THR44 4.7 32.9 1.0
CZ C:ARG335 4.8 30.6 1.0
OG1 C:THR44 5.0 31.8 1.0
C2 C:P6G600 5.0 45.5 1.0

Zinc binding site 7 out of 8 in 3s1l

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Zinc binding site 7 out of 8 in the Crystal Structure of Apo-Form Furx


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 Apo-Form Furx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:25.2
occ:1.00
 SG D:CYS99 2.4 24.1 1.0
SG D:CYS102 2.4 24.7 1.0
SG D:CYS110 2.4 25.7 1.0
CB D:CYS96 2.5 17.5 1.0
SG D:CYS96 2.8 69.7 1.0
N D:CYS96 3.2 27.6 1.0
CB D:CYS110 3.3 21.4 1.0
CB D:CYS99 3.3 28.2 1.0
CA D:CYS96 3.4 33.9 1.0
CB D:CYS102 3.5 23.9 1.0
N D:CYS99 3.8 24.6 1.0
N D:GLY97 3.9 26.2 1.0
CA D:CYS110 4.0 24.6 1.0
CA D:CYS99 4.1 23.6 1.0
C D:CYS96 4.2 35.0 1.0
O D:HOH364 4.2 29.2 1.0
N D:CYS102 4.3 25.8 1.0
C D:ALA95 4.4 24.1 1.0
CB D:ALA95 4.5 22.5 1.0
CA D:CYS102 4.5 24.7 1.0
N D:TYR98 4.5 24.3 1.0
C D:CYS99 4.8 25.5 1.0
O D:HOH406 4.8 32.3 1.0
O D:HOH469 4.9 48.9 1.0
CA D:ALA95 4.9 25.6 1.0
C D:CYS110 4.9 28.2 1.0
C D:TYR98 5.0 31.6 1.0

Zinc binding site 8 out of 8 in 3s1l

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Zinc binding site 8 out of 8 in the Crystal Structure of Apo-Form Furx


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 Apo-Form Furx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:35.7
occ:1.00
 OE2 D:GLU66 2.1 36.8 1.0
NE2 D:HIS65 2.3 34.0 1.0
SG D:CYS42 2.3 37.2 1.0
SG D:CYS152 2.4 32.2 1.0
CD2 D:HIS65 3.0 31.7 1.0
CB D:CYS152 3.2 29.2 1.0
CD D:GLU66 3.2 34.8 1.0
CE1 D:HIS65 3.2 37.8 1.0
CB D:CYS42 3.3 36.4 1.0
NH2 D:ARG335 3.6 39.6 1.0
CG D:GLU66 3.6 35.0 1.0
CG D:HIS65 4.1 34.0 1.0
ND1 D:HIS65 4.2 29.5 1.0
OE1 D:GLU66 4.3 35.6 1.0
O D:HOH391 4.3 35.8 1.0
CA D:CYS42 4.5 38.1 1.0
N D:CYS42 4.6 34.0 1.0
CA D:CYS152 4.6 27.4 1.0
CZ D:ARG335 4.7 34.1 1.0
O7 D:P6G600 4.8 46.2 1.0
C6 D:P6G600 4.8 52.2 1.0
CB D:THR44 4.8 39.0 1.0

Reference:

C.Kang, R.Hayes, E.J.Sanchez, B.N.Webb, Q.Li, T.Hooper, M.S.Nissen, L.Xun. Furfural Reduction Mechanism of A Zinc-Dependent Alcohol Dehydrogenase From Cupriavidus Necator JMP134. Mol.Microbiol. V. 83 85 2012.
ISSN: ISSN 0950-382X
PubMed: 22081946
DOI: 10.1111/J.1365-2958.2011.07914.X
Page generated: Wed Aug 20 13:47:22 2025

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