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Zinc in PDB 9fk6: The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant

Enzymatic activity of The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant

All present enzymatic activity of The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant:
3.2.1.8;

Protein crystallography data

The structure of The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant, PDB code: 9fk6 was solved by N.Hadad, O.Chmelnik, M.Dessau, Y.Shoham, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.55 / 1.95
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.133, 61.874, 110.956, 90, 105.37, 90
R / Rfree (%) 17.7 / 21.1

Other elements in 9fk6:

The structure of The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant (pdb code 9fk6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant, PDB code: 9fk6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 9fk6

Go back to Zinc Binding Sites List in 9fk6
Zinc binding site 1 out of 7 in the The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.0
occ:1.00
 OE1 A:GLU58 2.0 15.3 1.0
NE2 A:HIS322 2.0 14.4 1.0
O A:HOH525 2.0 12.5 1.0
CL A:CL408 2.2 17.2 1.0
CD A:GLU58 2.8 12.6 1.0
CE1 A:HIS322 2.9 19.7 1.0
OE2 A:GLU58 2.9 13.5 1.0
CD2 A:HIS322 3.1 14.5 1.0
OE2 A:GLU35 3.8 19.7 1.0
O A:HOH754 3.9 23.1 1.0
CG A:GLU35 4.0 12.3 1.0
ND1 A:HIS322 4.0 20.7 1.0
CG A:HIS322 4.1 14.6 1.0
CG A:GLU58 4.2 12.9 1.0
O A:HOH648 4.3 10.0 1.0
CD A:GLU35 4.4 17.9 1.0
CB A:GLU58 4.6 12.7 1.0
ND2 A:ASN59 4.6 15.9 1.0
O A:HOH834 4.8 29.0 1.0
O A:HOH963 4.9 33.1 1.0
O A:HOH715 5.0 9.3 1.0

Zinc binding site 2 out of 7 in 9fk6

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Zinc binding site 2 out of 7 in the The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:69.6
occ:1.00
 NE2 A:HIS378 2.2 19.6 1.0
O A:HOH856 2.4 24.3 1.0
CD2 A:HIS378 3.2 15.8 1.0
CE1 A:HIS378 3.2 20.4 1.0
O A:HOH816 3.8 25.7 1.0
CD A:ARG23 4.1 11.5 1.0
O A:ARG23 4.2 12.7 1.0
O A:HOH932 4.2 32.3 1.0
O A:HOH808 4.2 25.0 1.0
ND1 A:HIS378 4.2 20.6 1.0
CG A:HIS378 4.3 18.1 1.0
NH1 A:ARG23 4.3 12.3 1.0
O A:HOH903 4.4 25.2 1.0
NE A:ARG23 4.5 10.6 1.0
CZ A:ARG23 4.6 10.8 1.0

Zinc binding site 3 out of 7 in 9fk6

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Zinc binding site 3 out of 7 in the The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:25.9
occ:1.00
 O A:ALA374 2.3 11.2 1.0
OD1 A:ASP297 2.3 13.0 1.0
O A:HOH547 2.4 16.1 1.0
O A:LYS379 2.5 18.7 1.0
OD1 A:ASP377 2.5 13.5 1.0
C A:ALA374 3.5 12.1 1.0
CG A:ASP297 3.5 18.1 1.0
CG A:ASP377 3.5 19.1 1.0
C A:LYS379 3.6 26.4 1.0
OD2 A:ASP377 3.8 17.2 1.0
CE A:LYS301 4.1 23.0 1.0
N A:LYS379 4.3 22.8 1.0
CA A:ALA374 4.3 13.1 1.0
CB A:ASP297 4.3 12.2 1.0
OD2 A:ASP297 4.3 18.5 1.0
OXT A:LYS379 4.3 29.0 1.0
CA A:ASP297 4.4 11.0 1.0
N A:ILE375 4.4 8.1 1.0
CA A:ILE375 4.4 9.9 1.0
CA A:LYS379 4.5 24.6 1.0
O A:HOH823 4.5 30.2 1.0
O A:HOH680 4.5 11.7 1.0
O A:ASP377 4.6 11.3 1.0
O A:ASP297 4.6 11.4 1.0
NZ A:LYS301 4.6 30.1 1.0
C A:ASP377 4.8 17.5 1.0
CB A:ASP377 4.9 17.7 1.0
CB A:ALA374 4.9 14.5 1.0
C A:ASP297 4.9 9.9 1.0

Zinc binding site 4 out of 7 in 9fk6

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Zinc binding site 4 out of 7 in the The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:40.7
occ:1.00
 OD2 A:ASP282 2.2 21.6 1.0
O A:HOH826 2.5 21.7 1.0
CG A:ASP282 3.1 16.9 1.0
O A:HOH593 3.3 28.4 1.0
OD1 A:ASP282 3.7 23.7 1.0
CB A:ASP282 4.1 14.4 1.0
O A:HOH781 4.4 15.7 1.0
N A:ASP282 4.6 12.4 1.0
CB A:THR280 4.6 14.5 1.0
OG1 A:THR280 4.9 15.6 1.0
CA A:ASP282 5.0 14.1 1.0

Zinc binding site 5 out of 7 in 9fk6

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Zinc binding site 5 out of 7 in the The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:41.5
occ:1.00
 O A:SER307 2.3 12.7 1.0
O A:GLU27 2.3 10.6 1.0
O A:ILE310 2.4 12.3 1.0
O A:HOH861 2.5 14.4 1.0
O A:HOH870 2.5 15.6 1.0
O A:HOH813 2.6 16.2 1.0
C A:SER307 3.4 15.3 1.0
C A:ILE310 3.5 10.7 1.0
C A:GLU27 3.5 14.2 1.0
CA A:SER311 4.1 10.7 1.0
CA A:SER307 4.2 12.5 1.0
O A:HOH1015 4.2 30.4 1.0
N A:SER311 4.2 11.3 1.0
O A:HOH532 4.2 22.3 1.0
CB A:SER307 4.3 13.3 1.0
O A:HOH907 4.3 23.9 1.0
N A:PHE28 4.4 11.7 1.0
O A:HOH892 4.4 27.2 1.0
N A:ILE310 4.4 13.5 1.0
CA A:PHE28 4.4 9.0 1.0
CA A:GLU27 4.4 10.3 1.0
CB A:PHE28 4.4 8.4 1.0
N A:ASP308 4.4 12.4 1.0
CA A:ILE310 4.5 11.2 1.0
CA A:ASP308 4.5 18.6 1.0
O A:HOH641 4.8 22.4 1.0
CD2 A:PHE28 4.8 9.9 1.0
C A:ASP308 4.8 19.9 1.0
O A:ASN26 4.8 11.2 1.0
OG A:SER307 4.9 16.4 1.0
C A:SER311 4.9 8.9 1.0

Zinc binding site 6 out of 7 in 9fk6

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Zinc binding site 6 out of 7 in the The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:11.8
occ:1.00
 OD2 A:ASP21 2.1 10.1 1.0
O A:HOH597 2.1 10.6 1.0
O A:HOH784 2.1 13.5 1.0
O A:HOH914 2.1 13.1 1.0
O A:HOH562 2.2 8.2 1.0
O A:HOH780 2.2 12.4 1.0
CG A:ASP21 3.0 9.3 1.0
OD1 A:ASP21 3.3 10.1 1.0
O A:HOH862 4.2 28.2 1.0
O A:LYS49 4.2 11.7 1.0
O A:PHE52 4.2 9.2 1.0
O A:HOH887 4.2 28.3 1.0
O A:HOH872 4.3 22.3 1.0
O A:HOH639 4.3 12.8 1.0
O A:ARG50 4.4 10.7 1.0
CB A:ASP21 4.4 7.3 1.0
O A:HOH923 4.5 18.4 1.0
NE2 A:GLN22 4.5 15.4 1.0
O A:HOH860 4.6 24.5 1.0
CG A:GLN22 4.7 12.3 1.0
CB A:ASN53 4.7 7.6 1.0
C A:PHE52 4.8 8.3 1.0
O A:HOH942 4.8 35.7 1.0
C A:ARG50 5.0 12.2 1.0
O A:HOH889 5.0 34.8 1.0

Zinc binding site 7 out of 7 in 9fk6

Go back to Zinc Binding Sites List in 9fk6
Zinc binding site 7 out of 7 in the The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:12.6
occ:1.00
 OD2 A:ASP365 1.9 9.8 1.0
NE2 A:HIS11 2.1 10.5 1.0
CL A:CL409 2.2 13.7 1.0
CG A:ASP365 2.8 11.8 1.0
CD2 A:HIS11 2.9 9.8 1.0
OD1 A:ASP365 3.1 9.0 1.0
CE1 A:HIS11 3.2 9.6 1.0
CD A:LYS367 4.0 10.8 1.0
CG A:HIS11 4.1 10.9 1.0
ND1 A:HIS11 4.2 8.3 1.0
CB A:ASP365 4.2 11.8 1.0
O A:HOH927 4.3 24.9 1.0
O A:HOH845 4.4 12.2 1.0
CB A:LYS367 4.5 9.0 1.0
CG A:LYS367 4.7 8.9 1.0
NZ A:LYS367 4.7 18.5 1.0
CE A:LYS367 5.0 14.0 1.0

Reference:

N.Hadad, O.Chmelnik, M.Dessau, Y.Shoham, G.Shoham. The Structure of XT6 From G.Proteiniphilus T-6: the E265G/N158D Mutant To Be Published.
Page generated: Fri Aug 22 17:31:12 2025

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