Zinc in PDB 6rxf: Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate

The structure of Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate, PDB code: 6rxf was solved by I.M.Acquistapace, C.A.Brearley, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.77 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.508, 73.118, 88.987, 71.30, 72.99, 78.99
R / Rfree (%)	18.2 / 23.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate (pdb code 6rxf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 17 binding sites of Zinc where determined in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate, PDB code: 6rxf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 17 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate


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 Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:61.2 occ:1.00 OE2 A:GLU94 2.2 58.5 1.0 NE2 A:HIS326 2.3 66.4 1.0 CD2 A:HIS326 2.7 76.3 1.0 CD A:GLU94 3.0 59.9 1.0 OE1 A:GLU94 3.1 59.1 1.0 CE1 A:HIS326 3.6 55.5 1.0 CG A:HIS326 4.0 70.6 1.0 CG A:GLU94 4.4 42.9 1.0 ND1 A:HIS326 4.4 54.6 1.0 O A:HOH707 4.5 59.1 1.0

Zinc binding site 2 out of 17 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate


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 Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:30.8 occ:1.00 NE2 A:HIS242 2.0 24.1 1.0 OD2 B:ASP488 2.1 27.2 1.0 OE1 A:GLU251 2.4 39.8 1.0 O A:HOH784 2.5 36.0 1.0 OE2 A:GLU251 2.6 43.5 1.0 CD A:GLU251 2.8 32.2 1.0 CE1 A:HIS242 2.9 17.2 1.0 CG B:ASP488 2.9 33.8 1.0 CD2 A:HIS242 3.0 16.6 1.0 OD1 B:ASP488 3.1 32.5 1.0 OG A:SER246 3.5 25.2 0.5 ND1 A:HIS242 4.0 18.0 1.0 CG A:HIS242 4.1 19.3 1.0 CB A:SER246 4.3 16.1 1.0 CG A:GLU251 4.3 40.4 1.0 CB B:ASP488 4.4 36.2 1.0 OD1 A:ASP243 5.0 48.5 1.0 NH2 B:ARG514 5.0 38.0 1.0

Zinc binding site 3 out of 17 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate


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 Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:41.2 occ:1.00 O A:HOH768 1.9 27.7 1.0 O A:HOH758 2.1 23.4 1.0 OD1 A:ASP341 2.1 28.0 1.0 O A:HOH763 2.8 31.0 1.0 O A:HOH714 2.9 33.6 1.0 CG A:ASP341 3.0 25.9 1.0 OD2 A:ASP341 3.2 34.0 1.0 O A:HOH818 3.3 58.2 1.0 OD2 A:ASP243 3.4 55.4 1.0 OD2 A:ASP340 4.1 73.9 1.0 CB A:ASP243 4.1 23.3 1.0 CG A:ASP243 4.2 45.2 1.0 O A:HOH848 4.3 42.5 1.0 CB A:ASP341 4.4 26.7 1.0 CA A:ALA240 4.7 20.1 1.0 O A:ALA337 4.7 31.8 1.0 N A:ASP341 4.8 30.1 1.0 CG A:ASP340 4.8 65.4 1.0 CA A:ASP341 4.9 30.2 1.0

Zinc binding site 4 out of 17 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate


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 Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:33.9 occ:1.00 OE2 A:GLU258 1.9 66.2 1.0 ND1 A:HIS242 2.1 18.0 1.0 OE2 A:GLU301 2.3 51.7 1.0 CD A:GLU258 2.6 54.6 1.0 OE1 A:GLU301 2.6 37.6 1.0 CD A:GLU301 2.7 35.5 1.0 OE1 A:GLU258 3.0 62.8 1.0 CE1 A:HIS242 3.1 17.2 1.0 CG A:HIS242 3.1 19.3 1.0 CB A:HIS242 3.4 19.7 1.0 O A:HOH811 3.4 34.1 1.0 CG A:GLU258 3.6 63.8 1.0 CG A:GLU301 4.1 31.0 1.0 NE2 A:HIS242 4.2 24.1 1.0 CA A:HIS242 4.2 21.7 1.0 CD2 A:HIS242 4.2 16.6 1.0 CB A:LEU254 4.2 28.4 1.0 CB A:GLU258 4.4 33.3 1.0 O A:LEU254 4.4 28.8 1.0 C A:LEU254 4.7 28.0 1.0 CD1 A:LEU254 4.8 28.6 1.0

Zinc binding site 5 out of 17 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate


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 Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:70.6 occ:1.00 OE2 A:GLU356 2.0 56.2 1.0 OE1 A:GLU228 2.7 36.2 1.0 OE2 A:GLU228 3.1 55.0 1.0 CD A:GLU356 3.2 58.4 1.0 OE1 A:GLU352 3.3 66.4 1.0 ZN A:ZN608 3.3 0.5 1.0 CD A:GLU228 3.3 51.4 1.0 O A:HOH778 3.7 55.2 1.0 CG A:GLU352 3.7 51.3 1.0 OE1 A:GLU356 3.8 52.8 1.0 CD A:GLU352 3.9 61.0 1.0 CG A:GLU356 4.4 27.6 1.0 O A:HOH864 4.6 67.0 1.0 CG A:GLU228 4.8 31.2 1.0

Zinc binding site 6 out of 17 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate


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 Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:55.0 occ:1.00 OE2 A:GLU151 2.1 46.0 1.0 NZ A:LYS179 2.6 38.4 1.0 O A:ASN177 2.9 49.2 1.0 OD2 A:ASP180 2.9 58.0 1.0 CB A:ASP180 3.1 41.6 1.0 O A:HOH712 3.1 45.0 1.0 CD A:GLU151 3.2 39.9 1.0 ZN A:ZN607 3.2 75.5 1.0 CG A:ASP180 3.3 51.8 1.0 OE1 A:GLU151 3.5 44.0 1.0 CE A:LYS179 3.7 52.9 1.0 CE1 A:PHE181 3.8 28.2 1.0 CD A:LYS179 3.8 61.7 1.0 N A:ASP180 4.0 46.9 1.0 OD1 A:ASN177 4.0 86.8 1.0 CD1 A:PHE181 4.0 18.4 1.0 C A:ASN177 4.1 44.5 1.0 CA A:ASP180 4.1 44.5 1.0 CG A:GLU151 4.5 37.9 1.0 OD1 A:ASP180 4.5 58.5 1.0 CB A:GLU148 4.8 18.2 1.0 CA A:GLY178 4.8 43.4 1.0 N A:LYS179 4.9 40.0 1.0 CG A:ASN177 4.9 74.4 1.0 C A:GLY178 4.9 35.9 1.0 N A:GLY178 4.9 36.2 1.0 C A:ASP180 5.0 35.3 1.0 CB A:GLU151 5.0 24.4 1.0 CZ A:PHE181 5.0 31.1 1.0

Zinc binding site 7 out of 17 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate


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 Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn607 b:75.5 occ:1.00 OD2 A:ASP180 1.9 58.0 1.0 O A:HOH738 2.4 45.2 1.0 NZ A:LYS179 2.5 38.4 1.0 OE1 A:GLU151 2.8 44.0 1.0 CG A:ASP180 3.1 51.8 1.0 ZN A:ZN606 3.2 55.0 1.0 CD A:GLU151 3.3 39.9 1.0 CE A:LYS179 3.3 52.9 1.0 OE2 A:GLU151 3.4 46.0 1.0 O A:HOH712 3.4 45.0 1.0 OD1 A:ASP180 3.9 58.5 1.0 CB A:ASP180 4.1 41.6 1.0 CG A:GLU151 4.5 37.9 1.0 CD A:LYS179 4.5 61.7 1.0

Zinc binding site 8 out of 17 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate


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 Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn608 b:0.5 occ:1.00 O A:HOH778 2.4 55.2 1.0 O A:HOH864 2.5 67.0 1.0 ZN A:ZN605 3.3 70.6 1.0 OE1 A:GLU228 3.6 36.2 1.0 OE2 A:GLU356 3.8 56.2 1.0 O A:VAL218 4.2 34.6 1.0 CD A:GLU228 4.3 51.4 1.0 O A:HOH862 4.6 44.6 1.0 OE2 A:GLU228 4.6 55.0 1.0 CG2 A:ILE224 4.7 20.1 1.0 CD A:GLU356 4.8 58.4 1.0

Zinc binding site 9 out of 17 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate


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 Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:49.0 occ:1.00 NE2 B:HIS326 1.8 16.1 1.0 OE1 B:GLU94 2.1 50.3 1.0 OE2 B:GLU94 2.3 51.5 1.0 CD B:GLU94 2.4 49.4 1.0 CE1 B:HIS326 2.7 18.1 1.0 CD2 B:HIS326 2.9 21.1 1.0 CG B:GLU94 3.8 48.4 1.0 ND1 B:HIS326 3.8 31.1 1.0 CG B:HIS326 3.9 23.4 1.0 CB B:GLU94 4.3 26.0 1.0

Zinc binding site 10 out of 17 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate


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 Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Phosphohistidine Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:29.0 occ:1.00 OE1 B:GLU251 2.0 32.6 1.0 NE2 B:HIS242 2.1 28.7 1.0 O B:HOH807 2.2 35.3 1.0 OD2 A:ASP488 2.3 35.0 1.0 OE2 B:GLU251 2.5 30.4 1.0 CD B:GLU251 2.6 29.3 1.0 CE1 B:HIS242 3.0 18.7 1.0 CD2 B:HIS242 3.1 23.2 1.0 CG A:ASP488 3.2 35.9 1.0 OD1 A:ASP488 3.3 45.3 1.0 OG B:SER246 3.3 33.6 1.0 CG B:GLU251 4.0 23.3 1.0 ND1 B:HIS242 4.1 23.4 1.0 CG B:HIS242 4.2 19.5 1.0 O A:HOH804 4.3 39.5 1.0 CB B:SER246 4.5 20.7 1.0 CB A:ASP488 4.5 36.6 1.0 O B:HOH827 4.9 30.1 1.0

I.M.Acquistapace, A.W.H.Li, M.A.Z.Zietek, C.A.Brearley, A.M.Hemmings. Crystal Structures of Bifidobacterium Longum Multiple Inositol Phosphate Phosphatase Reveal An Alpha-Domain Induced-Fit Mechanism To Be Published.