Zinc in PDB 6rxd: Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Apo Form

Protein crystallography data

The structure of Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Apo Form, PDB code: 6rxd was solved by A.W.H.Li, 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) 46.53 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.660, 72.940, 88.160, 71.61, 72.10, 77.17
R / Rfree (%) 15.3 / 17.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Apo Form (pdb code 6rxd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Apo Form, PDB code: 6rxd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6rxd

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Zinc binding site 1 out of 4 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:21.8
occ:1.00
NE2 A:HIS242 2.2 18.4 1.0
OE2 A:GLU251 2.2 26.2 1.0
OD2 B:ASP488 2.2 28.9 1.0
O B:HOH1140 2.3 23.1 1.0
OD1 B:ASP488 2.8 29.5 1.0
CG B:ASP488 2.9 30.9 1.0
CD A:GLU251 2.9 27.7 1.0
CD2 A:HIS242 3.0 18.6 1.0
OE1 A:GLU251 3.0 23.3 1.0
CE1 A:HIS242 3.3 18.0 1.0
OG A:SER246 3.4 18.0 0.5
O A:HOH727 4.0 35.2 1.0
CB A:SER246 4.1 19.1 0.5
CB A:SER246 4.1 19.1 0.5
CG A:HIS242 4.2 16.8 1.0
O B:HOH1075 4.3 34.1 1.0
ND1 A:HIS242 4.3 17.2 1.0
CB B:ASP488 4.3 21.8 1.0
O B:HOH1020 4.3 49.4 1.0
CG A:GLU251 4.4 20.4 1.0
O A:HOH1007 4.4 34.5 1.0
OG A:SER246 4.5 21.8 0.5
NH1 B:ARG514 4.9 38.5 1.0

Zinc binding site 2 out of 4 in 6rxd

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Zinc binding site 2 out of 4 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:32.3
occ:1.00
NE2 A:HIS326 2.1 13.3 1.0
OE2 A:GLU94 2.3 30.2 1.0
O A:HOH1250 2.4 42.0 1.0
OE1 A:GLU94 2.5 43.2 1.0
CD A:GLU94 2.6 31.9 1.0
CD2 A:HIS326 2.7 15.9 1.0
CE1 A:HIS326 3.3 27.3 1.0
CG A:GLU94 4.0 23.2 1.0
CG A:HIS326 4.0 23.3 1.0
O A:HOH1368 4.1 49.0 1.0
ND1 A:HIS326 4.2 23.4 1.0
CB A:GLU94 4.3 17.7 1.0
O A:HOH772 4.4 26.6 1.0

Zinc binding site 3 out of 4 in 6rxd

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Zinc binding site 3 out of 4 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:20.2
occ:1.00
NE2 B:HIS242 2.2 17.9 1.0
OE2 B:GLU251 2.2 22.3 1.0
OD2 A:ASP488 2.2 25.7 1.0
O A:HOH1114 2.2 22.7 1.0
OD1 A:ASP488 2.8 23.8 1.0
CG A:ASP488 2.8 21.9 1.0
CD B:GLU251 2.9 28.4 1.0
OE1 B:GLU251 2.9 21.9 1.0
CD2 B:HIS242 3.0 14.6 1.0
OG B:SER246 3.1 20.9 0.5
CE1 B:HIS242 3.2 21.9 1.0
O B:HOH727 3.9 31.4 1.0
CB B:SER246 4.0 16.7 0.5
O A:HOH1209 4.0 45.3 1.0
CB B:SER246 4.0 17.5 0.5
O B:HOH735 4.0 41.9 1.0
NH2 A:ARG514 4.2 23.7 1.0
O A:HOH1221 4.2 48.5 1.0
CG B:HIS242 4.2 18.9 1.0
ND1 B:HIS242 4.2 19.8 1.0
O A:HOH911 4.3 29.2 1.0
CG B:GLU251 4.3 26.3 1.0
CB A:ASP488 4.3 19.3 1.0
OG B:SER246 4.4 15.2 0.5
O B:HOH1159 4.5 45.5 1.0
CZ A:ARG514 5.0 24.6 1.0

Zinc binding site 4 out of 4 in 6rxd

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Zinc binding site 4 out of 4 in the Crystal Structure of Bifidobacterium Longum Multiple Inositol Polyphosphate Phosphatase Apo Form


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 Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:22.1
occ:1.00
OE2 B:GLU94 2.2 21.5 1.0
O B:HOH1129 2.2 18.0 1.0
NE2 B:HIS326 2.2 22.1 1.0
OE1 B:GLU94 2.8 24.4 1.0
CD B:GLU94 2.8 24.7 1.0
CD2 B:HIS326 3.1 23.4 1.0
CE1 B:HIS326 3.3 22.4 1.0
O B:HOH891 4.1 21.5 1.0
CG B:GLU94 4.2 20.8 1.0
CG B:HIS326 4.3 24.9 1.0
ND1 B:HIS326 4.3 20.8 1.0
O B:HOH720 4.4 22.2 1.0

Reference:

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.
Page generated: Wed Dec 16 12:43:02 2020

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