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Zinc in PDB 5xwi: Crystal Structure of Spap, An Alkaline Phosphatase From Sphingomonas Showing Covalent Intermediate

Enzymatic activity of Crystal Structure of Spap, An Alkaline Phosphatase From Sphingomonas Showing Covalent Intermediate

All present enzymatic activity of Crystal Structure of Spap, An Alkaline Phosphatase From Sphingomonas Showing Covalent Intermediate:
3.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Spap, An Alkaline Phosphatase From Sphingomonas Showing Covalent Intermediate, PDB code: 5xwi was solved by S.C.Bihani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.38 / 1.87
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.600, 87.600, 168.030, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21

Other elements in 5xwi:

The structure of Crystal Structure of Spap, An Alkaline Phosphatase From Sphingomonas Showing Covalent Intermediate also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Spap, An Alkaline Phosphatase From Sphingomonas Showing Covalent Intermediate (pdb code 5xwi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Spap, An Alkaline Phosphatase From Sphingomonas Showing Covalent Intermediate, PDB code: 5xwi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5xwi

Go back to Zinc Binding Sites List in 5xwi
Zinc binding site 1 out of 2 in the Crystal Structure of Spap, An Alkaline Phosphatase From Sphingomonas Showing Covalent 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 Spap, An Alkaline Phosphatase From Sphingomonas Showing Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:23.3
occ:0.94
OD2 A:ASP345 2.0 19.7 1.0
OD1 A:ASP49 2.0 21.1 1.0
NE2 A:HIS346 2.0 22.8 1.0
OG1 A:TPO89 2.1 23.3 1.0
O3P A:TPO89 2.5 28.3 1.0
CG A:ASP49 2.8 25.4 1.0
CG A:ASP345 2.9 23.4 1.0
P A:TPO89 2.9 29.7 1.0
CD2 A:HIS346 3.0 24.3 1.0
CE1 A:HIS346 3.0 23.0 1.0
OD2 A:ASP49 3.1 25.1 1.0
OD1 A:ASP345 3.2 17.8 1.0
CB A:TPO89 3.2 26.3 1.0
CA A:TPO89 3.5 23.4 1.0
OD1 A:ASP300 3.7 20.4 1.0
CG2 A:TPO89 3.8 25.1 1.0
O2P A:TPO89 3.9 30.6 1.0
N A:TPO89 3.9 23.4 1.0
CG A:ASP300 4.0 23.6 1.0
ZN A:ZN602 4.0 23.8 1.0
ND1 A:HIS346 4.1 19.8 1.0
CG A:HIS346 4.1 19.1 1.0
NZ A:LYS171 4.1 27.4 1.0
O1P A:TPO89 4.1 28.8 1.0
CB A:ASP49 4.2 19.0 1.0
CE1 A:HIS491 4.2 26.2 1.0
CB A:ASP345 4.3 20.1 1.0
OD2 A:ASP300 4.3 23.6 1.0
NE2 A:HIS491 4.3 25.8 1.0
N A:GLN50 4.4 20.3 1.0
CA A:ASP49 4.5 21.1 1.0
CB A:ASP300 4.6 20.9 1.0
C A:GLU88 4.7 23.4 1.0
C A:ASP49 4.7 19.7 1.0
CE1 A:HIS93 4.8 23.3 1.0
C A:TPO89 4.9 21.3 1.0
O A:HOH702 4.9 39.2 1.0

Zinc binding site 2 out of 2 in 5xwi

Go back to Zinc Binding Sites List in 5xwi
Zinc binding site 2 out of 2 in the Crystal Structure of Spap, An Alkaline Phosphatase From Sphingomonas Showing Covalent 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 Spap, An Alkaline Phosphatase From Sphingomonas Showing Covalent Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:23.8
occ:0.99
O3P A:TPO89 1.9 28.3 1.0
NE2 A:HIS304 2.0 22.0 1.0
NE2 A:HIS491 2.1 25.8 1.0
OD1 A:ASP300 2.2 20.4 1.0
O A:HOH702 2.5 39.2 1.0
OD2 A:ASP300 2.5 23.6 1.0
CG A:ASP300 2.7 23.6 1.0
CD2 A:HIS304 2.9 26.8 1.0
CE1 A:HIS304 3.0 27.4 1.0
CE1 A:HIS491 3.0 26.2 1.0
CD2 A:HIS491 3.1 20.5 1.0
P A:TPO89 3.3 29.7 1.0
O2P A:TPO89 3.6 30.6 1.0
ZN A:ZN601 4.0 23.3 0.9
CE1 A:HIS346 4.0 23.0 1.0
NE2 A:GLN50 4.0 21.7 1.0
NE2 A:HIS346 4.1 22.8 1.0
NZ A:LYS171 4.1 27.4 1.0
ND1 A:HIS304 4.1 28.0 1.0
O1P A:TPO89 4.1 28.8 1.0
CG A:HIS304 4.1 27.2 1.0
CB A:ASP300 4.2 20.9 1.0
ND1 A:HIS491 4.2 24.6 1.0
O A:HOH959 4.2 47.7 1.0
CG A:HIS491 4.2 21.8 1.0
OG1 A:TPO89 4.3 23.3 1.0
OD1 A:ASP49 4.4 21.1 1.0
O A:ASP300 4.9 24.1 1.0
CA A:ASP300 5.0 23.5 1.0

Reference:

S.C.Bihani, S.C.Bihani. N/A N/A.
Page generated: Mon Oct 28 15:15:23 2024

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