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Sodium in PDB 2dho: Crystal Structure of Human Ipp Isomerase I in Space Group P212121

Enzymatic activity of Crystal Structure of Human Ipp Isomerase I in Space Group P212121

All present enzymatic activity of Crystal Structure of Human Ipp Isomerase I in Space Group P212121:
5.3.3.2;

Protein crystallography data

The structure of Crystal Structure of Human Ipp Isomerase I in Space Group P212121, PDB code: 2dho was solved by C.Zhang, Z.Wei, W.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.79 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.019, 62.947, 74.188, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.3

Other elements in 2dho:

The structure of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 also contains other interesting chemical elements:

Manganese (Mn) 8 atoms
Chlorine (Cl) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121 (pdb code 2dho). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121, PDB code: 2dho:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2dho

Go back to Sodium Binding Sites List in 2dho
Sodium binding site 1 out of 2 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2001

b:19.1
occ:1.00
O A:HOH3011 2.9 13.0 1.0
CL A:CL3001 2.9 19.9 1.0
CD2 A:TYR171 3.5 14.8 1.0
CE2 A:TYR171 3.5 15.2 1.0
CG A:PRO163 3.8 13.1 1.0
CA A:SER170 4.0 13.3 1.0
CD A:PRO163 4.0 13.2 1.0
N A:TYR171 4.3 13.5 1.0
C A:SER170 4.4 13.4 1.0
CB A:PRO163 4.4 12.4 1.0
O A:LYS169 4.4 13.0 1.0
N A:SER170 4.6 13.5 1.0
CG A:TYR171 4.6 13.6 1.0
CZ A:TYR171 4.6 13.5 1.0
O A:HOH3201 4.6 32.8 1.0
C A:LYS169 4.7 13.4 1.0
O A:HOH3272 4.8 38.1 1.0
CG2 A:ILE168 4.9 15.4 1.0

Sodium binding site 2 out of 2 in 2dho

Go back to Sodium Binding Sites List in 2dho
Sodium binding site 2 out of 2 in the Crystal Structure of Human Ipp Isomerase I in Space Group P212121


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Ipp Isomerase I in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2002

b:31.2
occ:1.00
O A:HOH3289 2.5 46.0 1.0
O A:HOH3045 3.1 17.5 1.0
O A:HOH3109 3.1 24.6 1.0
N A:ASN213 3.3 17.1 1.0
CA A:ASN211 3.6 17.7 1.0
ND1 A:HIS214 3.6 20.4 1.0
C A:ASN211 3.6 17.4 1.0
CB A:ASN213 3.6 17.4 1.0
O A:ASP210 3.7 19.6 1.0
N A:LEU212 3.7 17.6 1.0
OD1 A:ASN213 3.8 19.7 1.0
CA A:ASN213 3.9 17.8 1.0
CG A:ASN213 4.0 18.0 1.0
N A:HIS214 4.2 18.5 1.0
O A:ASN211 4.2 17.2 1.0
CE1 A:HIS214 4.3 21.4 1.0
N A:ASN211 4.3 17.9 1.0
C A:ASP210 4.3 18.2 1.0
C A:LEU212 4.4 17.0 1.0
C A:ASN213 4.4 18.3 1.0
CA A:LEU212 4.5 17.0 1.0
CG A:HIS214 4.7 19.6 1.0
CB A:ASN211 4.7 17.8 1.0
OD1 A:ASN211 4.8 18.6 1.0
CB A:HIS214 4.9 18.7 1.0

Reference:

C.Zhang, L.Liu, H.Xu, Z.Wei, Y.Wang, Y.Lin, W.Gong. Crystal Structures of Human Ipp Isomerase: New Insights Into the Catalytic Mechanism J.Mol.Biol. V. 366 1437 2007.
ISSN: ISSN 0022-2836
PubMed: 17137593
DOI: 10.1016/J.JMB.2006.10.092
Page generated: Thu Oct 29 04:09:08 2020

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