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Sodium in PDB 5i3j: Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase

Enzymatic activity of Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase

All present enzymatic activity of Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase:
5.3.1.1;

Protein crystallography data

The structure of Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase, PDB code: 5i3j was solved by E.J.Drake, A.M.Gulick, J.P.Richard, X.Zhai, K.Kim, C.J.Reinhardt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.30 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 40.030, 44.120, 71.700, 79.06, 77.49, 63.11
R / Rfree (%) 16.3 / 21.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase (pdb code 5i3j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase, PDB code: 5i3j:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5i3j

Go back to Sodium Binding Sites List in 5i3j
Sodium binding site 1 out of 4 in the Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:22.3
occ:1.00
 NH1 A:ARG54 2.2 43.7 1.0
CG A:ARG54 2.3 28.4 1.0
O A:HOH401 2.7 11.2 1.0
O A:HOH461 2.8 13.1 1.0
CZ A:ARG54 3.0 44.8 1.0
NA A:NA302 3.2 23.3 1.0
OG A:SER22 3.3 8.1 0.5
CD A:ARG54 3.4 19.4 1.0
NE A:ARG54 3.5 14.7 1.0
CB A:ARG54 3.5 19.9 1.0
NH2 A:ARG54 3.8 47.9 1.0
CA A:ARG54 4.1 18.3 1.0
O A:HOH537 4.4 29.3 1.0
OD2 A:ASP26 4.5 7.9 1.0
CB A:SER22 4.6 11.6 0.5
O A:HOH431 4.7 31.9 1.0
CB A:SER22 4.8 11.3 0.5
OD1 A:ASP26 4.8 9.2 1.0
N A:ARG54 4.9 16.7 1.0

Sodium binding site 2 out of 4 in 5i3j

Go back to Sodium Binding Sites List in 5i3j
Sodium binding site 2 out of 4 in the Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:23.3
occ:1.00
 CG2 A:ILE25 2.3 19.9 1.0
CB A:ARG54 2.3 19.9 1.0
CG A:ARG54 2.4 28.4 1.0
OG A:SER22 3.0 8.1 0.5
O A:SER22 3.0 9.2 1.0
NA A:NA301 3.2 22.3 1.0
CB A:ILE25 3.2 12.7 1.0
CA A:SER22 3.5 9.6 0.5
CA A:SER22 3.5 9.5 0.5
CD A:ARG54 3.6 19.4 1.0
CA A:ARG54 3.7 18.3 1.0
C A:SER22 3.7 6.7 1.0
CB A:SER22 3.8 11.6 0.5
OD1 A:ASP26 3.8 9.2 1.0
CB A:SER22 3.9 11.3 0.5
CG A:ASP26 4.0 9.4 1.0
OD2 A:ASP26 4.0 7.9 1.0
CD1 A:ILE25 4.0 9.8 1.0
O A:ARG54 4.0 10.6 1.0
N A:ASP26 4.0 12.0 1.0
C A:ARG54 4.1 13.7 1.0
CG1 A:ILE25 4.2 9.1 1.0
O A:HOH461 4.3 13.1 1.0
NE A:ARG54 4.3 14.7 1.0
CA A:ILE25 4.3 9.1 1.0
C A:ILE25 4.3 9.2 1.0
NH1 A:ARG54 4.6 43.7 1.0
O A:LEU21 4.7 10.2 1.0
ND2 A:ASN29 4.8 9.1 1.0
N A:SER22 4.8 14.3 1.0
CA A:ASP26 4.8 9.0 1.0
CB A:ASP26 4.8 10.9 1.0
CZ A:ARG54 4.8 44.8 1.0
N A:ARG54 4.8 16.7 1.0
N A:ILE25 4.9 7.2 1.0
N A:GLU23 5.0 7.3 1.0

Sodium binding site 3 out of 4 in 5i3j

Go back to Sodium Binding Sites List in 5i3j
Sodium binding site 3 out of 4 in the Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:35.8
occ:1.00
 CG2 A:THR221 2.3 16.3 0.5
OG1 A:THR221 2.5 16.0 0.5
NA A:NA304 3.2 47.4 1.0
CB A:THR221 3.3 16.9 0.5
CB A:THR221 3.3 16.9 0.5
CG2 A:THR221 3.4 14.2 0.5
CA A:THR221 3.7 17.7 0.5
CA A:THR221 3.7 17.7 0.5
N A:THR221 4.3 15.2 1.0
OG1 A:THR221 4.6 20.1 0.5
O A:HOH518 4.9 29.4 1.0
C A:THR221 4.9 21.8 1.0

Sodium binding site 4 out of 4 in 5i3j

Go back to Sodium Binding Sites List in 5i3j
Sodium binding site 4 out of 4 in the Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure-Function Studies on Role of Hydrophobic Clamping of A Basic Glutamate in Catalysis By Triosephosphate Isomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:47.4
occ:1.00
 CB A:GLN224 2.3 22.7 1.0
NA A:NA303 3.2 35.8 1.0
CA A:GLN224 3.9 24.7 1.0
CA A:THR221 3.9 17.7 0.5
CA A:THR221 3.9 17.7 0.5
O A:ARG220 4.1 16.4 1.0
O A:THR221 4.1 21.2 1.0
N A:GLN224 4.5 19.2 1.0
C A:THR221 4.5 21.8 1.0
CG2 A:THR221 4.5 16.3 0.5
CG2 A:THR221 4.5 14.2 0.5
CB A:THR221 4.6 16.9 0.5
CB A:THR221 4.6 16.9 0.5
N A:THR221 4.6 15.2 1.0
OG1 A:THR221 4.7 16.0 0.5
C A:ARG220 4.7 11.5 1.0
C A:GLN224 4.7 21.5 1.0

Reference:

J.P.Richard, T.L.Amyes, M.M.Malabanan, X.Zhai, K.J.Kim, C.J.Reinhardt, R.K.Wierenga, E.J.Drake, A.M.Gulick. Structure-Function Studies of Hydrophobic Residues That Clamp A Basic Glutamate Side Chain During Catalysis By Triosephosphate Isomerase. Biochemistry V. 55 3036 2016.
ISSN: ISSN 0006-2960
PubMed: 27149328
DOI: 10.1021/ACS.BIOCHEM.6B00311
Page generated: Mon Oct 7 21:31:23 2024

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