Sodium in PDB 8ing: Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution

Enzymatic activity of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution

All present enzymatic activity of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution:
1.11.1.7;

Protein crystallography data

The structure of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution, PDB code: 8ing was solved by M.I.Ahmad, V.Viswanathan, M.Kumar, R.P.Singh, A.K.Singh, M.Sinha, P.Kaur, P.Sharma, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.33 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.052, 80.342, 76.121, 90, 102.82, 90
R / Rfree (%) 18.3 / 23.4

Other elements in 8ing:

The structure of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Iodine (I) 13 atoms
Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution (pdb code 8ing). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution, PDB code: 8ing:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8ing

Go back to Sodium Binding Sites List in 8ing
Sodium binding site 1 out of 2 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na637

b:37.5
occ:1.00
 O2 A:NO2605 1.9 16.5 0.7
O A:HOH1007 1.9 42.9 1.0
O A:NO630 2.5 46.8 1.0
O A:HOH706 2.6 53.4 1.0
N A:NO2605 3.0 15.8 0.7
I A:IOD617 3.0 25.3 0.3
O A:HOH992 3.6 46.3 1.0
N A:NO630 3.7 42.1 1.0
CG A:GLU258 3.9 24.6 1.0
O1 A:NO2605 3.9 19.1 0.7
CZ A:PHE381 4.0 30.9 1.0
O A:HOH882 4.1 49.2 1.0
CB A:GLU258 4.2 24.6 1.0
CMA A:HEM626 4.3 26.0 1.0
CG A:ARG255 4.3 27.2 1.0
CB A:ARG255 4.5 27.8 1.0
C3A A:HEM626 4.7 24.6 1.0
CD A:ARG255 4.8 25.6 1.0
CE1 A:PHE381 4.8 31.0 1.0
CE2 A:PHE381 4.8 31.5 1.0

Sodium binding site 2 out of 2 in 8ing

Go back to Sodium Binding Sites List in 8ing
Sodium binding site 2 out of 2 in the Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na638

b:40.0
occ:1.00
 O2P A:SEP198 2.2 61.5 1.0
O3P A:SEP198 2.4 35.5 1.0
P A:SEP198 2.5 44.9 1.0
O1P A:SEP198 3.3 62.0 1.0
NH1 A:ARG202 3.9 83.8 1.0
OG A:SEP198 4.0 54.6 1.0
CD1 A:LEU199 4.2 37.1 1.0
CD A:ARG202 4.3 59.3 1.0
CZ A:ARG202 4.4 80.7 1.0
CA A:LEU199 4.5 35.2 1.0
CB A:LEU199 4.5 36.6 1.0
NE A:ARG202 4.6 69.5 1.0
N A:LEU199 4.7 38.0 1.0
CB A:SEP198 4.7 44.9 1.0
CG A:LEU199 5.0 38.6 1.0
C A:SEP198 5.0 43.1 1.0

Reference:

M.I.Ahmad, V.Viswanathan, M.Kumar, R.P.Singh, A.K.Singh, M.Sinha, P.Kaur, P.Sharma, S.Sharma, T.P.Singh. Structure of the Ternary Complex of Lactoperoxidase with Substrate Nitric Oxide (No) and Product Nitrite Ion (NO2) at 1.98 A Resolution To Be Published.
Page generated: Tue Apr 11 17:49:07 2023

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