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Sodium in PDB 6t7h: Crystal Structure of Thrombin in Complex with Macrocycle N14-PR4-A

Enzymatic activity of Crystal Structure of Thrombin in Complex with Macrocycle N14-PR4-A

All present enzymatic activity of Crystal Structure of Thrombin in Complex with Macrocycle N14-PR4-A:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Thrombin in Complex with Macrocycle N14-PR4-A, PDB code: 6t7h was solved by A.Angelini, M.G.Kumar, C.Heinis, L.Cendron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.96 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.664, 101.343, 119.129, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Thrombin in Complex with Macrocycle N14-PR4-A (pdb code 6t7h). 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 Thrombin in Complex with Macrocycle N14-PR4-A, PDB code: 6t7h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6t7h

Go back to Sodium Binding Sites List in 6t7h
Sodium binding site 1 out of 2 in the Crystal Structure of Thrombin in Complex with Macrocycle N14-PR4-A


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 Thrombin in Complex with Macrocycle N14-PR4-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:43.2
occ:1.00
O A:ARG221A 2.3 49.9 1.0
O A:HOH852 2.3 38.9 1.0
O A:LYS224 2.3 40.4 1.0
O A:HOH845 2.4 37.4 1.0
O A:HOH826 2.6 39.4 1.0
O A:HOH812 3.0 40.3 1.0
C A:LYS224 3.3 41.5 1.0
C A:ARG221A 3.4 50.4 1.0
N A:LYS224 3.7 48.9 1.0
N A:ARG221A 3.9 41.4 1.0
O A:HOH811 3.9 34.5 1.0
CA A:LYS224 3.9 48.5 1.0
C A:ASP221 4.1 41.2 1.0
N A:GLY223 4.2 47.8 1.0
N A:ASP222 4.2 53.9 1.0
O A:HOH828 4.2 38.6 1.0
CA A:ARG221A 4.3 44.8 1.0
O A:TYR184A 4.3 45.5 1.0
CA A:ASP221 4.3 40.1 1.0
O A:HOH835 4.3 33.7 1.0
N A:TYR225 4.3 39.0 1.0
CA A:ASP222 4.4 53.0 1.0
CB A:LYS224 4.4 47.5 1.0
C A:ASP222 4.5 53.7 1.0
O A:ASP221 4.5 39.9 1.0
O A:HOH846 4.6 43.3 1.0
O A:HOH817 4.7 42.8 1.0
OD1 A:ASP221 4.7 44.6 1.0
CA A:TYR225 4.7 38.0 1.0
C A:GLY223 4.7 50.6 1.0
N A:ASP221 4.9 39.2 1.0

Sodium binding site 2 out of 2 in 6t7h

Go back to Sodium Binding Sites List in 6t7h
Sodium binding site 2 out of 2 in the Crystal Structure of Thrombin in Complex with Macrocycle N14-PR4-A


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 Thrombin in Complex with Macrocycle N14-PR4-A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na604

b:45.1
occ:1.00
O H:HOH759 2.3 42.9 1.0
O H:ARG221A 2.3 52.6 1.0
O H:HOH747 2.3 40.8 1.0
O H:LYS224 2.4 39.4 1.0
O H:HOH743 2.4 38.8 1.0
O H:HOH754 2.8 48.2 1.0
C H:ARG221A 3.3 48.5 1.0
C H:LYS224 3.5 38.9 1.0
O H:HOH761 3.8 34.1 1.0
N H:ARG221A 3.9 44.0 1.0
O H:HOH709 3.9 53.3 1.0
N H:LYS224 3.9 46.2 1.0
O H:TYR184A 4.0 45.3 1.0
C H:ASP221 4.1 42.8 1.0
N H:ASP222 4.2 50.1 1.0
CA H:LYS224 4.2 43.6 1.0
CA H:ARG221A 4.3 45.6 1.0
CA H:ASP222 4.3 50.0 1.0
O H:HOH719 4.3 36.7 1.0
CA H:ASP221 4.3 44.8 1.0
N H:GLY223 4.4 53.1 1.0
N H:TYR225 4.6 40.1 1.0
C H:ASP222 4.6 49.2 1.0
O H:ASP221 4.6 47.2 1.0
CB H:LYS224 4.6 43.5 1.0
O H:HOH724 4.7 54.1 1.0
OD1 H:ASP221 4.8 44.0 1.0
O H:HOH745 4.8 45.5 1.0
CA H:TYR225 4.8 40.3 1.0
CD1 H:TYR225 5.0 42.2 1.0
N H:ASP221 5.0 40.8 1.0

Reference:

M.G.Kumar, S.S.Kale, C.L.Stenbrat, A.Zorzi, J.Vesin, J.B.Chapalay, K.Deyle, G.Turcatti, Cendron.L., A.Angelini, C.Heinis. Macrocycle Synthesis Strategy Based on Step-Wise “Adding and Reacting” Three Components Enables Screening of Large Combinatorial Libraries Chem Sci 2020.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC01944E
Page generated: Tue Dec 15 13:04:40 2020

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