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Sodium in PDB 6z48: Crystal Structure of Thrombin in Complex with Macrocycle X1VE

Protein crystallography data

The structure of Crystal Structure of Thrombin in Complex with Macrocycle X1VE, PDB code: 6z48 was solved by A.Angelini, S.Habeshian, C.Heinis, L.Cendron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.88 / 2.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.251, 100.573, 108.897, 90, 90.11, 90
R / Rfree (%) 18.9 / 24.3

Other elements in 6z48:

The structure of Crystal Structure of Thrombin in Complex with Macrocycle X1VE also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Thrombin in Complex with Macrocycle X1VE (pdb code 6z48). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Thrombin in Complex with Macrocycle X1VE, PDB code: 6z48:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6z48

Go back to Sodium Binding Sites List in 6z48
Sodium binding site 1 out of 4 in the Crystal Structure of Thrombin in Complex with Macrocycle X1VE


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 X1VE within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na301

b:27.2
occ:1.00
 O H:HOH452 2.3 34.2 1.0
O H:HOH405 2.3 23.5 1.0
O H:LYS224 2.5 25.2 1.0
O H:ARG221A 2.5 21.5 1.0
O H:HOH468 2.7 17.1 1.0
O H:HOH458 2.7 23.8 1.0
C H:ARG221A 3.5 21.5 1.0
C H:LYS224 3.6 22.4 1.0
O H:TYR184A 3.9 28.5 1.0
O H:HOH429 3.9 21.6 1.0
N H:LYS224 3.9 21.6 1.0
N H:ARG221A 4.0 19.2 1.0
O H:HOH411 4.0 27.7 1.0
C H:ASP221 4.1 18.9 1.0
O H:HOH441 4.1 24.5 1.0
CA H:LYS224 4.3 21.9 1.0
N H:ASP222 4.3 24.8 1.0
CA H:ASP221 4.3 21.2 1.0
CA H:ASP222 4.3 27.3 1.0
CA H:ARG221A 4.4 20.7 1.0
N H:GLY223 4.4 26.8 1.0
N H:TYR225 4.6 19.7 1.0
O H:ASP221 4.6 20.4 1.0
C H:ASP222 4.6 26.3 1.0
CB H:LYS224 4.7 19.3 1.0
CA H:TYR225 4.8 20.8 1.0
OD1 H:ASP221 4.8 18.4 1.0

Sodium binding site 2 out of 4 in 6z48

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Sodium binding site 2 out of 4 in the Crystal Structure of Thrombin in Complex with Macrocycle X1VE


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 X1VE within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:16.4
occ:1.00
 O B:ARG221A 2.3 20.2 1.0
O B:LYS224 2.3 16.2 1.0
O B:HOH465 2.4 22.6 1.0
O B:HOH477 2.5 14.4 1.0
O B:HOH444 2.6 17.1 1.0
O B:HOH417 2.6 21.1 1.0
C B:ARG221A 3.4 20.8 1.0
C B:LYS224 3.4 17.0 1.0
N B:LYS224 3.8 18.4 1.0
N B:ARG221A 3.9 18.3 1.0
O B:HOH455 3.9 17.7 1.0
C B:ASP221 4.0 18.8 1.0
CA B:LYS224 4.1 18.4 1.0
O B:HOH426 4.1 21.7 1.0
O B:TYR184A 4.1 22.6 1.0
O B:HOH456 4.1 18.3 1.0
N B:GLY223 4.2 21.4 1.0
CA B:ARG221A 4.2 19.5 1.0
N B:ASP222 4.3 20.9 1.0
CA B:ASP221 4.3 18.4 1.0
CA B:ASP222 4.4 20.0 1.0
N B:TYR225 4.4 17.9 1.0
CB B:LYS224 4.4 17.0 1.0
C B:ASP222 4.6 19.8 1.0
O B:ASP221 4.6 19.5 1.0
CA B:TYR225 4.7 18.1 1.0
OD1 B:ASP221 4.9 23.3 1.0
O B:HOH424 4.9 14.5 1.0
C B:GLY223 4.9 19.1 1.0
N B:ASP221 5.0 17.4 1.0

Sodium binding site 3 out of 4 in 6z48

Go back to Sodium Binding Sites List in 6z48
Sodium binding site 3 out of 4 in the Crystal Structure of Thrombin in Complex with Macrocycle X1VE


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Thrombin in Complex with Macrocycle X1VE within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:12.4
occ:1.00
 O D:HOH483 2.1 17.2 1.0
O D:HOH477 2.3 24.6 1.0
O D:ARG221A 2.3 17.3 1.0
O D:LYS224 2.3 14.2 1.0
O D:HOH439 2.3 16.4 1.0
C D:LYS224 3.4 17.2 1.0
C D:ARG221A 3.5 18.1 1.0
O D:HOH473 3.8 20.5 1.0
N D:LYS224 3.9 17.3 1.0
O D:HOH411 3.9 26.0 1.0
O D:TYR184A 4.0 24.8 1.0
O D:HOH421 4.0 17.6 1.0
N D:ARG221A 4.0 18.4 1.0
CA D:LYS224 4.1 17.0 1.0
C D:ASP221 4.2 18.0 1.0
N D:ASP222 4.3 18.9 1.0
CA D:ASP222 4.3 19.4 1.0
N D:GLY223 4.3 16.5 1.0
CA D:ARG221A 4.4 19.5 1.0
N D:TYR225 4.4 17.2 1.0
CA D:ASP221 4.4 16.6 1.0
CB D:LYS224 4.5 17.8 1.0
O D:ASP221 4.6 16.9 1.0
C D:ASP222 4.6 18.9 1.0
CA D:TYR225 4.7 19.6 1.0
O D:HOH440 4.8 16.7 1.0
CD1 D:TYR225 4.8 22.6 1.0
OD1 D:ASP221 4.9 15.1 1.0
C D:GLY223 5.0 18.1 1.0

Sodium binding site 4 out of 4 in 6z48

Go back to Sodium Binding Sites List in 6z48
Sodium binding site 4 out of 4 in the Crystal Structure of Thrombin in Complex with Macrocycle X1VE


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Thrombin in Complex with Macrocycle X1VE within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:25.7
occ:1.00
 O F:ARG221A 2.0 19.6 1.0
O F:HOH479 2.4 20.8 1.0
O F:HOH436 2.4 23.2 1.0
O F:LYS224 2.5 18.1 1.0
O F:HOH424 2.5 30.0 1.0
O F:HOH456 2.7 19.7 1.0
C F:ARG221A 3.2 20.6 1.0
C F:LYS224 3.5 18.2 1.0
N F:LYS224 3.6 20.7 1.0
O F:HOH434 3.9 20.2 1.0
N F:ARG221A 3.9 21.4 1.0
O F:HOH455 4.0 31.5 1.0
CA F:LYS224 4.0 19.5 1.0
N F:ASP222 4.0 19.8 1.0
C F:ASP221 4.1 21.5 1.0
CA F:ASP222 4.1 21.1 1.0
CA F:ARG221A 4.1 20.8 1.0
N F:GLY223 4.2 20.2 1.0
O F:TYR184A 4.2 23.9 1.0
O F:HOH430 4.3 22.4 1.0
CB F:LYS224 4.3 18.1 1.0
C F:ASP222 4.3 20.4 1.0
CA F:ASP221 4.4 17.7 1.0
N F:TYR225 4.5 18.6 1.0
O F:ASP221 4.6 22.1 1.0
C F:GLY223 4.7 21.2 1.0
OD1 F:ASP221 4.8 21.5 1.0
CA F:TYR225 4.8 19.8 1.0
O F:HOH419 4.9 21.4 1.0
CD1 F:TYR225 5.0 20.7 1.0

Reference:

S.Habeshian, M.L.Merz, G.Sangouard, G.K.Mothukuri, M.Schuttel, Z.Bognar, C.Diaz-Perlas, J.Vesin, J.Bortoli Chapalay, G.Turcatti, L.Cendron, A.Angelini, C.Heinis. Synthesis and Direct Assay of Large Macrocycle Diversities By Combinatorial Late-Stage Modification at Picomole Scale. Nat Commun V. 13 3823 2022.
ISSN: ESSN 2041-1723
PubMed: 35780129
DOI: 10.1038/S41467-022-31428-8
Page generated: Tue Oct 8 15:18:27 2024

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