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Sodium in PDB 7mj5: Complex of Human Thrombin with Xc-43

Enzymatic activity of Complex of Human Thrombin with Xc-43

All present enzymatic activity of Complex of Human Thrombin with Xc-43:
3.4.21.5;

Protein crystallography data

The structure of Complex of Human Thrombin with Xc-43, PDB code: 7mj5 was solved by S.Lu, L.Tirloni, J.F.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.24 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.35, 136.32, 193.95, 90, 90, 90
R / Rfree (%) 16.5 / 19.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Complex of Human Thrombin with Xc-43 (pdb code 7mj5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Complex of Human Thrombin with Xc-43, PDB code: 7mj5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 7mj5

Go back to Sodium Binding Sites List in 7mj5
Sodium binding site 1 out of 6 in the Complex of Human Thrombin with Xc-43


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:31.6
occ:1.00
 O H:ARG221 2.3 27.1 1.0
O H:HOH488 2.4 31.5 1.0
O H:HOH462 2.4 27.7 1.0
O H:LYS224 2.4 32.3 1.0
O H:HOH532 2.4 33.1 1.0
O H:HOH477 2.6 30.8 1.0
C H:ARG221 3.3 29.8 1.0
C H:LYS224 3.5 32.1 1.0
O H:HOH521 3.7 30.5 1.0
N H:ARG221 3.8 27.3 1.0
N H:LYS224 3.9 32.3 1.0
O H:TYR184A 4.0 33.1 1.0
C H:ASP220 4.1 27.7 1.0
O H:HOH441 4.1 29.1 1.0
CA H:ARG221 4.2 28.2 1.0
N H:ASP222 4.2 28.1 1.0
O H:HOH483 4.2 27.3 1.0
CA H:LYS224 4.2 31.5 1.0
CA H:ASP220 4.3 26.1 1.0
N H:GLY223 4.3 31.8 1.0
CA H:ASP222 4.3 28.4 1.0
N H:TYR225 4.5 27.5 1.0
C H:ASP222 4.6 33.1 1.0
CB H:LYS224 4.6 28.7 1.0
O H:ASP220 4.7 26.8 1.0
OD1 H:ASP220 4.7 27.5 1.0
CA H:TYR225 4.7 29.1 1.0
O H:HOH487 4.9 31.3 1.0
C H:GLY223 4.9 32.3 1.0
N H:ASP220 5.0 30.2 1.0

Sodium binding site 2 out of 6 in 7mj5

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Sodium binding site 2 out of 6 in the Complex of Human Thrombin with Xc-43


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:33.6
occ:1.00
 O C:ARG222 2.3 32.1 1.0
O C:HOH459 2.3 28.3 1.0
O C:HOH558 2.4 30.9 1.0
O C:HOH440 2.5 29.9 1.0
O C:LYS225 2.5 33.0 1.0
O C:HOH529 2.7 33.1 1.0
C C:ARG222 3.3 31.2 1.0
C C:LYS225 3.5 32.2 1.0
N C:ARG222 3.7 31.8 1.0
O C:HOH559 3.8 32.7 1.0
N C:LYS225 3.9 31.5 1.0
O C:HOH497 4.0 31.4 1.0
C C:ASP221 4.0 30.9 1.0
O C:TYR184A 4.0 33.0 1.0
CA C:ARG222 4.1 31.9 1.0
CA C:LYS225 4.2 28.9 1.0
CA C:ASP221 4.2 30.8 1.0
N C:ASP223 4.2 31.2 1.0
O C:HOH489 4.3 29.3 1.0
N C:GLY224 4.3 33.9 1.0
CA C:ASP223 4.4 32.9 1.0
N C:TYR226 4.5 31.8 1.0
O C:ASP221 4.6 30.9 1.0
CB C:LYS225 4.6 31.8 1.0
OD1 C:ASP221 4.6 29.8 1.0
C C:ASP223 4.6 34.7 1.0
CA C:TYR226 4.8 33.6 1.0
O C:HOH490 4.8 33.3 1.0
N C:ASP221 4.9 31.4 1.0
C C:GLY224 4.9 35.8 1.0

Sodium binding site 3 out of 6 in 7mj5

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Sodium binding site 3 out of 6 in the Complex of Human Thrombin with Xc-43


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:31.8
occ:1.00
 O E:ARG222 2.3 30.5 1.0
O E:HOH526 2.4 31.9 1.0
O E:LYS225 2.4 32.1 1.0
O E:HOH429 2.4 27.6 1.0
O E:HOH430 2.5 29.3 1.0
O E:HOH459 2.6 29.7 1.0
C E:ARG222 3.3 31.6 1.0
C E:LYS225 3.4 30.7 1.0
O E:HOH509 3.7 33.6 1.0
N E:ARG222 3.8 28.4 1.0
N E:LYS225 3.8 31.9 1.0
O E:TYR184A 4.0 30.8 1.0
C E:ASP221 4.1 31.1 1.0
O E:HOH444 4.1 30.4 1.0
CA E:LYS225 4.1 31.4 1.0
CA E:ARG222 4.2 29.8 1.0
O E:HOH479 4.2 28.9 1.0
N E:ASP223 4.2 29.3 1.0
N E:GLY224 4.3 31.5 1.0
CA E:ASP221 4.3 30.5 1.0
CA E:ASP223 4.4 29.3 1.0
N E:TYR226 4.4 33.9 1.0
C E:ASP223 4.6 31.2 1.0
CB E:LYS225 4.6 30.5 1.0
CA E:TYR226 4.7 29.7 1.0
OD1 E:ASP221 4.7 32.2 1.0
O E:ASP221 4.7 31.5 1.0
C E:GLY224 4.9 32.2 1.0
O E:HOH435 4.9 32.4 1.0
CD1 E:TYR226 5.0 30.0 1.0

Sodium binding site 4 out of 6 in 7mj5

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Sodium binding site 4 out of 6 in the Complex of Human Thrombin with Xc-43


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na302

b:38.1
occ:1.00
 O G:ARG222 2.4 35.0 1.0
O G:LYS225 2.4 36.4 1.0
O G:HOH493 2.4 35.9 1.0
O G:HOH481 2.4 33.9 1.0
O G:HOH511 2.5 36.5 1.0
O G:HOH440 2.7 35.9 1.0
C G:ARG222 3.4 37.1 1.0
C G:LYS225 3.5 40.4 1.0
N G:ARG222 3.8 35.3 1.0
O G:TYR184A 3.9 38.1 1.0
N G:LYS225 4.0 37.7 1.0
O G:HOH455 4.1 33.9 1.0
O G:HOH470 4.1 34.3 1.0
C G:ASP221 4.1 33.3 1.0
CA G:ARG222 4.2 33.4 1.0
CA G:LYS225 4.2 37.3 1.0
N G:ASP223 4.2 35.0 1.0
CA G:ASP221 4.3 32.5 1.0
N G:TYR226 4.4 36.6 1.0
CA G:ASP223 4.4 36.6 1.0
N G:GLY224 4.4 37.6 1.0
CA G:TYR226 4.6 37.5 1.0
C G:ASP223 4.7 39.6 1.0
CB G:LYS225 4.7 38.3 1.0
O G:HOH501 4.7 39.2 1.0
OD1 G:ASP221 4.7 32.9 1.0
O G:ASP221 4.8 37.6 1.0
CD1 G:TYR226 4.9 40.8 1.0
N G:ASP221 5.0 33.6 1.0
C G:GLY224 5.0 39.3 1.0

Sodium binding site 5 out of 6 in 7mj5

Go back to Sodium Binding Sites List in 7mj5
Sodium binding site 5 out of 6 in the Complex of Human Thrombin with Xc-43


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na302

b:36.0
occ:1.00
 O J:ARG222 2.3 33.4 1.0
O J:HOH475 2.4 31.4 1.0
O J:LYS225 2.4 35.0 1.0
O J:HOH534 2.5 31.1 1.0
O J:HOH451 2.5 33.9 1.0
O J:HOH460 2.5 33.6 1.0
C J:ARG222 3.3 33.4 1.0
C J:LYS225 3.5 34.5 1.0
N J:ARG222 3.8 31.3 1.0
N J:LYS225 3.9 34.1 1.0
O J:HOH514 3.9 34.2 1.0
O J:TYR184A 3.9 37.6 1.0
O J:HOH462 4.0 33.0 1.0
C J:ASP221 4.1 31.5 1.0
CA J:ARG222 4.1 32.7 1.0
CA J:LYS225 4.2 34.7 1.0
N J:ASP223 4.2 30.7 1.0
O J:HOH461 4.2 31.5 1.0
N J:GLY224 4.3 32.6 1.0
CA J:ASP223 4.3 32.8 1.0
CA J:ASP221 4.4 31.2 1.0
N J:TYR226 4.5 33.7 1.0
C J:ASP223 4.6 33.4 1.0
CB J:LYS225 4.6 33.0 1.0
O J:ASP221 4.7 32.1 1.0
CA J:TYR226 4.7 33.5 1.0
O J:HOH532 4.7 31.1 1.0
OD1 J:ASP221 4.8 35.0 1.0
C J:GLY224 4.9 34.1 1.0

Sodium binding site 6 out of 6 in 7mj5

Go back to Sodium Binding Sites List in 7mj5
Sodium binding site 6 out of 6 in the Complex of Human Thrombin with Xc-43


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Complex of Human Thrombin with Xc-43 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Na302

b:34.3
occ:1.00
 O M:ARG222 2.3 32.9 1.0
O M:HOH470 2.4 30.1 1.0
O M:LYS225 2.5 33.8 1.0
O M:HOH469 2.5 33.2 1.0
O M:HOH457 2.7 34.4 1.0
C M:ARG222 3.3 33.7 1.0
C M:LYS225 3.5 35.3 1.0
N M:ARG222 3.7 31.8 1.0
O M:HOH514 3.8 34.7 1.0
N M:LYS225 3.9 34.0 1.0
C M:ASP221 4.0 32.3 1.0
O M:TYR184A 4.1 33.3 1.0
O M:HOH441 4.1 32.1 1.0
CA M:ARG222 4.1 34.6 1.0
O M:HOH453 4.2 31.6 1.0
N M:ASP223 4.2 30.4 1.0
CA M:ASP221 4.2 30.8 1.0
CA M:LYS225 4.2 34.9 1.0
N M:GLY224 4.4 35.4 1.0
CA M:ASP223 4.4 34.4 1.0
N M:TYR226 4.5 34.2 1.0
O M:HOH522 4.6 33.8 1.0
O M:ASP221 4.6 31.9 1.0
OD1 M:ASP221 4.6 33.0 1.0
CB M:LYS225 4.6 37.7 1.0
C M:ASP223 4.7 35.0 1.0
CA M:TYR226 4.7 35.4 1.0
N M:ASP221 4.9 28.6 1.0
C M:GLY224 5.0 35.9 1.0

Reference:

S.Lu, L.Tirloni, M.B.Oliveira, C.F.Bosio, G.A.Nardone, Y.Zhang, B.J.Hinnebusch, J.M.Ribeiro, J.F.Andersen. Identification of A Substrate-Like Cleavage-Resistant Thrombin Inhibitor From the Saliva of the Flea Xenopsylla Cheopis. J.Biol.Chem. V. 297 01322 2021.
ISSN: ESSN 1083-351X
PubMed: 34688666
DOI: 10.1016/J.JBC.2021.101322
Page generated: Tue Oct 8 17:58:51 2024

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