Atomistry » Samarium » PDB 5lxr-7ml9 » 5nsj
Atomistry »
  Samarium »
    PDB 5lxr-7ml9 »
      5nsj »

Samarium in PDB 5nsj: GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus

Protein crystallography data

The structure of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus, PDB code: 5nsj was solved by A.Shimon, O.Shani, R.Diskin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.32 / 2.25
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 128.024, 128.352, 45.966, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.9

Samarium Binding Sites:

The binding sites of Samarium atom in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus (pdb code 5nsj). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 7 binding sites of Samarium where determined in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus, PDB code: 5nsj:
Jump to Samarium binding site number: 1; 2; 3; 4; 5; 6; 7;

Samarium binding site 1 out of 7 in 5nsj

Go back to Samarium Binding Sites List in 5nsj
Samarium binding site 1 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 1 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm305

b:41.5
occ:1.00
 SM A:SM308 1.7 62.9 0.6
O A:HOH469 2.2 20.7 1.0
OE2 A:GLU137 2.8 79.4 1.0
CB A:ASN134 3.0 0.6 1.0
OE1 A:GLU137 3.3 77.8 1.0
CD A:GLU137 3.4 66.2 1.0
CB A:ASP136 3.6 70.1 1.0
CA A:ASN134 4.0 0.9 1.0
CG A:ASN134 4.1 0.9 1.0
ND2 A:ASN134 4.1 0.2 1.0
N A:ASP136 4.4 62.9 1.0
OD2 A:ASP136 4.4 83.8 1.0
CG A:ASP136 4.5 76.8 1.0
CA A:ASP136 4.6 63.2 1.0
C A:ASN134 4.7 88.3 1.0
CG A:GLU137 4.7 66.1 1.0
N A:GLN135 4.9 91.1 1.0
N A:GLU137 4.9 64.1 1.0

Samarium binding site 2 out of 7 in 5nsj

Go back to Samarium Binding Sites List in 5nsj
Samarium binding site 2 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 2 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm306

b:68.0
occ:1.00
 CA A:GLU137 3.2 64.5 1.0
O A:HOH466 3.3 29.3 1.0
N A:ARG138 3.4 34.5 1.0
NE1 A:TRP102 3.4 23.8 1.0
N A:LEU139 3.4 25.1 1.0
C A:GLU137 3.5 79.2 1.0
CB A:GLU137 3.6 70.6 1.0
CZ2 A:TRP102 3.6 28.2 1.0
CB A:LEU139 3.7 27.3 1.0
CG A:LEU139 3.7 25.0 1.0
CE2 A:TRP102 3.9 23.2 1.0
CD1 A:LEU139 4.1 25.3 1.0
CA A:LEU139 4.2 24.9 1.0
C A:ARG138 4.4 32.3 1.0
CA A:ARG138 4.4 30.9 1.0
O A:GLU137 4.4 67.1 1.0
O A:ASP136 4.4 70.2 1.0
CG A:ARG138 4.4 35.5 1.0
N A:GLU137 4.5 64.1 1.0
CD1 A:TRP102 4.6 26.0 1.0
CH2 A:TRP102 4.9 26.3 1.0
C A:ASP136 4.9 69.7 1.0
C A:LEU139 4.9 30.7 1.0
CB A:ARG138 5.0 28.1 1.0
CG A:GLU137 5.0 66.1 1.0

Samarium binding site 3 out of 7 in 5nsj

Go back to Samarium Binding Sites List in 5nsj
Samarium binding site 3 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 3 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm307

b:11.8
occ:0.07
 NE2 A:HIS155 2.4 34.4 1.0
CD2 A:HIS155 3.0 34.4 1.0
CE1 A:HIS156 3.3 27.6 1.0
NE2 A:HIS156 3.4 27.7 1.0
CE1 A:HIS155 3.6 36.5 1.0
ND1 A:HIS156 4.2 27.5 1.0
CG A:HIS155 4.2 33.9 1.0
CD2 A:HIS156 4.4 27.0 1.0
ND1 A:HIS155 4.5 36.3 1.0
CG A:HIS156 4.8 29.4 1.0

Samarium binding site 4 out of 7 in 5nsj

Go back to Samarium Binding Sites List in 5nsj
Samarium binding site 4 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 4 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm308

b:62.9
occ:0.63
 SM A:SM305 1.7 41.5 1.0
OE2 A:GLU137 2.3 79.4 1.0
CB A:ASN134 2.7 0.6 1.0
O A:HOH469 3.1 20.7 1.0
ND2 A:ASN134 3.1 0.2 1.0
CD A:GLU137 3.4 66.2 1.0
CG A:ASN134 3.4 0.9 1.0
OE1 A:GLU137 3.9 77.8 1.0
CA A:ASN134 4.0 0.9 1.0
OD1 A:ASN134 4.6 0.0 1.0
CG A:GLU137 4.6 66.1 1.0
N A:ASN134 4.9 0.6 1.0
ND2 A:ASN133 4.9 68.8 1.0
O A:HOH422 4.9 23.3 1.0

Samarium binding site 5 out of 7 in 5nsj

Go back to Samarium Binding Sites List in 5nsj
Samarium binding site 5 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 5 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm305

b:31.9
occ:0.74
 OE2 A:GLU180 2.0 63.0 1.0
CB B:ASP136 2.8 38.4 1.0
OE1 B:GLU137 3.0 55.6 1.0
O B:HOH412 3.0 31.2 1.0
CD A:GLU180 3.1 64.1 1.0
OD2 B:ASP136 3.1 49.4 1.0
CG B:ASP136 3.4 50.9 1.0
OE2 B:GLU137 3.5 45.9 1.0
CD B:GLU137 3.6 41.9 1.0
CG A:GLU180 3.8 55.9 1.0
O A:HOH456 3.8 13.3 1.0
O A:CYS201 3.8 27.4 1.0
CB B:ASN134 3.9 45.5 1.0
OE1 A:GLU180 4.0 66.1 1.0
CA B:ASP136 4.1 45.6 1.0
N B:ASP136 4.3 53.6 1.0
ND1 A:HIS204 4.6 25.4 1.0
OD1 B:ASP136 4.6 55.6 1.0
O A:SER203 4.7 29.4 1.0
N B:GLU137 4.7 42.9 1.0
ND2 B:ASN134 4.7 44.6 1.0
C B:ASP136 4.7 44.8 1.0
CE1 A:HIS204 4.8 26.6 1.0
CG B:ASN134 4.8 46.9 1.0
CA B:ASN134 4.9 50.3 1.0
C A:CYS201 5.0 23.4 1.0

Samarium binding site 6 out of 7 in 5nsj

Go back to Samarium Binding Sites List in 5nsj
Samarium binding site 6 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 6 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm306

b:0.5
occ:1.00
 O B:HOH489 2.5 35.5 1.0
CE1 B:HIS156 2.6 61.6 1.0
NE2 B:HIS155 2.8 72.3 1.0
ND1 B:HIS156 3.5 59.7 1.0
NE2 B:HIS156 3.5 61.2 1.0
CE1 B:HIS155 3.7 71.0 1.0
CD2 B:HIS155 3.8 69.0 1.0
O B:HOH514 4.3 23.4 1.0
CG B:HIS156 4.7 53.1 1.0
CD2 B:HIS156 4.7 54.4 1.0
O B:HOH555 4.7 77.4 1.0
ND1 B:HIS155 4.8 66.4 1.0
CG B:HIS155 4.9 65.7 1.0

Samarium binding site 7 out of 7 in 5nsj

Go back to Samarium Binding Sites List in 5nsj
Samarium binding site 7 out of 7 in the GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 7 of GP1 Receptor-Binding Domain From Whitewater Arroyo Mammarenavirus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm307

b:7.4
occ:0.15
 O B:HOH441 1.9 5.0 1.0
O B:HOH459 2.9 21.6 1.0
NE1 B:TRP102 3.5 36.0 1.0
CZ2 B:TRP102 3.7 21.8 1.0
CE2 B:TRP102 3.9 22.7 1.0
CD1 B:LEU139 4.2 23.8 1.0
CG B:LEU139 4.3 30.4 1.0
CA B:GLU137 4.3 33.8 1.0
CB B:LEU139 4.4 27.2 1.0
CB B:GLU137 4.4 31.6 1.0
CB B:ALA100 4.6 26.8 1.0
N B:ARG138 4.6 32.1 1.0
N B:LEU139 4.6 19.9 1.0
CD1 B:TRP102 4.7 38.7 1.0
C B:GLU137 4.7 35.3 1.0
CH2 B:TRP102 4.9 20.0 1.0
O B:PRO97 5.0 28.4 1.0

Reference:

A.Shimon, O.Shani, R.Diskin. Structural Basis For Receptor Selectivity By the Whitewater Arroyo Mammarenavirus. J. Mol. Biol. V. 429 2825 2017.
ISSN: ESSN 1089-8638
PubMed: 28736175
DOI: 10.1016/J.JMB.2017.07.011
Page generated: Thu Oct 10 13:57:02 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy