Calcium in PDB 4i9x: Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2

Protein crystallography data

The structure of Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2, PDB code: 4i9x was solved by I.Nemcovicova, D.M.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.83 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.916, 97.043, 141.422, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 27.4

Other elements in 4i9x:

The structure of Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2 (pdb code 4i9x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2, PDB code: 4i9x:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4i9x

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Calcium binding site 1 out of 4 in the Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:93.5
occ:1.00
 NE2 A:HIS122 2.8 53.8 1.0
OG1 B:THR191 3.0 52.7 1.0
N B:ALA58 3.3 52.2 1.0
CE1 A:HIS122 3.5 49.8 1.0
CG1 B:VAL57 3.7 48.3 1.0
CG B:GLU61 3.7 62.4 1.0
CA B:VAL57 3.8 45.5 1.0
CG B:PRO190 3.9 40.7 1.0
CD2 A:HIS122 4.0 49.6 1.0
CB B:ALA58 4.0 52.6 1.0
OE2 B:GLU61 4.0 68.9 1.0
CG2 B:ILE213 4.0 46.7 1.0
CG2 B:THR191 4.0 45.5 1.0
C B:VAL57 4.0 51.2 1.0
CB B:THR191 4.1 46.5 1.0
CD B:GLU61 4.1 63.7 1.0
CA B:ALA58 4.2 54.7 1.0
CB B:VAL57 4.3 46.5 1.0
NH2 B:ARG194 4.3 65.7 1.0
CD B:PRO190 4.4 42.3 1.0
N B:THR191 4.5 48.8 1.0
CB B:GLU61 4.6 57.0 1.0
O B:LEU56 4.7 41.5 1.0
OG B:SER189 4.7 38.4 1.0
CB B:ILE213 4.7 50.6 1.0
ND1 A:HIS122 4.8 47.6 1.0
CG2 B:VAL57 4.8 43.5 1.0
CB B:PRO190 4.8 42.3 1.0
CA B:THR191 4.9 47.0 1.0
CG1 B:ILE213 5.0 49.1 1.0
O B:ALA58 5.0 59.5 1.0
N B:VAL57 5.0 43.2 1.0

Calcium binding site 2 out of 4 in 4i9x

Go back to Calcium Binding Sites List in 4i9x
Calcium binding site 2 out of 4 in the Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:65.4
occ:1.00
 OE1 B:GLU142 2.7 27.6 1.0
O B:MSE140 2.8 39.9 1.0
NE B:ARG82 3.0 34.7 1.0
O B:ARG80 3.3 32.5 1.0
NH2 B:ARG82 3.4 41.0 1.0
N B:ARG82 3.5 33.0 1.0
C B:MSE140 3.5 37.8 1.0
CD B:GLU142 3.6 27.1 1.0
CZ B:ARG82 3.6 37.0 1.0
C B:ARG80 3.7 30.0 1.0
CG B:ARG82 3.8 35.0 1.0
CG B:ARG80 3.8 28.6 1.0
C B:ALA81 3.9 34.7 1.0
CD B:ARG80 3.9 31.2 1.0
CB B:ARG82 3.9 31.7 1.0
CD B:ARG82 4.0 33.2 1.0
CA B:ALA81 4.0 35.4 1.0
NH1 B:ARG80 4.0 37.2 1.0
CB B:MSE140 4.0 40.6 1.0
N B:ALA81 4.0 31.3 1.0
N B:TYR141 4.1 38.0 1.0
CB B:GLU142 4.1 31.3 1.0
N B:GLU142 4.2 35.2 1.0
CG B:GLU142 4.2 29.2 1.0
CB B:ARG80 4.2 28.0 1.0
CA B:ARG82 4.3 33.5 1.0
CA B:TYR141 4.3 37.1 1.0
CA B:MSE140 4.4 39.9 1.0
NE B:ARG80 4.5 31.6 1.0
OE2 B:GLU142 4.5 28.4 1.0
C B:TYR141 4.5 38.1 1.0
CZ B:ARG80 4.5 32.9 1.0
O B:ALA81 4.6 39.0 1.0
CA B:ARG80 4.7 28.5 1.0
CA B:GLU142 4.8 33.9 1.0
NH1 B:ARG82 4.9 38.6 1.0

Calcium binding site 3 out of 4 in 4i9x

Go back to Calcium Binding Sites List in 4i9x
Calcium binding site 3 out of 4 in the Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:74.4
occ:1.00
 O D:ASP102 2.8 38.7 1.0
N D:GLY100 3.0 35.5 1.0
C D:THR130 3.1 40.1 1.0
O D:THR130 3.2 42.4 1.0
CA D:TYR99 3.4 39.6 1.0
N D:THR131 3.4 39.8 1.0
O D:LYS98 3.4 42.2 1.0
SG D:CYS116 3.5 46.0 1.0
SG D:CYS129 3.6 46.1 1.0
C D:TYR99 3.6 41.6 1.0
CA D:THR130 3.7 39.2 1.0
C D:ASP102 3.7 39.4 1.0
N D:ASP102 3.7 39.9 1.0
CA D:THR131 3.8 35.3 1.0
N D:GLN101 3.8 38.4 1.0
N D:THR130 3.9 38.7 1.0
CA D:GLY100 3.9 34.5 1.0
CB D:CYS129 4.1 39.5 1.0
C D:CYS129 4.1 40.1 1.0
C D:LYS98 4.1 41.0 1.0
N D:TYR99 4.1 40.3 1.0
CD1 D:TYR99 4.2 38.9 1.0
C D:GLY100 4.2 39.1 1.0
CG2 D:THR131 4.2 31.9 1.0
CA D:ASP102 4.3 40.4 1.0
O D:CYS129 4.3 45.0 1.0
CB D:TYR103 4.4 34.4 1.0
C D:GLN101 4.4 42.1 1.0
CB D:TYR99 4.5 36.8 1.0
CB D:THR131 4.7 35.7 1.0
N D:TYR103 4.7 36.4 1.0
CA D:GLN101 4.7 42.5 1.0
CA D:CYS129 4.7 39.8 1.0
O D:TYR99 4.8 38.3 1.0
CG D:TYR99 4.8 37.7 1.0
CA D:TYR103 4.9 36.6 1.0
C D:THR131 4.9 38.7 1.0

Calcium binding site 4 out of 4 in 4i9x

Go back to Calcium Binding Sites List in 4i9x
Calcium binding site 4 out of 4 in the Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:92.5
occ:1.00
 O D:ARG115 2.8 35.6 1.0
OH D:TYR103 2.9 39.6 1.0
O A:ASP37 3.0 42.0 1.0
O A:HOH436 3.0 43.3 1.0
OG1 D:THR117 3.0 38.8 1.0
OD1 D:ASN134 3.4 40.6 1.0
N D:THR117 3.5 37.8 1.0
N A:ALA39 3.5 38.1 1.0
CE2 D:TYR103 3.6 39.8 1.0
C A:ASP37 3.6 40.8 1.0
CZ D:TYR103 3.7 39.5 1.0
CB A:ALA39 3.7 33.7 1.0
CG D:ASN134 3.7 43.4 1.0
CA A:ALA39 3.7 42.4 1.0
ND2 D:ASN134 3.8 45.6 1.0
C D:ARG115 3.9 39.6 1.0
C D:CYS116 4.0 39.3 1.0
C A:ILE38 4.0 41.1 1.0
N A:ASP37 4.1 38.6 1.0
CB D:THR117 4.1 38.4 1.0
CA D:CYS116 4.2 39.1 1.0
CA D:THR117 4.2 36.5 1.0
CA A:ASP37 4.2 38.7 1.0
N A:ILE38 4.4 36.3 1.0
CB A:ASP37 4.4 39.4 1.0
N D:CYS116 4.5 38.8 1.0
CA A:ILE38 4.5 37.8 1.0
O A:ILE38 4.6 38.4 1.0
CB D:ASN134 4.8 41.8 1.0
O D:CYS116 4.8 41.9 1.0
O D:HOH301 4.8 34.8 1.0
CD2 D:TYR103 4.9 35.8 1.0

Reference:

I.Nemcovicova, C.A.Benedict, D.M.Zajonc. Structure of Human Cytomegalovirus UL141 Binding to Trail-R2 Reveals Novel, Non-Canonical Death Receptor Interactions. Plos Pathog. V. 9 03224 2013.
ISSN: ISSN 1553-7366
PubMed: 23555243
DOI: 10.1371/JOURNAL.PPAT.1003224
Page generated: Sat Dec 12 04:51:32 2020

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