Atomistry » Platinum » PDB 5yky-7bpr » 7bpr
Atomistry »
  Platinum »
    PDB 5yky-7bpr »
      7bpr »

Platinum in PDB 7bpr: Crystal Structure of Human TEX101

Protein crystallography data

The structure of Crystal Structure of Human TEX101, PDB code: 7bpr was solved by M.Masutani, S.Sakurai, T.Shimizu, U.Ohto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.03 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.053, 49.480, 57.202, 81.70, 87.84, 61.41
R / Rfree (%) 19.1 / 23.5

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of Human TEX101 (pdb code 7bpr). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 6 binding sites of Platinum where determined in the Crystal Structure of Human TEX101, PDB code: 7bpr:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6;

Platinum binding site 1 out of 6 in 7bpr

Go back to Platinum Binding Sites List in 7bpr
Platinum binding site 1 out of 6 in the Crystal Structure of Human TEX101


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of Human TEX101 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt302

b:75.0
occ:0.75
CB A:CYS81 3.7 52.0 1.0
N A:ASP55 3.8 69.3 1.0
CB A:ALA58 3.9 64.2 1.0
CG A:ASP55 3.9 77.1 1.0
CB A:ASP55 4.0 69.9 1.0
N A:PRO83 4.1 59.9 1.0
OD1 A:ASP55 4.1 76.3 1.0
CA A:PRO83 4.1 59.7 1.0
OD2 A:ASP55 4.2 76.9 1.0
CA A:CYS54 4.2 56.5 1.0
CB A:CYS54 4.3 56.4 1.0
C A:ILE82 4.3 53.5 1.0
CB A:PRO83 4.4 64.2 1.0
CA A:ASP55 4.5 73.1 1.0
C A:CYS54 4.5 66.1 1.0
CD A:PRO83 4.5 58.0 1.0
C A:CYS81 4.6 42.7 1.0
N A:ILE82 4.6 47.1 1.0
O A:ILE82 4.7 47.4 1.0
O A:ASP55 4.7 85.6 1.0
SG A:CYS81 4.8 46.7 1.0
CA A:ILE82 4.8 51.0 1.0
CA A:CYS81 4.8 46.7 1.0
CG A:PRO83 5.0 64.6 1.0

Platinum binding site 2 out of 6 in 7bpr

Go back to Platinum Binding Sites List in 7bpr
Platinum binding site 2 out of 6 in the Crystal Structure of Human TEX101


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of Human TEX101 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt303

b:41.3
occ:0.55
OE1 A:GLN122 3.6 46.0 1.0
CD1 A:ILE91 3.8 33.5 1.0
CD A:GLN122 4.5 42.5 1.0
NE2 A:GLN122 4.6 37.9 1.0
CG2 A:ILE89 4.6 43.5 1.0
NZ A:LYS117 4.9 45.4 1.0

Platinum binding site 3 out of 6 in 7bpr

Go back to Platinum Binding Sites List in 7bpr
Platinum binding site 3 out of 6 in the Crystal Structure of Human TEX101


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Crystal Structure of Human TEX101 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt304

b:34.0
occ:0.90
O A:HOH413 3.4 42.0 1.0
N A:GLY70 3.6 36.1 1.0
N A:CYS185 3.7 29.7 1.0
C A:GLY99 3.8 31.6 1.0
N A:LEU100 3.8 30.9 1.0
CA A:GLY99 3.9 34.1 1.0
CB A:CYS185 4.0 31.1 1.0
SG A:CYS185 4.0 36.5 1.0
CD2 A:LEU100 4.1 26.8 1.0
O A:GLY99 4.2 29.9 1.0
O A:HOH445 4.2 29.3 1.0
CA A:GLY184 4.2 29.4 1.0
O A:CYS185 4.3 29.6 1.0
CA A:ALA69 4.3 34.4 1.0
CG A:LEU100 4.3 28.3 1.0
CA A:LEU100 4.4 29.4 1.0
CA A:CYS185 4.4 32.4 1.0
C A:ALA69 4.4 35.7 1.0
CA A:GLY70 4.5 37.7 1.0
C A:GLY184 4.5 31.2 1.0
CG2 A:THR142 4.5 36.7 1.0
O A:HOH404 4.7 38.1 1.0
C A:CYS185 4.8 32.5 1.0
CD A:PRO158 4.9 40.1 1.0
CB A:LEU100 5.0 29.4 1.0

Platinum binding site 4 out of 6 in 7bpr

Go back to Platinum Binding Sites List in 7bpr
Platinum binding site 4 out of 6 in the Crystal Structure of Human TEX101


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Crystal Structure of Human TEX101 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt301

b:33.2
occ:0.70
O B:HOH443 3.3 38.3 1.0
N B:GLY70 3.6 34.0 1.0
N B:CYS185 3.6 28.0 1.0
N B:LEU100 3.7 31.2 1.0
C B:GLY99 3.7 30.3 1.0
CA B:GLY99 3.8 32.5 1.0
CB B:CYS185 4.1 30.8 1.0
CD2 B:LEU100 4.1 29.5 1.0
O B:CYS185 4.1 28.6 1.0
O B:GLY99 4.2 31.1 1.0
O B:HOH437 4.3 39.3 1.0
CG B:LEU100 4.3 28.7 1.0
CA B:LEU100 4.3 30.6 1.0
CA B:GLY184 4.3 27.0 1.0
CA B:ALA69 4.3 30.0 1.0
SG B:CYS185 4.4 36.6 1.0
CA B:CYS185 4.4 27.6 1.0
CG2 B:THR142 4.4 27.3 1.0
C B:ALA69 4.4 28.6 1.0
CA B:GLY70 4.5 33.3 1.0
C B:GLY184 4.5 26.8 1.0
C B:CYS185 4.8 28.8 1.0
CB B:LEU100 4.9 27.5 1.0
OG1 B:THR142 4.9 29.2 1.0

Platinum binding site 5 out of 6 in 7bpr

Go back to Platinum Binding Sites List in 7bpr
Platinum binding site 5 out of 6 in the Crystal Structure of Human TEX101


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Crystal Structure of Human TEX101 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt302

b:52.2
occ:0.50
CB B:MET188 4.0 42.3 1.0
N B:ILE189 4.1 44.7 1.0
CA B:MET188 4.1 39.8 1.0
C B:MET188 4.6 40.7 1.0
CG B:MET188 4.7 48.9 1.0
O B:ILE189 4.8 44.2 1.0
CB B:ARG192 4.8 35.4 1.0

Platinum binding site 6 out of 6 in 7bpr

Go back to Platinum Binding Sites List in 7bpr
Platinum binding site 6 out of 6 in the Crystal Structure of Human TEX101


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Crystal Structure of Human TEX101 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt303

b:72.1
occ:0.50
CB B:CYS81 3.6 37.2 1.0
CB B:ALA58 3.7 49.4 1.0
N B:ASP55 3.9 51.8 1.0
N B:PRO83 4.0 44.0 1.0
CB B:ASP55 4.0 53.7 1.0
C B:ILE82 4.1 39.8 1.0
CA B:PRO83 4.2 48.0 1.0
CG B:ASP55 4.2 56.2 1.0
OD2 B:ASP55 4.2 59.4 1.0
C B:CYS81 4.3 41.0 1.0
N B:ILE82 4.3 38.6 1.0
O B:ILE82 4.5 38.5 1.0
O B:HOH401 4.5 55.0 1.0
CD B:PRO83 4.5 42.0 1.0
CA B:ILE82 4.5 42.1 1.0
CB B:CYS54 4.5 44.3 1.0
CA B:CYS81 4.6 36.0 1.0
CA B:CYS54 4.6 47.4 1.0
CA B:ASP55 4.6 50.9 1.0
O B:CYS81 4.7 40.2 1.0
CB B:PRO83 4.7 49.2 1.0
C B:CYS54 4.8 52.5 1.0
SG B:CYS81 4.8 38.4 1.0
O B:ASP55 4.8 55.0 1.0
OD1 B:ASP55 4.9 59.7 1.0
CA B:ALA58 4.9 47.7 1.0
OE2 B:GLU52 5.0 49.1 1.0

Reference:

M.Masutani, S.Sakurai, T.Shimizu, U.Ohto. Crystal Structure of TEX101, A Glycoprotein Essential For Male Fertility, Reveals the Presence of Tandemly Arranged LY6/Upar Domains. Febs Lett. 2020.
ISSN: ISSN 0014-5793
PubMed: 32608065
DOI: 10.1002/1873-3468.13875
Page generated: Thu Oct 10 11:49:36 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