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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

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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

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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

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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

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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

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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

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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: Wed Dec 16 02:05:44 2020

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