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Bromine in PDB 7ta2: Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6

Protein crystallography data

The structure of Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6, PDB code: 7ta2 was solved by T.D.R.Vance, P.Yip, E.Jimenez, I.Uson, J.E.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.83 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 28.984, 46.522, 167.67, 90, 90, 90
R / Rfree (%) 20.1 / 25.5

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6 (pdb code 7ta2). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 10 binding sites of Bromine where determined in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6, PDB code: 7ta2:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 10 in 7ta2

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Bromine binding site 1 out of 10 in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br301

b:38.8
occ:0.59
 H A:TYR183 2.4 24.6 1.0
H A:GLY208 2.7 46.8 1.0
HA A:THR182 3.0 41.7 1.0
HD1 A:TYR183 3.2 32.4 1.0
N A:TYR183 3.2 20.5 1.0
HB A:THR182 3.4 44.9 1.0
N A:GLY208 3.5 39.0 1.0
HA2 A:GLY208 3.5 40.4 1.0
HB2 A:TYR183 3.6 34.0 1.0
CA A:THR182 3.7 34.7 1.0
O A:TYR183 3.8 25.8 1.0
HB2 A:GLU207 3.8 66.8 1.0
HG22 A:THR182 3.8 42.3 1.0
CB A:THR182 4.0 37.4 1.0
C A:THR182 4.0 29.9 1.0
CA A:GLY208 4.0 33.6 1.0
CD1 A:TYR183 4.1 27.0 1.0
CA A:TYR183 4.1 28.7 1.0
CB A:TYR183 4.2 28.4 1.0
HA A:GLU207 4.2 58.6 1.0
C A:TYR183 4.4 24.1 1.0
CG2 A:THR182 4.4 35.3 1.0
CB A:GLU207 4.5 55.7 1.0
HB3 A:GLU207 4.5 66.8 1.0
C A:GLU207 4.5 39.2 1.0
CA A:GLU207 4.6 48.8 1.0
CG A:TYR183 4.7 32.3 1.0
HA3 A:GLY208 4.7 40.4 1.0
O A:ILE181 4.8 31.0 1.0
HG21 A:THR182 4.8 42.3 1.0
C A:GLY208 5.0 35.5 1.0

Bromine binding site 2 out of 10 in 7ta2

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Bromine binding site 2 out of 10 in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br302

b:43.4
occ:0.61
 H A:ASP202 2.3 26.5 1.0
HB2 A:ASP202 2.9 33.0 1.0
N A:ASP202 3.1 22.1 1.0
HA A:ARG201 3.4 26.3 1.0
HB2 A:ARG201 3.4 24.6 1.0
CB A:ASP202 3.6 27.5 1.0
CG A:ASP202 3.7 38.6 1.0
CA A:ASP202 4.0 32.7 1.0
OD2 A:ASP202 4.0 49.3 1.0
CA A:ARG201 4.0 21.9 1.0
C A:ARG201 4.1 19.6 1.0
CB A:ARG201 4.1 20.5 1.0
OD1 A:ASP202 4.2 37.4 1.0
HB3 A:ASP202 4.4 33.0 1.0
HB3 A:ARG201 4.5 24.6 1.0
O A:HOH458 4.6 37.1 1.0
HA A:ASP202 4.6 39.2 1.0
O A:ASP202 4.9 33.6 1.0
C A:ASP202 4.9 25.2 1.0

Bromine binding site 3 out of 10 in 7ta2

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Bromine binding site 3 out of 10 in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br303

b:39.3
occ:0.50
 H A:LYS178 2.6 40.9 1.0
HZ A:PHE133 2.9 46.4 1.0
HA A:PRO177 3.1 38.9 1.0
N A:LYS178 3.4 34.1 1.0
HG3 A:LYS178 3.5 77.0 1.0
HB2 A:LYS178 3.6 54.7 1.0
HB3 A:PRO177 3.7 39.5 1.0
CZ A:PHE133 3.7 38.7 1.0
CA A:PRO177 3.9 32.4 1.0
C A:PRO177 4.2 32.1 1.0
CB A:LYS178 4.2 45.6 1.0
HE1 A:PHE133 4.2 41.2 1.0
CB A:PRO177 4.3 32.9 1.0
HG2 A:GLU179 4.3 88.8 1.0
CG A:LYS178 4.3 64.1 1.0
CE1 A:PHE133 4.4 34.4 1.0
CA A:LYS178 4.4 40.0 1.0
H A:GLU179 4.5 56.6 1.0
HE2 A:PHE133 4.6 47.4 1.0
CE2 A:PHE133 4.6 39.5 1.0
HE3 A:LYS178 4.7 97.8 1.0
HD2 A:LYS178 4.7 79.6 1.0
HB2 A:PRO177 4.8 39.5 1.0

Bromine binding site 4 out of 10 in 7ta2

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Bromine binding site 4 out of 10 in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br304

b:48.7
occ:0.63
 H A:ARG205 2.7 45.1 1.0
HD2 A:PRO204 2.8 33.4 1.0
HG2 A:MET203 2.8 52.7 1.0
HA A:MET203 2.9 40.4 1.0
HB2 A:ARG205 2.9 37.3 1.0
HD3 A:ARG205 2.9 54.2 1.0
HG3 A:ARG205 3.2 45.1 1.0
HG3 A:MET203 3.2 52.7 1.0
CG A:MET203 3.4 43.9 1.0
CD A:PRO204 3.5 27.8 1.0
N A:ARG205 3.6 37.6 1.0
CA A:MET203 3.6 33.7 1.0
CG A:ARG205 3.6 37.5 1.0
CB A:ARG205 3.6 31.1 1.0
CD A:ARG205 3.7 45.2 1.0
N A:PRO204 3.7 27.7 1.0
C A:MET203 3.7 25.8 1.0
HH12 A:ARG201 3.7 58.9 1.0
HD3 A:PRO204 3.8 33.4 1.0
HD2 A:ARG205 4.1 54.2 1.0
CB A:MET203 4.1 36.2 1.0
CA A:ARG205 4.3 33.6 1.0
NH1 A:ARG201 4.4 49.1 1.0
O A:MET203 4.4 29.9 1.0
HB3 A:ARG205 4.4 37.3 1.0
C A:PRO204 4.6 39.0 1.0
HG2 A:ARG205 4.6 45.1 1.0
HH11 A:ARG201 4.6 58.9 1.0
CA A:PRO204 4.6 33.7 1.0
HB2 A:MET203 4.7 43.4 1.0
H A:ALA206 4.7 31.4 1.0
O A:ASP202 4.7 33.6 1.0
HB3 A:MET203 4.7 43.4 1.0
HH11 A:ARG205 4.8 82.5 1.0
CG A:PRO204 4.8 37.5 1.0
NE A:ARG205 4.8 59.6 1.0
N A:MET203 4.9 26.2 1.0
HA A:ARG205 4.9 40.4 1.0
HG2 A:PRO204 4.9 45.0 1.0
HH22 A:ARG201 5.0 51.5 1.0
SD A:MET203 5.0 56.8 1.0

Bromine binding site 5 out of 10 in 7ta2

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Bromine binding site 5 out of 10 in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br305

b:43.3
occ:0.56
 H A:ALA121 2.4 36.5 1.0
HE A:ARG136 3.1 72.2 1.0
HA A:GLU120 3.1 38.5 1.0
HG2 A:ARG136 3.3 53.5 1.0
N A:ALA121 3.3 30.5 1.0
HB3 A:ALA121 3.4 34.3 1.0
HH21 A:ARG136 3.4 64.7 1.0
NE A:ARG136 3.4 60.1 1.0
HB2 A:ASN72 3.5 38.9 1.0
H A:ASN72 3.6 45.6 1.0
HB3 A:GLU120 3.6 37.9 1.0
N A:ASN72 3.7 38.0 1.0
HA A:ASN72 3.7 40.8 1.0
NH2 A:ARG136 3.8 53.9 1.0
HG2 A:GLU120 3.8 48.8 1.0
CZ A:ARG136 3.8 67.6 1.0
CA A:GLU120 3.8 32.1 1.0
HB2 A:ALA121 3.9 34.3 1.0
CB A:ALA121 4.0 28.6 1.0
HA A:ILE71 4.0 40.2 1.0
C A:ILE71 4.0 34.5 1.0
CA A:ASN72 4.0 34.0 1.0
CG A:ARG136 4.0 44.6 1.0
O A:HOH416 4.0 28.1 1.0
C A:GLU120 4.1 34.0 1.0
CB A:GLU120 4.1 31.6 1.0
CA A:ALA121 4.2 29.5 1.0
CB A:ASN72 4.2 32.4 1.0
HG3 A:ARG136 4.2 53.5 1.0
CD A:ARG136 4.3 47.4 1.0
HH22 A:ARG136 4.4 64.7 1.0
CG A:GLU120 4.5 40.7 1.0
O A:ILE71 4.5 33.1 1.0
HD3 A:ARG136 4.5 56.8 1.0
CA A:ILE71 4.5 33.5 1.0
O A:GLU70 4.5 46.7 1.0
O A:ALA121 4.6 29.2 1.0
NH1 A:ARG136 4.8 35.1 1.0
HB3 A:ASN72 4.8 38.9 1.0
C A:ALA121 4.9 32.6 1.0
HB1 A:ALA121 4.9 34.3 1.0
O A:LYS119 4.9 29.4 1.0
HG3 A:GLU120 4.9 48.8 1.0
HA A:ALA121 5.0 35.5 1.0

Bromine binding site 6 out of 10 in 7ta2

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Bromine binding site 6 out of 10 in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br306

b:55.3
occ:0.54
 HD3 A:ARG237 2.8 39.5 1.0
HG11 A:VAL227 3.0 27.9 1.0
HH11 A:ARG237 3.3 76.7 1.0
HG3 A:PRO234 3.4 43.9 1.0
HG21 A:VAL227 3.6 28.6 1.0
CD A:ARG237 3.6 32.9 1.0
HD2 A:ARG237 3.7 39.5 1.0
HE2 A:LYS229 3.8 72.3 1.0
HG2 A:PRO234 3.9 43.9 1.0
CG1 A:VAL227 3.9 23.2 1.0
NH1 A:ARG237 3.9 63.9 1.0
HG13 A:VAL227 3.9 27.9 1.0
HB3 A:PRO234 3.9 34.9 1.0
CG A:PRO234 4.0 36.6 1.0
HZ3 A:LYS186 4.0 62.8 1.0
O A:HOH451 4.1 38.9 1.0
NE A:ARG237 4.3 33.3 1.0
HH12 A:ARG237 4.3 76.7 1.0
CG2 A:VAL227 4.4 23.8 1.0
HG22 A:VAL227 4.4 28.6 1.0
CZ A:ARG237 4.4 48.1 1.0
CB A:PRO234 4.4 29.1 1.0
HZ1 A:LYS229 4.5 95.5 1.0
HG12 A:VAL227 4.5 27.9 1.0
HZ1 A:LYS186 4.5 62.8 1.0
CE A:LYS229 4.6 60.3 1.0
HG2 A:ARG237 4.6 35.4 1.0
HE3 A:LYS229 4.6 72.3 1.0
NZ A:LYS186 4.7 52.4 1.0
CB A:VAL227 4.7 27.8 1.0
CG A:ARG237 4.7 29.5 1.0
HB2 A:PRO234 4.8 34.9 1.0
HD13 A:LEU197 4.9 60.5 1.0
NZ A:LYS229 5.0 79.6 1.0
HE A:ARG237 5.0 40.0 1.0

Bromine binding site 7 out of 10 in 7ta2

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Bromine binding site 7 out of 10 in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br307

b:46.9
occ:0.58
 HD1 A:HIS80 2.6 41.6 1.0
HG3 A:ARG76 3.2 55.8 1.0
HA A:SER77 3.2 37.8 1.0
HB2 A:HIS80 3.3 30.5 1.0
ND1 A:HIS80 3.4 34.6 1.0
HE1 A:PHE31 3.7 41.8 1.0
HB3 A:HIS80 3.8 30.5 1.0
CB A:HIS80 3.9 25.4 1.0
CA A:SER77 4.0 31.5 1.0
CG A:ARG76 4.1 46.5 1.0
N A:SER77 4.1 28.4 1.0
CG A:HIS80 4.1 37.6 1.0
HB2 A:ARG76 4.1 40.5 1.0
OG A:SER77 4.2 46.4 1.0
C A:ARG76 4.3 29.5 1.0
HD2 A:ARG76 4.4 55.9 1.0
H A:SER77 4.4 34.1 1.0
O A:ARG76 4.4 32.1 1.0
HD1 A:PHE31 4.4 42.4 1.0
CE1 A:PHE31 4.5 34.9 1.0
CE1 A:HIS80 4.5 33.3 1.0
CB A:ARG76 4.6 33.8 1.0
HE A:ARG76 4.6 54.1 1.0
CD A:ARG76 4.7 46.5 1.0
HE1 A:HIS80 4.7 40.0 1.0
HG2 A:ARG76 4.7 55.8 1.0
CB A:SER77 4.7 29.9 1.0
HG A:SER77 4.9 55.7 1.0
CD1 A:PHE31 4.9 35.3 1.0
NE A:ARG76 4.9 45.1 1.0

Bromine binding site 8 out of 10 in 7ta2

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Bromine binding site 8 out of 10 in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br308

b:39.4
occ:0.49
 H A:ARG193 2.5 33.2 1.0
HB3 A:ARG193 3.3 31.2 1.0
HA A:LEU192 3.3 35.0 1.0
N A:ARG193 3.3 27.7 1.0
HD22 A:LEU192 3.6 46.4 1.0
O A:ARG193 3.9 26.1 1.0
CB A:ARG193 3.9 26.0 1.0
HB2 A:ARG193 4.0 31.2 1.0
CA A:ARG193 4.1 28.8 1.0
CA A:LEU192 4.1 29.1 1.0
C A:LEU192 4.2 25.4 1.0
HD23 A:LEU192 4.3 46.4 1.0
C A:ARG193 4.4 23.2 1.0
O A:GLY191 4.4 25.4 1.0
CD2 A:LEU192 4.4 38.6 1.0
HB3 A:LEU192 4.7 32.8 1.0
CB A:LEU192 4.9 27.3 1.0
HA A:ARG193 5.0 34.5 1.0

Bromine binding site 9 out of 10 in 7ta2

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Bromine binding site 9 out of 10 in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br309

b:91.0
occ:0.74
 HG11 A:VAL102 2.4 106.4 1.0
H A:SER99 2.7 75.0 1.0
CG1 A:VAL102 2.9 88.7 1.0
HG13 A:VAL102 2.9 106.4 1.0
HG12 A:VAL102 3.0 106.4 1.0
HA2 A:GLY98 3.3 99.1 1.0
N A:SER99 3.4 62.5 1.0
HD21 A:LEU93 3.7 93.8 1.0
HB3 A:SER99 3.9 99.0 1.0
CA A:GLY98 3.9 82.6 1.0
HA3 A:GLY98 3.9 99.1 1.0
O A:SER99 4.0 77.5 1.0
C A:GLY98 4.2 75.1 1.0
CB A:VAL102 4.3 82.9 1.0
CA A:SER99 4.4 66.3 1.0
CB A:SER99 4.4 82.5 1.0
HB2 A:SER99 4.5 99.0 1.0
CD2 A:LEU93 4.5 78.2 1.0
HB A:VAL102 4.6 99.4 1.0
HG21 A:VAL102 4.6 92.9 1.0
HD23 A:LEU93 4.6 93.8 1.0
C A:SER99 4.7 81.9 1.0
HB2 A:ALA103 4.7 82.3 1.0
HD11 A:LEU93 4.8 88.0 1.0
CG2 A:VAL102 4.9 77.4 1.0
H A:ALA103 4.9 92.4 1.0
HG22 A:VAL102 4.9 92.9 1.0

Bromine binding site 10 out of 10 in 7ta2

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Bromine binding site 10 out of 10 in the Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of the Human Sperm-Expressed Surface Protein SPACA6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br310

b:62.7
occ:1.00
 HH22 A:ARG212 2.5 51.8 1.0
HH12 A:ARG212 2.6 50.4 1.0
HD23 A:LEU210 3.2 65.1 1.0
HB3 A:LEU210 3.2 43.5 1.0
NH2 A:ARG212 3.3 43.1 1.0
NH1 A:ARG212 3.4 42.0 1.0
HB2 A:LEU210 3.7 43.5 1.0
CZ A:ARG212 3.8 48.1 1.0
HD22 A:LEU210 3.8 65.1 1.0
CB A:LEU210 3.9 36.2 1.0
CD2 A:LEU210 3.9 54.2 1.0
HH21 A:ARG212 4.0 51.8 1.0
HH11 A:ARG212 4.1 50.4 1.0
HE1 A:TYR209 4.1 38.3 1.0
CG A:LEU210 4.6 45.0 1.0
CE1 A:TYR209 4.6 31.9 1.0
H A:LEU210 4.7 34.8 1.0
HD21 A:LEU210 4.7 65.1 1.0
O A:LEU210 4.9 34.1 1.0
HD1 A:TYR209 5.0 44.2 1.0

Reference:

T.D.R.Vance, P.Yip, E.Jimenez, S.Li, D.Gawol, J.Byrnes, I.Uson, A.Ziyyat, J.E.Lee. SPACA6 Ectodomain Structure Reveals A Conserved Superfamily of Gamete Fusion-Associated Proteins. Commun Biol V. 5 984 2022.
ISSN: ESSN 2399-3642
PubMed: 36115925
DOI: 10.1038/S42003-022-03883-Y
Page generated: Tue Apr 4 17:40:09 2023

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