Chlorine in PDB 7rgf: Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface

Protein crystallography data

The structure of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface, PDB code: 7rgf was solved by K.M.Goodman, S.Mannepalli, B.Honig, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.16 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.944, 103.948, 200.592, 90, 90, 90
R / Rfree (%) 19.6 / 24.1

Other elements in 7rgf:

The structure of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface also contains other interesting chemical elements:

Calcium (Ca) 18 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface (pdb code 7rgf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface, PDB code: 7rgf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 7rgf

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Chlorine binding site 1 out of 7 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl514

b:56.4
occ:1.00
 N A:VAL37 3.1 51.6 1.0
N A:VAL48 3.4 50.8 1.0
CA A:GLN36 3.7 53.7 1.0
CA A:ARG47 3.8 54.8 1.0
CB A:VAL37 3.9 48.3 1.0
CG2 A:VAL37 3.9 46.5 1.0
C A:GLN36 3.9 53.7 1.0
CB A:GLN36 3.9 56.8 1.0
CA A:VAL37 4.1 47.9 1.0
C A:ARG47 4.1 56.6 1.0
CB A:VAL48 4.2 46.4 1.0
CB A:ARG47 4.2 52.3 1.0
CG A:GLN36 4.3 63.1 1.0
CA A:VAL48 4.3 47.7 1.0
CG2 A:VAL48 4.3 45.4 1.0
O A:VAL48 4.5 53.4 1.0
O A:VAL37 4.6 59.8 1.0
O A:LEU35 4.8 55.0 1.0
O A:PHE46 4.8 57.8 1.0
C A:VAL37 4.9 52.5 1.0
N A:ARG47 4.9 52.7 1.0
C A:VAL48 4.9 52.9 1.0
N A:GLN36 5.0 50.8 1.0

Chlorine binding site 2 out of 7 in 7rgf

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Chlorine binding site 2 out of 7 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl515

b:75.0
occ:1.00
 N A:TYR141 3.3 64.4 1.0
CG2 A:VAL153 3.5 64.1 1.0
CA A:SER140 3.6 72.5 1.0
CB A:VAL153 3.8 67.0 1.0
CG1 A:VAL153 3.8 67.5 1.0
CB A:SER140 3.9 78.5 1.0
O A:TYR141 3.9 63.3 1.0
C A:SER140 4.0 64.2 1.0
CA A:TYR141 4.3 64.0 1.0
CB A:TYR141 4.5 60.0 1.0
CD1 A:LEU161 4.5 65.1 1.0
C A:TYR141 4.6 63.2 1.0
O A:SER139 4.6 72.8 1.0
N A:SER140 4.8 65.7 1.0
CD1 A:TYR141 4.9 56.8 1.0

Chlorine binding site 3 out of 7 in 7rgf

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Chlorine binding site 3 out of 7 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl516

b:74.3
occ:1.00
 NH1 A:ARG33 3.0 55.2 1.0
N A:ASP26 3.3 66.2 1.0
CD2 A:LEU25 3.6 61.4 1.0
OD2 A:ASP26 3.7 97.5 1.0
CG A:ARG33 3.8 55.2 1.0
CG A:ASP26 3.9 94.7 1.0
CB A:ASP26 4.0 84.1 1.0
CD A:ARG33 4.0 56.5 1.0
CA A:LEU25 4.0 56.0 1.0
CZ A:ARG33 4.2 56.4 1.0
C A:LEU25 4.2 62.3 1.0
CA A:ASP26 4.2 72.3 1.0
CB A:LEU25 4.3 55.5 1.0
CB A:SER29 4.5 77.3 1.0
NE A:ARG33 4.5 60.0 1.0
CG A:LEU25 4.6 60.0 1.0
OD1 A:ASP26 4.6 97.8 1.0
O A:ASP26 4.7 68.7 1.0

Chlorine binding site 4 out of 7 in 7rgf

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Chlorine binding site 4 out of 7 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl513

b:48.8
occ:1.00
 N B:THR411 3.4 45.4 1.0
CD B:ARG410 3.8 55.7 1.0
O B:THR411 3.9 54.2 1.0
CB B:THR411 4.1 58.9 1.0
CA B:THR411 4.2 54.2 1.0
CA B:ARG410 4.2 46.4 1.0
C B:ARG410 4.3 45.0 1.0
NE B:ARG410 4.4 62.2 1.0
OG1 B:THR411 4.5 61.9 1.0
C B:THR411 4.5 53.2 1.0
CE1 B:PHE413 4.6 62.7 1.0
CG B:ARG410 4.6 51.1 1.0
CB B:ARG410 4.9 47.9 1.0
O B:HIS409 5.0 44.4 1.0

Chlorine binding site 5 out of 7 in 7rgf

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Chlorine binding site 5 out of 7 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl514

b:64.8
occ:1.00
 NH2 B:ARG261 3.2 49.6 1.0
NH1 B:ARG261 3.9 58.8 1.0
CZ B:ARG261 4.0 57.9 1.0
CB B:SER251 4.1 44.3 1.0
N B:PHE252 4.2 56.9 1.0
CB B:PHE252 4.6 57.4 1.0
O B:PHE252 4.7 59.4 1.0
CA B:SER251 4.8 54.9 1.0
OG B:SER251 4.8 61.0 1.0
CD2 B:PHE252 4.9 59.0 1.0
CA B:PHE252 4.9 51.8 1.0

Chlorine binding site 6 out of 7 in 7rgf

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Chlorine binding site 6 out of 7 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl515

b:69.3
occ:1.00
 N B:TYR141 3.3 61.1 1.0
CA B:SER140 3.6 66.3 1.0
CB B:SER140 3.7 68.9 1.0
CG2 B:VAL153 3.8 62.4 1.0
O B:TYR141 3.9 60.4 1.0
CB B:VAL153 3.9 61.4 1.0
C B:SER140 4.0 61.9 1.0
CG1 B:VAL153 4.0 64.8 1.0
CD1 B:LEU161 4.1 63.2 1.0
CA B:TYR141 4.3 54.2 1.0
CB B:TYR141 4.6 50.9 1.0
C B:TYR141 4.6 57.3 1.0
O B:SER139 4.7 70.7 1.0
N B:SER140 4.8 65.5 1.0
OG B:SER140 5.0 73.1 1.0

Chlorine binding site 7 out of 7 in 7rgf

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Chlorine binding site 7 out of 7 in the Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Protocadherin GAMMAC4 EC1-4 Crystal Structure Disrupted Trans Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl516

b:74.2
occ:1.00
 N B:VAL323 3.3 52.2 1.0
NH2 B:ARG410 3.4 56.9 1.0
NH1 B:ARG410 3.6 55.5 1.0
CA B:THR322 3.7 51.7 1.0
O B:ILE321 4.0 48.6 1.0
C B:THR322 4.0 52.9 1.0
CZ B:ARG410 4.0 59.1 1.0
CG2 B:THR322 4.1 59.7 1.0
O B:VAL323 4.2 56.0 1.0
CA B:VAL323 4.2 56.3 1.0
CB B:THR322 4.4 56.7 1.0
CB B:VAL323 4.4 55.0 1.0
C B:VAL323 4.5 63.9 1.0
N B:THR322 4.7 44.5 1.0
OG1 B:THR322 4.7 67.8 1.0
C B:ILE321 4.7 46.3 1.0
CG2 B:VAL323 4.8 51.1 1.0

Reference:

K.M.Goodman, P.S.Katsamba, R.Rubinstein, G.Ahlsen, F.Bahna, S.Mannepalli, H.Dan, R.V.Sampogna, L.Shapiro, B.Honig. How Clustered Protocadherin Binding Specificity Is Tuned For Neuronal Self-/Nonself-Recognition. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35253643
DOI: 10.7554/ELIFE.72416
Page generated: Tue Jul 30 03:36:13 2024

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