Calcium in PDB 7amk: Zebrafish Ret Cadherin Like Domains 1 to 4.

Enzymatic activity of Zebrafish Ret Cadherin Like Domains 1 to 4.

All present enzymatic activity of Zebrafish Ret Cadherin Like Domains 1 to 4.:
2.7.10.1;

Protein crystallography data

The structure of Zebrafish Ret Cadherin Like Domains 1 to 4., PDB code: 7amk was solved by A.G.Purkiss, N.Q.Mcdonald, K.M.Goodman, A.Narowtek, P.P.Knowles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.96 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.167, 70.499, 105.438, 105.41, 100.93, 100.25
R / Rfree (%) 22.5 / 26.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Zebrafish Ret Cadherin Like Domains 1 to 4. (pdb code 7amk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Zebrafish Ret Cadherin Like Domains 1 to 4., PDB code: 7amk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7amk

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Calcium binding site 1 out of 6 in the Zebrafish Ret Cadherin Like Domains 1 to 4.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Zebrafish Ret Cadherin Like Domains 1 to 4. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:22.0
occ:1.00
OD2 A:ASP253 2.3 22.2 1.0
OE1 A:GLU164 2.3 21.3 1.0
OD1 A:ASP216 2.3 27.8 1.0
OE1 A:GLU218 2.3 23.1 1.0
O A:HOH708 2.3 21.8 1.0
O A:HOH782 2.3 32.2 1.0
CG A:ASP253 3.1 21.8 1.0
CD A:GLU164 3.3 21.5 1.0
OD1 A:ASP253 3.3 22.0 1.0
CG A:ASP216 3.3 24.9 1.0
CD A:GLU218 3.5 24.1 1.0
OE2 A:GLU164 3.6 22.4 1.0
CA A:CA602 3.9 18.0 1.0
OD2 A:ASP216 4.1 25.3 1.0
O A:HOH726 4.1 24.9 1.0
ND2 A:ASN165 4.2 24.3 1.0
N A:ARG217 4.2 26.6 1.0
N A:GLU218 4.2 20.0 1.0
CA A:ASP216 4.3 19.3 1.0
CB A:ASP216 4.3 25.9 1.0
OD1 A:ASN165 4.3 23.1 1.0
CB A:GLU218 4.3 22.2 1.0
OE2 A:GLU218 4.4 23.6 1.0
ND2 A:ASN254 4.4 21.7 1.0
CG A:GLU218 4.4 23.3 1.0
C A:ASP216 4.5 22.3 1.0
CG A:GLU164 4.5 20.7 1.0
CB A:ASP253 4.6 25.7 1.0
O A:HOH784 4.6 36.6 1.0
CG A:ASN165 4.7 23.6 1.0
CB A:GLU164 4.9 19.5 1.0
CA A:GLU218 4.9 24.6 1.0

Calcium binding site 2 out of 6 in 7amk

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Calcium binding site 2 out of 6 in the Zebrafish Ret Cadherin Like Domains 1 to 4.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Zebrafish Ret Cadherin Like Domains 1 to 4. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:18.0
occ:1.00
OE2 A:GLU164 2.4 22.4 1.0
OD1 A:ASP287 2.4 21.3 1.0
O A:GLU251 2.4 19.5 1.0
OD1 A:ASP250 2.4 22.3 1.0
OD1 A:ASP253 2.5 22.0 1.0
OE2 A:GLU218 2.6 23.6 1.0
OE1 A:GLU218 2.9 23.1 1.0
CD A:GLU218 3.1 24.1 1.0
CG A:ASP253 3.2 21.8 1.0
CG A:ASP250 3.3 22.6 1.0
CD A:GLU164 3.4 21.5 1.0
CG A:ASP287 3.5 20.9 1.0
OD2 A:ASP250 3.5 24.0 1.0
C A:GLU251 3.6 20.1 1.0
OD2 A:ASP253 3.6 22.2 1.0
OE1 A:GLU164 3.7 21.3 1.0
ND2 A:ASN254 3.7 21.7 1.0
N A:GLU251 3.8 22.0 1.0
CA A:CA601 3.9 22.0 1.0
N A:ASP253 4.0 21.2 1.0
CB A:ASP287 4.2 17.8 1.0
OD2 A:ASP287 4.3 21.3 1.0
CA A:GLU251 4.4 23.8 1.0
CB A:ASP253 4.4 25.7 1.0
CA A:ASP287 4.4 17.5 1.0
CB A:ASP250 4.5 21.5 1.0
NH2 A:ARG217 4.6 22.7 1.0
N A:ASP252 4.6 26.5 1.0
CG A:GLU218 4.6 23.3 1.0
CA A:ASP253 4.7 25.2 1.0
CA A:ASP250 4.7 20.8 1.0
C A:ASP250 4.7 22.0 1.0
CG A:GLU164 4.7 20.7 1.0
NE A:ARG217 4.7 20.5 1.0
CA A:ASP252 4.8 23.0 1.0
CG A:GLU251 4.8 29.2 1.0
C A:ASP252 4.9 21.6 1.0
CB A:ARG217 4.9 18.9 1.0

Calcium binding site 3 out of 6 in 7amk

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Calcium binding site 3 out of 6 in the Zebrafish Ret Cadherin Like Domains 1 to 4.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Zebrafish Ret Cadherin Like Domains 1 to 4. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:13.2
occ:1.00
O A:ASN254 2.3 20.7 1.0
OD1 A:ASN299 2.3 18.7 1.0
OD1 A:ASP252 2.3 20.7 1.0
OD2 A:ASP287 2.4 21.3 1.0
OD2 A:ASP285 2.4 18.9 1.0
OD2 A:ASP363 2.5 20.9 1.0
OD1 A:ASP285 2.6 22.5 1.0
CG A:ASP285 2.8 18.2 1.0
CG A:ASP252 3.4 21.1 1.0
CG A:ASN299 3.4 18.2 1.0
CG A:ASP287 3.4 20.9 1.0
C A:ASN254 3.4 21.7 1.0
CG A:ASP363 3.7 25.2 1.0
CB A:ASP287 3.7 17.8 1.0
ND2 A:ASN299 3.9 18.7 1.0
OD2 A:ASP252 4.0 21.7 1.0
N A:ASN254 4.0 21.5 1.0
OD1 A:ASP363 4.2 21.8 1.0
CA A:ASN254 4.2 21.7 1.0
CB A:ASP285 4.3 17.9 1.0
CB A:ASP252 4.4 21.0 1.0
CB A:ASN254 4.5 20.7 1.0
N A:SER255 4.5 22.9 1.0
OD1 A:ASP287 4.5 21.3 1.0
CA A:ASP252 4.5 23.0 1.0
CB A:ASN299 4.6 18.8 1.0
CA A:SER255 4.6 24.3 1.0
N A:ASP253 4.7 21.2 1.0
C A:ASP252 4.7 21.6 1.0
N A:ASP287 4.8 17.8 1.0
CA A:ASP287 4.8 17.5 1.0
CB A:ASP363 4.9 22.4 1.0
CA A:ASN299 4.9 19.8 1.0
CD A:PRO256 4.9 21.8 1.0
C A:SER255 4.9 28.1 1.0
CD1 A:PHE366 5.0 24.8 1.0

Calcium binding site 4 out of 6 in 7amk

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Calcium binding site 4 out of 6 in the Zebrafish Ret Cadherin Like Domains 1 to 4.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Zebrafish Ret Cadherin Like Domains 1 to 4. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:20.1
occ:1.00
O B:ASN254 2.3 24.9 1.0
OD1 B:ASN299 2.3 37.3 1.0
OD2 B:ASP363 2.5 25.4 1.0
OD1 B:ASP252 2.5 26.6 1.0
OD2 B:ASP285 2.5 25.6 1.0
OD2 B:ASP287 2.6 25.5 1.0
OD1 B:ASP285 2.6 30.0 1.0
CG B:ASP285 2.9 28.7 1.0
CG B:ASP252 3.5 30.9 1.0
CG B:ASN299 3.5 31.1 1.0
C B:ASN254 3.5 25.3 1.0
CG B:ASP287 3.6 26.0 1.0
CG B:ASP363 3.6 29.1 1.0
CB B:ASP287 3.9 26.6 1.0
OD2 B:ASP252 4.0 30.6 1.0
N B:ASN254 4.0 25.3 1.0
ND2 B:ASN299 4.0 28.3 1.0
OD1 B:ASP363 4.2 28.3 1.0
CA B:ASN254 4.2 25.3 1.0
CB B:ASN254 4.4 25.6 1.0
CB B:ASP285 4.4 25.2 1.0
N B:SER255 4.6 25.4 1.0
CB B:ASP252 4.6 27.7 1.0
CA B:SER255 4.6 25.4 1.0
OD1 B:ASP287 4.6 26.3 1.0
CA B:ASP252 4.7 26.5 1.0
CB B:ASN299 4.7 36.8 1.0
CD B:PRO256 4.7 28.8 1.0
CB B:ASP363 4.8 28.0 1.0
C B:SER255 4.8 25.5 1.0
N B:ASP253 4.8 26.9 1.0
C B:ASP252 4.8 28.3 1.0
N B:ASP287 4.9 26.8 1.0
N B:PRO256 4.9 25.9 1.0
CD1 B:PHE366 4.9 29.0 1.0

Calcium binding site 5 out of 6 in 7amk

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Calcium binding site 5 out of 6 in the Zebrafish Ret Cadherin Like Domains 1 to 4.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Zebrafish Ret Cadherin Like Domains 1 to 4. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:22.1
occ:1.00
O B:GLU251 2.3 27.0 1.0
OD1 B:ASP287 2.3 26.3 1.0
OD1 B:ASP250 2.4 30.0 1.0
OE2 B:GLU218 2.4 32.2 1.0
OE2 B:GLU164 2.5 29.3 1.0
OD1 B:ASP253 2.6 26.2 1.0
OE1 B:GLU218 2.7 31.8 1.0
CD B:GLU218 2.9 32.4 1.0
CG B:ASP250 3.3 30.0 1.0
CG B:ASP287 3.4 26.0 1.0
CD B:GLU164 3.5 28.5 1.0
C B:GLU251 3.5 27.3 1.0
CG B:ASP253 3.6 26.2 1.0
OD2 B:ASP250 3.7 31.4 1.0
N B:GLU251 3.7 28.8 1.0
OE1 B:GLU164 3.7 28.9 1.0
ND2 B:ASN254 3.8 26.3 1.0
CA B:CA603 4.0 23.0 1.0
CB B:ASP287 4.0 26.6 1.0
OD2 B:ASP253 4.1 26.6 1.0
N B:ASP253 4.1 26.9 1.0
CA B:GLU251 4.2 28.2 1.0
OD2 B:ASP287 4.2 25.5 1.0
CA B:ASP287 4.3 35.2 1.0
CG B:GLU218 4.3 33.5 1.0
CB B:ASP250 4.5 28.5 1.0
N B:ASP252 4.6 27.1 1.0
NH2 B:ARG217 4.6 31.9 1.0
NE B:ARG217 4.6 29.0 1.0
C B:ASP250 4.6 31.5 1.0
CA B:ASP250 4.6 27.4 1.0
CB B:ARG217 4.7 29.6 1.0
CB B:ASP253 4.7 25.9 1.0
CB B:GLU251 4.8 32.6 1.0
CA B:ASP252 4.8 26.5 1.0
CG B:GLU164 4.8 27.2 1.0
CA B:ASP253 4.8 25.6 1.0
C B:ASP252 5.0 28.3 1.0

Calcium binding site 6 out of 6 in 7amk

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Calcium binding site 6 out of 6 in the Zebrafish Ret Cadherin Like Domains 1 to 4.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Zebrafish Ret Cadherin Like Domains 1 to 4. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:23.0
occ:1.00
OE1 B:GLU164 2.3 28.9 1.0
OD2 B:ASP253 2.4 26.6 1.0
O B:HOH720 2.4 17.1 1.0
OD1 B:ASP216 2.4 32.0 1.0
O B:HOH776 2.4 24.0 1.0
OE1 B:GLU218 2.4 31.8 1.0
CG B:ASP253 3.1 26.2 1.0
OD1 B:ASP253 3.1 26.2 1.0
CD B:GLU164 3.3 28.5 1.0
CG B:ASP216 3.3 30.8 1.0
CD B:GLU218 3.6 32.4 1.0
OE2 B:GLU164 3.7 29.3 1.0
O B:HOH777 3.7 26.2 1.0
CA B:CA602 4.0 22.1 1.0
OD2 B:ASP216 4.0 37.3 1.0
CB B:ASP216 4.1 30.0 1.0
CA B:ASP216 4.1 27.9 1.0
ND2 B:ASN165 4.1 30.7 1.0
N B:GLU218 4.2 29.7 1.0
N B:ARG217 4.2 27.1 1.0
ND2 B:ASN254 4.2 26.3 1.0
OD1 B:ASN165 4.3 34.4 1.0
CB B:GLU218 4.4 32.8 1.0
CG B:GLU218 4.4 33.5 1.0
C B:ASP216 4.5 29.5 1.0
CG B:GLU164 4.5 27.2 1.0
OE2 B:GLU218 4.5 32.2 1.0
CB B:ASP253 4.6 25.9 1.0
CG B:ASN165 4.6 31.0 1.0
CB B:GLU164 4.8 26.2 1.0
CA B:GLU218 4.9 33.5 1.0

Reference:

S.E.Adams, A.G.Purkiss, P.P.Knowles, A.Nans, D.C.Briggs, A.Borg, C.P.Earl, K.M.Goodman, A.Nawrotek, A.J.Borg, P.B.Mcintosh, F.M.Houghton, S.Kjaer, N.Q.Mcdonald. A Two-Site Flexible Clamp Mechanism For Ret-Gdnf-Gfr Alpha 1 Assembly Reveals Both Conformational Adaptation and Strict Geometric Spacing. Structure 2021.
ISSN: ISSN 0969-2126
PubMed: 33484636
DOI: 10.1016/J.STR.2020.12.012
Page generated: Sat Apr 17 14:05:59 2021

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