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Calcium in PDB 7vut: Crystal Structure of ALLEYCAT10

Protein crystallography data

The structure of Crystal Structure of ALLEYCAT10, PDB code: 7vut was solved by J.R.H.Tame, I.V.Korendovych, E.Margheritis, K.Takahashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.50 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 27.313, 50.499, 88.246, 90, 90, 90
R / Rfree (%) 19.7 / 24.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of ALLEYCAT10 (pdb code 7vut). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of ALLEYCAT10, PDB code: 7vut:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7vut

Go back to Calcium Binding Sites List in 7vut
Calcium binding site 1 out of 6 in the Crystal Structure of ALLEYCAT10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of ALLEYCAT10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca101

b:4.5
occ:1.00
 O A:TYR24 2.3 5.8 1.0
OD1 A:ASP20 2.3 5.3 1.0
O A:HOH236 2.4 3.6 1.0
OD1 A:ASP18 2.4 3.6 1.0
OE1 A:GLU29 2.4 5.9 1.0
OE2 A:GLU29 2.5 7.9 1.0
OD1 A:ASN22 2.5 3.7 1.0
CD A:GLU29 2.8 7.4 1.0
CG A:ASP20 3.2 8.9 1.0
CG A:ASN22 3.3 3.7 1.0
C A:TYR24 3.4 3.7 1.0
CG A:ASP18 3.5 5.3 1.0
ND2 A:ASN22 3.6 6.9 1.0
OD2 A:ASP20 3.6 11.1 1.0
O A:HOH209 4.0 7.7 1.0
CA A:ASP18 4.1 6.8 1.0
N A:TYR24 4.2 2.7 1.0
N A:ASN22 4.2 4.2 1.0
CB A:ASP18 4.2 5.2 1.0
N A:ILE25 4.2 3.9 1.0
CG A:GLU29 4.3 5.0 1.0
N A:ASP20 4.3 9.8 1.0
CA A:ILE25 4.3 4.3 1.0
CA A:TYR24 4.3 2.9 1.0
OD2 A:ASP18 4.3 5.3 1.0
N A:GLY21 4.4 5.3 1.0
C A:ASP18 4.4 5.3 1.0
CB A:ASP20 4.5 5.1 1.0
CB A:ASN22 4.5 2.6 1.0
N A:SER26 4.5 4.0 1.0
C A:ASP20 4.7 5.0 1.0
N A:LYS19 4.7 7.5 1.0
CA A:ASP20 4.7 5.2 1.0
CB A:TYR24 4.7 3.1 1.0
O A:HOH257 4.8 4.7 1.0
CA A:ASN22 4.8 5.9 1.0
C A:ILE25 4.9 4.7 1.0
O A:ASP18 4.9 5.5 1.0
OG A:SER26 5.0 4.7 1.0

Calcium binding site 2 out of 6 in 7vut

Go back to Calcium Binding Sites List in 7vut
Calcium binding site 2 out of 6 in the Crystal Structure of ALLEYCAT10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of ALLEYCAT10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:4.1
occ:1.00
 OD1 A:ASP54 2.3 7.5 1.0
OD1 A:ASP56 2.3 5.7 1.0
O A:GLN60 2.3 4.0 1.0
OE1 A:GLU65 2.4 6.2 1.0
OE2 A:GLU65 2.4 4.5 1.0
OD1 A:ASP58 2.4 6.8 1.0
O A:HOH206 2.5 5.5 1.0
CD A:GLU65 2.8 4.5 1.0
CG A:ASP56 3.2 7.5 1.0
CG A:ASP58 3.3 4.5 1.0
CG A:ASP54 3.5 8.0 1.0
C A:GLN60 3.5 4.9 1.0
OD2 A:ASP56 3.6 8.4 1.0
OD2 A:ASP58 3.6 5.8 1.0
N A:GLN60 4.1 3.3 1.0
N A:ASP58 4.2 8.3 1.0
N A:ASP56 4.2 10.2 1.0
CG A:GLU65 4.3 3.3 1.0
OD2 A:ASP54 4.3 6.2 1.0
CA A:GLN60 4.4 2.9 1.0
N A:GLY57 4.4 6.8 1.0
CA A:ASP54 4.4 7.4 1.0
N A:VAL61 4.4 4.7 1.0
CA A:VAL61 4.4 5.0 1.0
CB A:ASP54 4.4 7.5 1.0
CB A:ASP58 4.4 5.1 1.0
CB A:ASP56 4.5 7.1 1.0
N A:ASN62 4.5 3.9 1.0
N A:ILE55 4.6 5.0 1.0
C A:ASP54 4.6 8.0 1.0
ND2 A:ASN62 4.7 5.9 1.0
CA A:ASP56 4.7 11.3 1.0
CA A:ASP58 4.8 5.7 1.0
C A:ASP56 4.8 10.2 1.0
CB A:GLN60 4.8 3.0 1.0
N A:GLY59 4.8 4.4 1.0
CG A:ASN62 4.9 3.8 1.0
O A:HOH229 4.9 7.3 1.0
C A:ASP58 5.0 3.8 1.0

Calcium binding site 3 out of 6 in 7vut

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Calcium binding site 3 out of 6 in the Crystal Structure of ALLEYCAT10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of ALLEYCAT10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca103

b:30.6
occ:1.00
 OE1 A:GLU52 2.3 15.9 1.0
O A:HOH207 3.0 34.0 1.0
CD A:GLU52 3.5 15.1 1.0
OE2 A:GLU52 4.2 19.9 1.0
CB A:GLU52 4.4 9.9 1.0
CG A:GLU52 4.5 12.0 1.0
CA A:GLU52 4.7 10.2 1.0

Calcium binding site 4 out of 6 in 7vut

Go back to Calcium Binding Sites List in 7vut
Calcium binding site 4 out of 6 in the Crystal Structure of ALLEYCAT10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of ALLEYCAT10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca101

b:3.5
occ:1.00
 O B:TYR24 2.3 5.2 1.0
OD1 B:ASP20 2.3 5.7 1.0
OD1 B:ASP18 2.4 4.9 1.0
O B:HOH227 2.4 7.7 1.0
OE1 B:GLU29 2.4 4.1 1.0
OD1 B:ASN22 2.4 4.0 1.0
OE2 B:GLU29 2.6 3.9 1.0
CD B:GLU29 2.8 4.6 1.0
CG B:ASP18 3.4 4.2 1.0
CG B:ASP20 3.4 4.6 1.0
CG B:ASN22 3.4 3.5 1.0
C B:TYR24 3.5 4.0 1.0
OD2 B:ASP20 3.9 5.9 1.0
ND2 B:ASN22 4.0 3.1 1.0
OD2 B:ASP18 4.1 3.3 1.0
CA B:ASP18 4.2 4.8 1.0
N B:ASP20 4.2 3.1 1.0
N B:ASN22 4.2 3.0 1.0
N B:TYR24 4.2 4.6 1.0
CB B:ASP18 4.3 5.3 1.0
CG B:GLU29 4.4 2.6 1.0
CA B:TYR24 4.4 4.8 1.0
O B:HOH228 4.4 3.6 1.0
N B:LYS19 4.4 5.1 1.0
N B:ILE25 4.5 3.6 1.0
N B:GLY21 4.5 4.0 1.0
CB B:ASN22 4.5 3.4 1.0
C B:ASP18 4.5 3.4 1.0
CA B:ILE25 4.5 3.7 1.0
N B:SER26 4.6 2.7 1.0
CB B:ASP20 4.6 7.4 1.0
CB B:TYR24 4.7 4.0 1.0
O B:HOH204 4.7 6.0 1.0
CA B:ASP20 4.8 3.2 1.0
CA B:ASN22 4.8 4.1 1.0
N B:GLY23 4.9 4.2 1.0
C B:ASP20 4.9 4.5 1.0

Calcium binding site 5 out of 6 in 7vut

Go back to Calcium Binding Sites List in 7vut
Calcium binding site 5 out of 6 in the Crystal Structure of ALLEYCAT10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of ALLEYCAT10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca102

b:5.8
occ:1.00
 OD1 B:ASP54 2.3 8.0 1.0
O B:GLN60 2.3 6.0 1.0
OE2 B:GLU65 2.3 6.9 1.0
OD1 B:ASP58 2.4 6.0 1.0
OD1 B:ASP56 2.4 6.0 1.0
O B:HOH229 2.4 9.1 1.0
OE1 B:GLU65 2.5 7.9 1.0
CD B:GLU65 2.7 6.5 1.0
CG B:ASP56 3.3 10.2 1.0
CG B:ASP58 3.3 8.5 1.0
CG B:ASP54 3.4 7.4 1.0
C B:GLN60 3.5 5.6 1.0
OD2 B:ASP56 3.6 11.1 1.0
OD2 B:ASP58 3.7 11.5 1.0
N B:ASP58 4.2 8.5 1.0
OD2 B:ASP54 4.2 6.0 1.0
CA B:ASP54 4.2 5.6 1.0
N B:ASP56 4.2 7.4 1.0
N B:GLN60 4.2 6.7 1.0
CB B:ASP54 4.2 6.8 1.0
CG B:GLU65 4.3 6.8 1.0
CA B:GLN60 4.3 6.0 1.0
N B:VAL61 4.4 3.8 1.0
N B:ASN62 4.4 6.6 1.0
N B:GLY57 4.4 5.9 1.0
CA B:VAL61 4.4 4.4 1.0
C B:ASP54 4.5 7.5 1.0
CB B:ASP56 4.5 13.1 1.0
CB B:ASP58 4.5 6.0 1.0
N B:ILE55 4.6 7.5 1.0
CB B:GLN60 4.6 8.4 1.0
CA B:ASP56 4.7 6.3 1.0
C B:ASP56 4.7 9.2 1.0
CA B:ASP58 4.8 5.0 1.0
CG B:ASN62 4.8 9.8 1.0
C B:VAL61 4.9 8.9 1.0
N B:GLY59 4.9 4.9 1.0
OD1 B:ASN62 4.9 11.7 1.0
ND2 B:ASN62 5.0 6.4 1.0
O B:ASP54 5.0 7.4 1.0

Calcium binding site 6 out of 6 in 7vut

Go back to Calcium Binding Sites List in 7vut
Calcium binding site 6 out of 6 in the Crystal Structure of ALLEYCAT10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of ALLEYCAT10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca103

b:7.3
occ:1.00
 O B:HOH237 2.3 5.4 1.0
O B:ASP18 2.3 4.0 1.0
O B:ARG15 2.4 6.8 1.0
O B:HOH248 2.4 10.7 1.0
C B:ARG15 3.5 7.0 1.0
C B:ASP18 3.5 3.4 1.0
CA B:ARG15 4.1 7.2 1.0
O B:LYS19 4.3 6.1 1.0
N B:LYS19 4.4 5.1 1.0
CA B:LYS19 4.4 2.6 1.0
CB B:ARG15 4.4 6.7 1.0
CA B:ASP18 4.4 4.8 1.0
C B:LYS19 4.5 3.8 1.0
N B:VAL16 4.5 6.9 1.0
CB B:ASP18 4.5 5.3 1.0
N B:ASP18 4.7 5.2 1.0
N B:GLY21 4.7 4.0 1.0
CA B:GLY21 4.7 3.6 1.0
CA B:VAL16 4.8 7.6 1.0
O B:VAL16 4.8 5.2 1.0
C B:VAL16 4.9 8.0 1.0
O B:HOH261 4.9 25.7 1.0
O B:HOH208 4.9 4.7 1.0
CG B:ASP18 5.0 4.2 1.0

Reference:

S.Bhattacharya, E.G.Margheritis, K.Takahashi, A.Kulesha, A.D'souza, I.Kim, J.H.Yoon, J.R.H.Tame, A.N.Volkov, O.V.Makhlynets, I.V.Korendovych. uc(Nmr)-Guided Directed Evolution. Nature V. 610 389 2022.
ISSN: ESSN 1476-4687
PubMed: 36198791
DOI: 10.1038/S41586-022-05278-9
Page generated: Fri Jul 19 05:29:40 2024

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