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Calcium in PDB 7vuu: Crystal Structure of ALLEYCAT10 with Inhibitor

Protein crystallography data

The structure of Crystal Structure of ALLEYCAT10 with Inhibitor, PDB code: 7vuu 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) 13.19 / 1.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.919, 82.919, 104.948, 90, 90, 90
R / Rfree (%) 24.9 / 27.8

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of ALLEYCAT10 with Inhibitor (pdb code 7vuu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 17 binding sites of Calcium where determined in the Crystal Structure of ALLEYCAT10 with Inhibitor, PDB code: 7vuu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 17 in 7vuu

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Calcium binding site 1 out of 17 in the Crystal Structure of ALLEYCAT10 with Inhibitor


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 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:12.0
occ:1.00
 OD1 A:ASN22 2.3 9.0 1.0
OD1 A:ASP20 2.3 16.9 1.0
O A:TYR24 2.3 11.7 1.0
O A:HOH218 2.4 17.3 1.0
OD1 A:ASP18 2.4 11.9 1.0
OE1 A:GLU29 2.5 10.2 1.0
OE2 A:GLU29 2.6 13.8 1.0
CD A:GLU29 2.9 13.4 1.0
CG A:ASN22 3.2 13.5 1.0
CG A:ASP20 3.3 17.1 1.0
C A:TYR24 3.5 11.2 1.0
CG A:ASP18 3.5 12.0 1.0
OD2 A:ASP20 3.7 16.5 1.0
ND2 A:ASN22 3.8 10.0 1.0
N A:ASN22 4.1 13.2 1.0
CA A:ASP18 4.2 16.2 1.0
N A:TYR24 4.2 11.0 1.0
N A:ASP20 4.2 19.6 1.0
CB A:ASN22 4.3 8.1 1.0
CA A:TYR24 4.3 9.8 1.0
OD2 A:ASP18 4.3 10.6 1.0
CG A:GLU29 4.4 13.1 1.0
CB A:ASP18 4.4 14.2 1.0
C A:ASP18 4.4 18.8 1.0
N A:LYS19 4.5 15.9 1.0
N A:ILE25 4.5 12.0 1.0
CB A:TYR24 4.5 10.3 1.0
CB A:ASP20 4.5 16.4 1.0
N A:GLY21 4.5 16.7 1.0
CA A:ILE25 4.6 10.7 1.0
N A:SER26 4.6 7.8 1.0
CA A:ASN22 4.6 7.3 1.0
CA A:ASP20 4.7 20.3 1.0
C A:ASP20 4.7 17.8 1.0
C A:ASN22 4.9 11.6 1.0
N A:GLY23 5.0 9.2 1.0

Calcium binding site 2 out of 17 in 7vuu

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Calcium binding site 2 out of 17 in the Crystal Structure of ALLEYCAT10 with Inhibitor


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 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca103

b:10.6
occ:1.00
 O A:GLN60 2.2 10.3 1.0
OD1 A:ASP56 2.3 15.1 1.0
OD1 A:ASP54 2.3 15.5 1.0
O A:HOH204 2.4 12.2 1.0
OE1 A:GLU65 2.4 12.8 1.0
OE2 A:GLU65 2.5 17.1 1.0
OD1 A:ASP58 2.5 13.6 1.0
CD A:GLU65 2.8 14.8 1.0
CG A:ASP56 3.0 20.2 1.0
OD2 A:ASP56 3.0 22.5 1.0
CG A:ASP58 3.4 18.3 1.0
C A:GLN60 3.4 12.3 1.0
CG A:ASP54 3.4 14.8 1.0
OD2 A:ASP58 3.7 12.9 1.0
OD2 A:ASP54 4.2 13.4 1.0
N A:GLN60 4.2 9.0 1.0
N A:ASP58 4.3 12.4 1.0
N A:ASP56 4.3 18.1 1.0
CA A:GLN60 4.3 10.5 1.0
N A:VAL61 4.3 6.9 1.0
CG A:GLU65 4.3 16.9 1.0
CB A:ASP56 4.3 15.6 1.0
CA A:ASP54 4.3 12.0 1.0
CB A:ASP54 4.4 12.7 1.0
N A:ASN62 4.4 9.7 1.0
CA A:VAL61 4.4 9.3 1.0
N A:GLY57 4.5 18.1 1.0
C A:ASP54 4.5 14.6 1.0
CB A:ASP58 4.5 15.4 1.0
CB A:GLN60 4.6 12.4 1.0
CA A:ASP56 4.7 14.8 1.0
N A:ILE55 4.7 16.6 1.0
ND2 A:ASN62 4.7 10.8 1.0
CG A:ASN62 4.8 13.8 1.0
C A:ASP56 4.8 16.6 1.0
CA A:ASP58 4.8 16.6 1.0
C A:VAL61 4.9 10.4 1.0
N A:GLY59 4.9 13.5 1.0

Calcium binding site 3 out of 17 in 7vuu

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Calcium binding site 3 out of 17 in the Crystal Structure of ALLEYCAT10 with Inhibitor


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 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca104

b:18.4
occ:1.00
 OD2 A:ASP56 2.6 22.5 1.0
CG A:ASP56 3.5 20.2 1.0
ND2 A:ASN62 3.7 10.8 1.0
CB A:ASP56 3.8 15.6 1.0
O A:HOH204 4.3 12.2 1.0
OD1 A:ASP56 4.6 15.1 1.0
O A:HOH212 4.8 12.4 1.0
OE2 A:GLU65 4.8 17.1 1.0
CG A:ASN62 5.0 13.8 1.0

Calcium binding site 4 out of 17 in 7vuu

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Calcium binding site 4 out of 17 in the Crystal Structure of ALLEYCAT10 with Inhibitor


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 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca105

b:36.5
occ:1.00
 O A:HOH219 2.4 16.8 1.0
O A:ARG51 2.5 14.5 1.0
O A:HOH208 2.5 17.9 1.0
O A:ASP54 2.6 13.7 1.0
O A:HOH209 2.8 22.7 1.0
C A:ASP54 3.5 14.6 1.0
C A:ARG51 3.7 16.8 1.0
CG A:ARG51 4.2 21.9 1.0
CB A:ASP54 4.3 12.7 1.0
CA A:ASP54 4.3 12.0 1.0
O A:ILE55 4.3 19.2 1.0
CA A:GLY57 4.4 18.6 1.0
O A:GLU52 4.4 15.8 1.0
N A:ASP54 4.4 12.7 1.0
N A:ILE55 4.4 16.6 1.0
CA A:GLU52 4.4 18.1 1.0
N A:GLU52 4.5 11.6 1.0
N A:GLY57 4.6 18.1 1.0
CA A:ILE55 4.6 18.0 1.0
C A:GLU52 4.6 16.2 1.0
CA A:ARG51 4.6 11.8 1.0
C A:ILE55 4.6 19.6 1.0
NH2 A:ARG51 4.7 20.6 1.0
CG A:ASP54 4.7 14.8 1.0
O A:HOH211 4.9 17.2 1.0
OD2 A:ASP54 5.0 13.4 1.0

Calcium binding site 5 out of 17 in 7vuu

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Calcium binding site 5 out of 17 in the Crystal Structure of ALLEYCAT10 with Inhibitor


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 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca102

b:8.6
occ:1.00
 OD1 B:ASP56 2.2 14.5 1.0
OD1 B:ASP54 2.3 11.2 1.0
O B:GLN60 2.3 10.8 1.0
OE1 B:GLU65 2.4 10.2 1.0
OD1 B:ASP58 2.5 12.3 1.0
OE2 B:GLU65 2.6 11.7 1.0
CD B:GLU65 2.9 14.5 1.0
CG B:ASP54 3.3 10.7 1.0
CG B:ASP56 3.3 19.7 1.0
CG B:ASP58 3.4 11.2 1.0
C B:GLN60 3.5 12.1 1.0
OD2 B:ASP58 3.8 16.0 1.0
OD2 B:ASP56 3.9 24.0 1.0
OD2 B:ASP54 4.1 10.9 1.0
CB B:ASP54 4.1 10.4 1.0
N B:ASP56 4.1 15.4 1.0
CA B:ASP54 4.1 8.9 1.0
N B:ASP58 4.3 15.2 1.0
N B:GLN60 4.3 8.3 1.0
C B:ASP54 4.3 12.3 1.0
N B:GLY57 4.4 12.1 1.0
CG B:GLU65 4.4 12.6 1.0
CA B:GLN60 4.4 13.4 1.0
N B:VAL61 4.4 9.6 1.0
N B:ILE55 4.5 8.9 1.0
CB B:ASP56 4.5 16.1 1.0
CA B:VAL61 4.5 11.3 1.0
CB B:ASP58 4.6 12.7 1.0
CA B:ASP56 4.6 18.9 1.0
N B:ASN62 4.6 10.8 1.0
C B:ASP56 4.7 18.4 1.0
O B:ASP54 4.9 12.9 1.0
CB B:GLN60 4.9 11.3 1.0
ND2 B:ASN62 4.9 10.9 1.0
O B:HOH203 4.9 9.2 1.0
CA B:ASP58 4.9 13.0 1.0
N B:GLY59 5.0 12.2 1.0

Calcium binding site 6 out of 17 in 7vuu

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Calcium binding site 6 out of 17 in the Crystal Structure of ALLEYCAT10 with Inhibitor


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 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca103

b:8.0
occ:1.00
 OD1 B:ASP20 2.3 13.6 1.0
O B:TYR24 2.3 6.9 1.0
OD1 B:ASP18 2.3 12.1 1.0
OD1 B:ASN22 2.4 13.7 1.0
O B:HOH218 2.4 14.7 1.0
OE2 B:GLU29 2.5 9.0 1.0
OE1 B:GLU29 2.5 10.0 1.0
CD B:GLU29 2.8 10.2 1.0
CG B:ASN22 3.3 14.8 1.0
CG B:ASP18 3.4 10.2 1.0
CG B:ASP20 3.4 15.8 1.0
C B:TYR24 3.5 11.7 1.0
ND2 B:ASN22 3.8 12.5 1.0
OD2 B:ASP20 3.9 18.8 1.0
CA B:ASP18 4.1 8.9 1.0
OD2 B:ASP18 4.2 12.8 1.0
N B:ASP20 4.2 19.7 1.0
N B:TYR24 4.2 9.8 1.0
CB B:ASP18 4.2 9.5 1.0
CA B:TYR24 4.3 8.8 1.0
N B:ASN22 4.3 12.8 1.0
N B:LYS19 4.3 12.2 1.0
CG B:GLU29 4.4 10.6 1.0
N B:ILE25 4.4 8.8 1.0
C B:ASP18 4.4 13.0 1.0
CA B:ILE25 4.5 6.6 1.0
CB B:ASN22 4.5 11.2 1.0
N B:GLY21 4.6 15.2 1.0
CB B:TYR24 4.6 11.0 1.0
CB B:ASP20 4.6 13.4 1.0
N B:SER26 4.6 6.8 1.0
CA B:ASP20 4.7 12.9 1.0
C B:ASP20 4.8 17.1 1.0
CA B:ASN22 4.9 11.6 1.0
OE1 B:GLN60 4.9 12.9 1.0
C B:ILE25 5.0 8.0 1.0

Calcium binding site 7 out of 17 in 7vuu

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Calcium binding site 7 out of 17 in the Crystal Structure of ALLEYCAT10 with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of ALLEYCAT10 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca104

b:18.9
occ:1.00
 O B:HOH206 2.4 20.1 1.0
OE1 B:GLU64 2.5 17.1 1.0
OE2 B:GLU64 2.7 16.6 1.0
CD B:GLU64 3.0 15.4 1.0
CG B:GLU64 4.5 19.5 1.0

Calcium binding site 8 out of 17 in 7vuu

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Calcium binding site 8 out of 17 in the Crystal Structure of ALLEYCAT10 with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of ALLEYCAT10 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca105

b:29.4
occ:1.00
 O B:ARG51 2.3 10.1 1.0
O B:ASP54 2.5 12.9 1.0
O B:HOH221 2.5 24.0 1.0
O B:HOH208 2.6 16.0 1.0
C B:ASP54 3.4 12.3 1.0
C B:ARG51 3.4 13.6 1.0
CA B:GLU52 4.2 15.0 1.0
CA B:ASP54 4.2 8.9 1.0
CG B:ARG51 4.2 17.6 1.0
O B:GLU52 4.2 10.7 1.0
CB B:ASP54 4.2 10.4 1.0
N B:GLU52 4.3 11.2 1.0
N B:ASP54 4.3 8.1 1.0
C B:GLU52 4.3 12.7 1.0
N B:ILE55 4.4 8.9 1.0
CA B:ARG51 4.4 8.6 1.0
O B:ILE55 4.5 15.9 1.0
CA B:ILE55 4.5 14.7 1.0
CG B:ASP54 4.6 10.7 1.0
C B:ILE55 4.6 13.2 1.0
N B:GLY57 4.7 12.1 1.0
CA B:GLY57 4.7 15.0 1.0
OD2 B:ASP54 4.8 10.9 1.0
NH1 B:ARG51 4.8 20.1 1.0
CB B:ARG51 4.9 11.8 1.0
OE1 B:GLU52 5.0 22.3 1.0

Calcium binding site 9 out of 17 in 7vuu

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Calcium binding site 9 out of 17 in the Crystal Structure of ALLEYCAT10 with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of ALLEYCAT10 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca106

b:24.6
occ:1.00
 O B:ARG15 2.2 15.7 1.0
O B:ASP18 2.5 10.5 1.0
C B:ARG15 3.4 15.6 1.0
C B:ASP18 3.5 13.0 1.0
CA B:ARG15 4.2 15.8 1.0
CA B:LYS19 4.3 11.8 1.0
N B:LYS19 4.3 12.2 1.0
N B:VAL16 4.3 13.6 1.0
O B:VAL16 4.3 12.0 1.0
CA B:ASP18 4.4 8.9 1.0
CA B:VAL16 4.4 13.4 1.0
C B:VAL16 4.5 15.3 1.0
N B:ASP18 4.5 8.4 1.0
O B:HOH201 4.5 11.5 1.0
CB B:ASP18 4.6 9.5 1.0
O B:LYS19 4.6 15.7 1.0
C B:LYS19 4.6 12.5 1.0
CB B:ARG15 4.6 20.7 1.0
N B:GLY21 4.9 15.2 1.0

Calcium binding site 10 out of 17 in 7vuu

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Calcium binding site 10 out of 17 in the Crystal Structure of ALLEYCAT10 with Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of ALLEYCAT10 with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca102

b:14.6
occ:1.00
 O C:HOH204 2.3 18.3 1.0
OD1 C:ASP18 2.3 13.1 1.0
O C:TYR24 2.4 17.2 1.0
OD1 C:ASP20 2.4 20.0 1.0
OD1 C:ASN22 2.4 16.8 1.0
OE2 C:GLU29 2.5 17.8 1.0
OE1 C:GLU29 2.5 15.5 1.0
CD C:GLU29 2.8 17.6 1.0
CG C:ASN22 3.4 14.9 1.0
CG C:ASP18 3.4 16.2 1.0
CG C:ASP20 3.4 15.0 1.0
C C:TYR24 3.5 17.4 1.0
OD2 C:ASP20 3.9 15.8 1.0
ND2 C:ASN22 3.9 14.3 1.0
CA C:ASP18 4.1 14.0 1.0
N C:ASN22 4.2 13.5 1.0
N C:ASP20 4.2 12.7 1.0
OD2 C:ASP18 4.2 12.6 1.0
N C:TYR24 4.2 15.1 1.0
CB C:ASP18 4.3 15.2 1.0
N C:LYS19 4.3 12.6 1.0
CG C:GLU29 4.3 14.2 1.0
CA C:TYR24 4.4 16.6 1.0
C C:ASP18 4.4 17.3 1.0
N C:GLY21 4.4 14.3 1.0
N C:ILE25 4.5 12.4 1.0
CA C:ILE25 4.5 10.0 1.0
CB C:ASN22 4.5 11.7 1.0
N C:SER26 4.5 11.1 1.0
CB C:ASP20 4.6 13.7 1.0
CB C:TYR24 4.7 15.8 1.0
CA C:ASP20 4.8 14.4 1.0
C C:ASP20 4.8 16.2 1.0
CA C:ASN22 4.8 14.0 1.0
C C:ILE25 5.0 15.5 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 05:31:19 2024

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