Calcium in PDB 7vur: Crystal Structure of ALLEYCAT9 with Calcium But No Inhibitor

Protein crystallography data

The structure of Crystal Structure of ALLEYCAT9 with Calcium But No Inhibitor, PDB code: 7vur was solved by E.Margheritis, K.Takahashi, I.V.Korendovych, J.R.H.Tame, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.75 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 27.376, 58.711, 87.51, 90, 90, 90
R / Rfree (%) 17.9 / 21.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of ALLEYCAT9 with Calcium But No Inhibitor (pdb code 7vur). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of ALLEYCAT9 with Calcium But No Inhibitor, PDB code: 7vur:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 7vur

Go back to Calcium Binding Sites List in 7vur
Calcium binding site 1 out of 5 in the Crystal Structure of ALLEYCAT9 with Calcium But No 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 ALLEYCAT9 with Calcium But No Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:4.7
occ:1.00
 OD1 A:ASP20 2.3 5.9 1.0
O A:TYR24 2.3 6.7 1.0
OD1 A:ASP18 2.3 5.8 1.0
OD1 A:ASN22 2.4 6.3 1.0
OE1 A:GLU29 2.5 4.2 1.0
O A:HOH216 2.5 5.8 1.0
OE2 A:GLU29 2.5 6.6 1.0
CD A:GLU29 2.8 6.6 1.0
CG A:ASP20 3.3 9.6 1.0
CG A:ASP18 3.4 5.1 1.0
CG A:ASN22 3.4 8.0 1.0
C A:TYR24 3.5 5.2 1.0
OD2 A:ASP20 3.8 7.4 1.0
ND2 A:ASN22 4.1 5.4 1.0
OD2 A:ASP18 4.1 6.4 1.0
N A:ASN22 4.2 5.8 1.0
N A:TYR24 4.2 6.5 1.0
CA A:ASP18 4.2 5.7 1.0
N A:ASP20 4.2 6.6 1.0
CB A:ASP18 4.3 5.4 1.0
CG A:GLU29 4.4 5.5 1.0
N A:LYS19 4.4 5.0 1.0
CA A:TYR24 4.4 5.5 1.0
N A:GLY21 4.4 6.3 1.0
O A:HOH217 4.4 5.7 1.0
N A:ILE25 4.5 6.6 1.0
O A:HOH210 4.5 6.8 1.0
C A:ASP18 4.5 6.4 1.0
CB A:ASN22 4.5 5.9 1.0
CA A:ILE25 4.6 5.1 1.0
CB A:ASP20 4.6 6.2 1.0
N A:SER26 4.7 5.2 1.0
CB A:TYR24 4.7 6.0 1.0
CA A:ASP20 4.8 5.8 1.0
CA A:ASN22 4.8 6.5 1.0
C A:ASP20 4.9 7.1 1.0
N A:GLY23 4.9 4.7 1.0

Calcium binding site 2 out of 5 in 7vur

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Calcium binding site 2 out of 5 in the Crystal Structure of ALLEYCAT9 with Calcium But No 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 ALLEYCAT9 with Calcium But No Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca103

b:5.4
occ:1.00
 OD1 A:ASP54 2.3 6.6 1.0
OD1 A:ASP56 2.3 7.7 1.0
O A:HOH214 2.3 7.7 1.0
O A:GLN60 2.3 6.5 1.0
OD1 A:ASP58 2.4 7.1 1.0
OE1 A:GLU65 2.5 6.5 1.0
OE2 A:GLU65 2.5 6.9 1.0
CD A:GLU65 2.8 7.6 1.0
CG A:ASP56 3.3 10.6 1.0
CG A:ASP58 3.3 8.6 1.0
CG A:ASP54 3.4 6.8 1.0
C A:GLN60 3.5 6.0 1.0
OD2 A:ASP56 3.7 14.7 1.0
OD2 A:ASP58 3.8 9.1 1.0
N A:ASP58 4.2 6.8 1.0
OD2 A:ASP54 4.2 6.8 1.0
N A:GLN60 4.2 5.2 1.0
N A:ASP56 4.2 7.8 1.0
CA A:ASP54 4.3 7.2 1.0
CB A:ASP54 4.3 6.1 1.0
N A:GLY57 4.3 7.9 1.0
CG A:GLU65 4.4 7.5 1.0
CA A:GLN60 4.4 6.8 1.0
N A:VAL61 4.4 5.3 1.0
CA A:VAL61 4.4 4.5 1.0
N A:ASN62 4.4 5.9 1.0
CB A:ASP56 4.5 8.1 1.0
C A:ASP54 4.5 7.8 1.0
CB A:ASP58 4.5 7.4 1.0
N A:ILE55 4.6 7.5 1.0
CA A:ASP56 4.7 7.4 1.0
C A:ASP56 4.7 12.0 1.0
CB A:GLN60 4.7 7.1 1.0
CA A:ASP58 4.8 7.4 1.0
ND2 A:ASN62 4.9 8.7 1.0
CG A:ASN62 4.9 8.5 1.0
C A:VAL61 4.9 6.5 1.0
N A:GLY59 4.9 7.0 1.0
O A:ASP54 5.0 8.2 1.0

Calcium binding site 3 out of 5 in 7vur

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Calcium binding site 3 out of 5 in the Crystal Structure of ALLEYCAT9 with Calcium But No 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 ALLEYCAT9 with Calcium But No Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca104

b:8.2
occ:1.00
 O A:ARG15 2.3 7.9 1.0
O A:ASP18 2.3 7.7 1.0
O A:HOH221 2.4 19.6 1.0
O A:HOH240 2.4 19.6 1.0
C A:ARG15 3.4 7.2 1.0
C A:ASP18 3.5 6.4 1.0
CA A:ARG15 4.1 7.0 1.0
O A:LYS19 4.3 7.9 1.0
CB A:ARG15 4.4 9.4 1.0
N A:LYS19 4.4 5.0 1.0
CA A:ASP18 4.4 5.7 1.0
CA A:LYS19 4.4 5.9 1.0
CB A:ASP18 4.4 5.4 1.0
N A:VAL16 4.5 8.0 1.0
C A:LYS19 4.6 8.9 1.0
N A:ASP18 4.6 5.0 1.0
CA A:VAL16 4.7 7.2 1.0
CA A:GLY21 4.8 6.0 1.0
N A:GLY21 4.8 6.3 1.0
C A:VAL16 4.8 6.9 1.0
O A:VAL16 4.9 8.0 1.0
CG A:ASP18 5.0 5.1 1.0

Calcium binding site 4 out of 5 in 7vur

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Calcium binding site 4 out of 5 in the Crystal Structure of ALLEYCAT9 with Calcium But No 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 ALLEYCAT9 with Calcium But No Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca102

b:5.4
occ:1.00
 O B:TYR24 2.3 5.3 1.0
OD1 B:ASP20 2.3 8.5 1.0
OD1 B:ASP18 2.4 5.3 1.0
OE2 B:GLU29 2.4 10.2 1.0
O B:HOH236 2.4 5.2 1.0
OD1 B:ASN22 2.5 6.5 1.0
OE1 B:GLU29 2.5 7.0 1.0
CD B:GLU29 2.8 6.9 1.0
CG B:ASN22 3.3 7.5 1.0
CG B:ASP20 3.3 10.0 1.0
C B:TYR24 3.4 5.1 1.0
CG B:ASP18 3.4 6.5 1.0
ND2 B:ASN22 3.6 6.9 1.0
OD2 B:ASP20 3.7 12.1 1.0
O B:HOH215 4.0 17.1 1.0
CA B:ASP18 4.1 8.3 1.0
N B:ASN22 4.2 5.8 1.0
N B:TYR24 4.2 4.5 1.0
CB B:ASP18 4.2 5.7 1.0
CG B:GLU29 4.3 6.5 1.0
N B:ASP20 4.3 8.1 1.0
N B:ILE25 4.3 4.9 1.0
OD2 B:ASP18 4.3 7.4 1.0
CA B:TYR24 4.3 5.2 1.0
CA B:ILE25 4.3 3.9 1.0
N B:GLY21 4.3 6.2 1.0
C B:ASP18 4.4 5.9 1.0
CB B:ASN22 4.5 7.4 1.0
CB B:ASP20 4.5 7.6 1.0
N B:SER26 4.5 4.8 1.0
C B:ASP20 4.6 8.4 1.0
CA B:ASP20 4.7 6.3 1.0
N B:LYS19 4.7 9.2 1.0
CB B:TYR24 4.7 5.7 1.0
CA B:ASN22 4.8 8.2 1.0
O B:HOH241 4.8 6.0 1.0
O B:ASP18 4.8 6.4 1.0
C B:ILE25 4.9 4.5 1.0
N B:GLY23 4.9 6.7 1.0

Calcium binding site 5 out of 5 in 7vur

Go back to Calcium Binding Sites List in 7vur
Calcium binding site 5 out of 5 in the Crystal Structure of ALLEYCAT9 with Calcium But No 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 ALLEYCAT9 with Calcium But No Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca103

b:6.5
occ:1.00
 O B:GLN60 2.2 9.8 1.0
OD1 B:ASP54 2.3 8.6 1.0
OD1 B:ASP56 2.3 6.7 1.0
O B:HOH210 2.4 7.4 1.0
OD1 B:ASP58 2.4 6.8 1.0
OE1 B:GLU65 2.5 6.5 1.0
OE2 B:GLU65 2.6 7.3 1.0
CD B:GLU65 2.9 8.3 1.0
CG B:ASP56 3.2 12.2 1.0
CG B:ASP58 3.3 8.4 1.0
C B:GLN60 3.4 7.7 1.0
CG B:ASP54 3.5 7.1 1.0
OD2 B:ASP56 3.6 16.3 1.0
OD2 B:ASP58 3.7 7.8 1.0
N B:GLN60 4.1 5.5 1.0
N B:ASP58 4.2 6.9 1.0
N B:ASP56 4.3 8.3 1.0
OD2 B:ASP54 4.3 7.7 1.0
CA B:GLN60 4.3 6.7 1.0
N B:VAL61 4.4 4.3 1.0
CA B:ASP54 4.4 6.6 1.0
CA B:VAL61 4.4 4.8 1.0
CG B:GLU65 4.4 5.6 1.0
CB B:ASP54 4.4 7.0 1.0
N B:GLY57 4.5 8.9 1.0
CB B:ASP56 4.5 12.0 1.0
CB B:ASP58 4.5 7.2 1.0
N B:ASN62 4.5 4.9 1.0
C B:ASP54 4.6 6.6 1.0
N B:ILE55 4.7 7.8 1.0
CA B:ASP56 4.7 9.5 1.0
C B:ASP56 4.8 9.3 1.0
CB B:GLN60 4.8 6.6 1.0
CA B:ASP58 4.8 5.6 1.0
ND2 B:ASN62 4.8 7.0 1.0
N B:GLY59 4.9 6.1 1.0
CG B:ASN62 4.9 5.9 1.0
C B:VAL61 5.0 5.5 1.0
O B:HOH211 5.0 12.4 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: Tue Apr 4 19:04:07 2023

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