Calcium in PDB 8qvo: L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris

Protein crystallography data

The structure of L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris, PDB code: 8qvo was solved by V.I.Timofeev, P.V.Dorovatovskii, V.A.Lazarenko, V.K.Akparov, I.P.Kuranova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.91 / 1.96
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 158.085, 158.085, 104.589, 90, 90, 120
R / Rfree (%) 14.6 / 16.6

Other elements in 8qvo:

The structure of L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris (pdb code 8qvo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris, PDB code: 8qvo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8qvo

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Calcium binding site 1 out of 5 in the L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:14.8
occ:1.00
 O A:SER7 2.3 14.7 1.0
O A:HOH722 2.4 16.4 1.0
O A:HOH793 2.4 19.7 1.0
O A:TYR9 2.4 10.8 1.0
O A:HOH709 2.5 23.0 1.0
OE1 A:GLU14 2.5 14.2 1.0
OE2 A:GLU14 2.5 16.9 1.0
CD A:GLU14 2.9 17.8 1.0
C A:SER7 3.5 14.0 1.0
C A:TYR9 3.6 13.3 1.0
CA A:SER7 4.2 15.1 1.0
O A:HOH526 4.2 21.8 1.0
C A:GLY8 4.3 12.8 1.0
CG A:GLU14 4.3 15.6 1.0
N A:TYR9 4.4 12.2 1.0
CA A:HIS10 4.4 12.2 1.0
N A:HIS10 4.4 12.0 1.0
O A:HOH734 4.5 40.5 1.0
O A:HOH724 4.5 41.9 1.0
N A:GLY8 4.5 15.1 1.0
O A:HOH655 4.6 16.8 1.0
CA A:TYR9 4.6 11.0 1.0
O A:GLY8 4.6 12.8 1.0
CB A:SER7 4.6 16.2 1.0
N A:ASN11 4.7 11.3 1.0
CA A:GLY8 4.7 15.0 1.0
CB A:GLU14 4.9 15.0 1.0
O A:HOH862 4.9 32.7 1.0
OD1 A:ASP1 5.0 17.9 1.0
C A:HIS10 5.0 13.2 1.0

Calcium binding site 2 out of 5 in 8qvo

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Calcium binding site 2 out of 5 in the L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:15.5
occ:1.00
 OD1 A:ASP51 2.2 17.5 1.0
OE1 A:GLU57 2.3 18.9 1.0
O A:ASP51 2.3 13.9 1.0
OG A:SER50 2.4 13.6 1.0
O A:HOH575 2.4 14.6 1.0
OE1 A:GLU59 2.4 17.4 1.0
OE2 A:GLU59 2.7 22.5 1.0
CD A:GLU59 2.9 19.4 1.0
C A:ASP51 3.3 15.9 1.0
CG A:ASP51 3.4 16.8 1.0
CD A:GLU57 3.4 23.2 1.0
CB A:SER50 3.4 14.0 1.0
N A:ASP51 3.7 16.2 1.0
CA A:CA407 3.9 19.7 1.0
CA A:ASP51 3.9 16.4 1.0
CG A:GLU57 4.1 19.0 1.0
C A:SER50 4.2 15.1 1.0
CB A:ASP51 4.2 17.6 1.0
CB A:GLU57 4.3 18.2 1.0
CA A:SER50 4.3 12.5 1.0
CG A:GLU104 4.3 15.1 1.0
OD2 A:ASP51 4.4 17.8 1.0
CG A:GLU59 4.4 19.3 1.0
N A:ASN52 4.4 16.7 1.0
OE2 A:GLU104 4.4 15.7 1.0
OE2 A:GLU57 4.4 28.9 1.0
CB A:ASN52 4.4 18.7 1.0
O A:HOH557 4.5 27.2 1.0
O A:ASN52 4.5 15.6 1.0
O A:ARG103 4.5 12.1 1.0
OD1 A:ASN52 4.6 33.1 1.0
C A:ASN52 4.6 16.1 1.0
O A:VAL100 4.7 13.7 1.0
CA A:ASN52 4.7 16.8 1.0
CD A:GLU104 4.8 15.6 1.0
O A:ASN101 4.8 15.7 1.0
O A:SER50 4.9 14.7 1.0
CG A:ASN52 5.0 24.0 1.0

Calcium binding site 3 out of 5 in 8qvo

Go back to Calcium Binding Sites List in 8qvo
Calcium binding site 3 out of 5 in the L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:19.7
occ:1.00
 O A:ASN101 2.3 15.7 1.0
O A:HOH774 2.3 32.6 1.0
OE2 A:GLU59 2.3 22.5 1.0
OD2 A:ASP51 2.4 17.8 1.0
O A:HOH738 2.4 22.1 1.0
O A:HOH557 2.4 27.2 1.0
OD1 A:ASP51 2.6 17.5 1.0
CG A:ASP51 2.8 16.8 1.0
C A:ASN101 3.5 16.5 1.0
CD A:GLU59 3.6 19.4 1.0
OE1 A:GLU57 3.8 18.9 1.0
CA A:CA406 3.9 15.5 1.0
CA A:ASN101 4.3 15.9 1.0
CB A:ASP51 4.4 17.6 1.0
CG A:GLU59 4.4 19.3 1.0
N A:ASN102 4.4 14.4 1.0
OE1 A:GLU59 4.4 17.4 1.0
CD A:GLU57 4.5 23.2 1.0
OD1 A:ASN52 4.5 33.1 1.0
OE2 A:GLU57 4.5 28.9 1.0
CA A:ASN102 4.5 14.5 1.0
O A:HOH585 4.6 46.2 1.0
O A:HOH723 4.7 41.4 1.0
OD1 A:ASN102 4.8 19.2 1.0
CB A:ASN101 4.8 17.6 1.0
O A:HOH663 4.9 32.6 1.0

Calcium binding site 4 out of 5 in 8qvo

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Calcium binding site 4 out of 5 in the L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:16.1
occ:1.00
 OE1 A:GLU104 2.2 17.1 1.0
OD1 A:ASP56 2.3 16.9 1.0
OE2 A:GLU61 2.3 13.7 1.0
O A:HOH518 2.4 17.9 1.0
O A:GLU57 2.4 16.6 1.0
O A:HOH611 2.4 14.8 1.0
CG A:ASP56 3.4 19.7 1.0
CD A:GLU104 3.4 15.6 1.0
CD A:GLU61 3.4 13.7 1.0
C A:GLU57 3.6 20.8 1.0
NH2 A:ARG189 3.8 19.5 1.0
OD2 A:ASP56 3.8 17.8 1.0
CG A:GLU61 3.9 15.3 1.0
OE2 A:GLU104 3.9 15.7 1.0
O A:GLU59 3.9 14.4 1.0
N A:GLU57 4.0 17.4 1.0
O A:HOH511 4.0 24.3 1.0
N A:GLU59 4.3 17.1 1.0
C A:ASP56 4.4 21.1 1.0
O A:HOH690 4.4 28.4 1.0
CA A:GLU57 4.5 17.6 1.0
OE1 A:GLN196 4.5 14.6 1.0
OE1 A:GLU61 4.5 12.4 1.0
CG A:GLU104 4.6 15.1 1.0
CB A:ASP56 4.6 18.8 1.0
N A:ASN58 4.6 19.7 1.0
CA A:ASP56 4.6 17.7 1.0
CG A:GLN196 4.7 14.7 1.0
CA A:ASN58 4.7 24.5 1.0
CB A:GLN196 4.8 13.8 1.0
CB A:GLU104 4.9 13.9 1.0
C A:GLU59 4.9 15.5 1.0

Calcium binding site 5 out of 5 in 8qvo

Go back to Calcium Binding Sites List in 8qvo
Calcium binding site 5 out of 5 in the L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:19.7
occ:1.00
 O A:TYR5 2.3 15.4 1.0
OE2 A:GLU292 2.4 21.1 1.0
OD1 A:ASP291 2.4 12.3 1.0
O A:HOH646 2.4 18.0 1.0
O A:HOH821 2.4 20.9 1.0
OE1 A:GLU292 2.6 14.3 1.0
O A:HOH804 2.7 27.5 1.0
O A:HOH597 2.7 32.5 1.0
CD A:GLU292 2.8 18.1 1.0
CG A:ASP291 3.4 15.0 1.0
C A:TYR5 3.5 16.2 1.0
OD2 A:ASP291 3.8 14.3 1.0
CA A:TYR5 4.3 17.4 1.0
OD1 A:ASP6 4.3 14.0 1.0
CG A:GLU292 4.3 17.8 1.0
N A:ASP291 4.4 12.3 1.0
N A:ASP6 4.5 14.1 1.0
N A:GLU292 4.5 12.2 1.0
O A:HOH505 4.6 24.1 1.0
CB A:TYR5 4.6 19.1 1.0
CB A:ASP291 4.6 13.6 1.0
O A:HOH904 4.7 44.9 1.0
CA A:ASP6 4.8 13.5 1.0
CA A:ASP291 4.9 12.3 1.0
CB A:PRO290 4.9 16.1 1.0

Reference:

V.I.Timofeev, P.V.Dorovatovskii, V.A.Lazarenko, V.K.Akparov, I.P.Kuranova. L211Q, L254N, T262G Mutant of Carboxypeptidase T From Thermoactinomyces Vulgaris To Be Published.
Page generated: Fri Jul 19 11:19:56 2024

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