Calcium in PDB 6r7v: Tannerella Forsythia Promirolysin Mutant E225A

Protein crystallography data

The structure of Tannerella Forsythia Promirolysin Mutant E225A, PDB code: 6r7v was solved by A.Rodriguez-Banqueri, T.Guevara, M.Ksiazek, J.Potempa, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.34 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.330, 67.250, 79.640, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.8

Other elements in 6r7v:

The structure of Tannerella Forsythia Promirolysin Mutant E225A also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Tannerella Forsythia Promirolysin Mutant E225A (pdb code 6r7v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tannerella Forsythia Promirolysin Mutant E225A, PDB code: 6r7v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6r7v

Go back to Calcium Binding Sites List in 6r7v
Calcium binding site 1 out of 2 in the Tannerella Forsythia Promirolysin Mutant E225A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tannerella Forsythia Promirolysin Mutant E225A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:18.2
occ:1.00
O A:TRP236 2.3 17.9 1.0
O A:SER242 2.3 20.7 1.0
OD2 A:ASP239 2.4 20.9 1.0
O A:GLY256 2.4 19.2 1.0
O A:HOH562 2.4 19.3 1.0
O A:GLN255 2.4 20.0 1.0
OD1 A:ASP239 2.4 19.0 1.0
CG A:ASP239 2.7 18.8 1.0
C A:GLY256 3.3 20.1 1.0
C A:SER242 3.4 23.8 1.0
C A:TRP236 3.5 18.9 1.0
C A:GLN255 3.5 20.0 1.0
CA A:GLY256 3.6 17.9 1.0
N A:GLY256 4.0 18.9 1.0
N A:SER242 4.2 22.8 1.0
CA A:TRP236 4.2 16.4 1.0
CB A:TRP236 4.2 15.6 1.0
CB A:ASP239 4.3 19.4 1.0
CA A:CYS243 4.3 24.8 1.0
N A:CYS243 4.3 25.0 1.0
C A:GLY241 4.3 23.8 1.0
O A:HOH637 4.4 22.3 1.0
CA A:SER242 4.4 23.2 1.0
N A:GLY237 4.5 17.4 1.0
N A:GLY257 4.6 19.1 1.0
CD1 A:TRP236 4.6 18.5 1.0
O A:GLY245 4.7 23.6 1.0
CA A:GLY237 4.7 17.9 1.0
OD1 A:ASN254 4.7 35.0 1.0
O A:GLY241 4.7 23.2 1.0
CA A:GLN255 4.8 18.2 1.0
N A:GLY245 4.8 22.2 1.0
C A:CYS243 4.8 31.6 1.0
CA A:GLY241 4.8 20.4 1.0
OG A:SER242 4.8 31.8 1.0
SG A:CYS271 4.8 29.2 1.0
CG A:TRP236 4.8 15.5 1.0
N A:GLY241 4.9 21.0 1.0
N A:GLN255 4.9 19.6 1.0
N A:SER244 4.9 26.7 1.0
N A:ASP239 4.9 17.6 1.0

Calcium binding site 2 out of 2 in 6r7v

Go back to Calcium Binding Sites List in 6r7v
Calcium binding site 2 out of 2 in the Tannerella Forsythia Promirolysin Mutant E225A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tannerella Forsythia Promirolysin Mutant E225A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:17.8
occ:0.97
O A:HOH642 2.4 28.7 1.0
OD1 A:ASP247 2.4 18.0 1.0
O A:ILE249 2.4 18.1 1.0
O A:THR252 2.5 16.8 1.0
O A:HOH594 2.5 17.7 1.0
OG1 A:THR252 2.5 16.8 1.0
O A:HOH601 2.6 21.3 1.0
O A:HOH722 2.6 22.2 1.0
CG A:ASP247 3.4 17.6 1.0
C A:THR252 3.5 18.6 1.0
C A:ILE249 3.6 18.8 1.0
CB A:THR252 3.6 16.5 1.0
OD2 A:ASP247 3.8 16.0 1.0
CA A:THR252 3.9 14.8 1.0
N A:THR252 4.1 16.7 1.0
N A:ILE249 4.1 17.9 1.0
CA A:ILE249 4.2 15.5 1.0
O A:PRO253 4.4 19.6 1.0
CB A:ILE249 4.4 16.8 1.0
C A:PRO253 4.5 21.1 1.0
O A:HOH672 4.5 30.2 0.5
N A:ASP247 4.6 17.8 1.0
N A:PRO253 4.6 18.3 1.0
N A:ALA250 4.6 17.7 1.0
N A:ASN254 4.7 19.7 1.0
CB A:ASP247 4.7 17.2 1.0
O A:HOH637 4.7 22.3 1.0
CA A:ALA250 4.8 19.1 1.0
OG1 A:THR246 4.8 23.0 1.0
C A:ALA250 4.8 23.1 1.0
O A:ALA250 4.9 24.1 1.0
O A:ILE235 4.9 17.9 1.0
CG2 A:THR252 4.9 15.3 1.0
CA A:ASN254 5.0 20.0 1.0
O A:HOH740 5.0 32.4 1.0

Reference:

T.Guevara, A.Rodriguez-Banqueri, M.Ksiazek, J.Potempa, F.X.Gomis-Ruth. Structure-Based Mechanism of Cysteine-Switch Latency and of Catalysis By Pappalysin-Family Metallopeptidases Iucrj 2019.
ISSN: ESSN 2052-2525
Page generated: Sat Dec 12 07:29:51 2020

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