Calcium in PDB 6ya1: Zinc Metalloprotease Proa

Protein crystallography data

The structure of Zinc Metalloprotease Proa, PDB code: 6ya1 was solved by S.Schmelz, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.39 / 1.48
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.262, 108.213, 47.39, 90, 90, 90
R / Rfree (%) 16.8 / 18.7

Other elements in 6ya1:

The structure of Zinc Metalloprotease Proa also contains other interesting chemical elements:

Zinc (Zn) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Zinc Metalloprotease Proa (pdb code 6ya1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Zinc Metalloprotease Proa, PDB code: 6ya1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6ya1

Go back to Calcium Binding Sites List in 6ya1
Calcium binding site 1 out of 4 in the Zinc Metalloprotease Proa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Zinc Metalloprotease Proa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:27.5
occ:1.00
OD1 A:ASP156 2.2 27.8 1.0
O A:HOH618 2.2 26.8 1.0
CG A:ASP156 3.1 24.6 1.0
OD2 A:ASP156 3.4 30.5 1.0
HG22 A:THR157 3.5 24.1 1.0
HG23 A:THR157 3.9 24.1 1.0
O A:HOH801 4.1 37.3 1.0
CG2 A:THR157 4.2 20.0 1.0
HA A:ASP156 4.3 18.6 1.0
CB A:ASP156 4.5 19.7 1.0
HG21 A:THR157 4.6 24.1 1.0
CA A:ASP156 4.8 15.5 1.0
C A:ASP156 4.8 16.1 1.0
N A:THR157 4.9 18.4 1.0
H A:THR157 4.9 22.1 1.0
HB3 A:ASP156 5.0 23.7 1.0

Calcium binding site 2 out of 4 in 6ya1

Go back to Calcium Binding Sites List in 6ya1
Calcium binding site 2 out of 4 in the Zinc Metalloprotease Proa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Zinc Metalloprotease Proa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:12.6
occ:1.00
O A:HOH806 2.1 28.5 1.0
OD2 A:ASP224 2.1 21.0 1.0
O A:HOH522 2.2 20.8 1.0
O A:HOH747 2.2 24.3 1.0
CG A:ASP224 3.0 33.0 1.0
OD1 A:ASP224 3.3 24.5 1.0
O A:HOH690 4.1 31.0 1.0
O A:HOH714 4.3 41.2 1.0
CB A:ASP224 4.3 23.6 1.0
HB2 A:ASP224 4.3 28.3 1.0
O A:THR157 4.3 20.4 1.0
HB A:THR157 4.3 23.4 1.0
HB3 A:ASP224 4.8 28.3 1.0
HD3 A:LYS222 4.8 24.7 1.0
HA A:THR157 4.8 25.8 1.0

Calcium binding site 3 out of 4 in 6ya1

Go back to Calcium Binding Sites List in 6ya1
Calcium binding site 3 out of 4 in the Zinc Metalloprotease Proa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Zinc Metalloprotease Proa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca410

b:17.7
occ:1.00
OE2 A:GLU42 2.1 19.7 1.0
O A:HOH658 2.1 36.5 1.0
O A:HOH820 2.1 40.6 1.0
O A:HOH577 2.2 25.8 1.0
O A:HOH539 2.2 24.0 1.0
O A:HOH726 2.2 47.0 1.0
CD A:GLU42 3.0 16.8 1.0
OE1 A:GLU42 3.3 21.2 1.0
HE22 A:GLN129 3.4 19.3 1.0
HZ3 A:LYS47 3.5 27.7 1.0
HD3 A:LYS47 3.7 20.2 1.0
O A:HOH778 3.8 44.4 1.0
O A:HOH777 4.0 42.2 1.0
OE1 A:GLN129 4.2 14.5 1.0
NE2 A:GLN129 4.2 16.1 1.0
NZ A:LYS47 4.3 23.1 1.0
CG A:GLU42 4.4 15.8 1.0
HG2 A:GLU42 4.6 18.9 1.0
CD A:LYS47 4.6 16.8 1.0
CD A:GLN129 4.6 15.6 1.0
HG3 A:GLU42 4.6 18.9 1.0
HE2 A:LYS47 4.6 22.4 1.0
HZ2 A:LYS47 4.7 27.7 1.0
CE A:LYS47 4.8 18.7 1.0
HB2 A:LYS47 4.8 15.1 1.0
O A:HOH798 4.8 36.8 1.0
HZ1 A:LYS47 4.8 27.7 1.0
HE21 A:GLN129 4.8 19.3 1.0
HD3 A:PRO61 5.0 23.8 1.0
O A:HOH774 5.0 36.0 1.0
HD2 A:LYS47 5.0 20.2 1.0

Calcium binding site 4 out of 4 in 6ya1

Go back to Calcium Binding Sites List in 6ya1
Calcium binding site 4 out of 4 in the Zinc Metalloprotease Proa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Zinc Metalloprotease Proa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca411

b:26.9
occ:0.74
O A:HOH687 2.2 28.3 1.0
O A:HOH503 2.3 44.9 1.0
HZ1 A:LYS148 2.7 55.4 1.0
NZ A:LYS148 3.4 46.2 1.0
HZ2 A:LYS148 3.5 55.4 1.0
HZ3 A:LYS148 3.7 55.4 1.0
O A:ASP146 3.9 17.3 1.0
HD3 A:LYS148 4.4 27.5 1.0
O A:HOH660 4.4 36.4 1.0
HG2 A:LYS148 4.4 24.3 1.0
OD2 A:ASP146 4.6 18.2 1.0
HB2 A:ASP146 4.6 16.1 1.0
CE A:LYS148 4.7 31.4 1.0
CG A:ASP146 4.8 16.1 1.0
CD A:LYS148 4.9 22.9 1.0
HE3 A:LYS148 5.0 37.7 1.0
C A:ASP146 5.0 17.6 1.0

Reference:

L.Scheithauer, S.Thiem, S.Schmelz, A.Dellmann, K.Bussow, R.M.H.J.Brouwer, C.M.Unal, W.Blankenfeldt, M.Steinert. Zinc Metalloprotease Proa of Legionella Pneumophila Increases Alveolar Septal Thickness in Human Lung Tissue Explants By Collagen IV Degradation. Cell.Microbiol. 13313 2021.
ISSN: ESSN 1462-5822
PubMed: 33491325
DOI: 10.1111/CMI.13313
Page generated: Sat Apr 17 14:00:51 2021

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