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Calcium in PDB 6ew9: Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide

Enzymatic activity of Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide

All present enzymatic activity of Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide:
3.4.21.107;

Protein crystallography data

The structure of Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide, PDB code: 6ew9 was solved by I.R.Vetter, A.T.Porfetye, P.Stege, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.38 / 2.20
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.600, 53.650, 132.500, 90.00, 101.80, 90.00
R / Rfree (%) 22.6 / 27.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide (pdb code 6ew9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide, PDB code: 6ew9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6ew9

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Calcium binding site 1 out of 8 in the Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide


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 Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:77.2
occ:1.00
 O A:HOH501 2.9 52.8 1.0
OD2 A:ASP221 3.1 70.9 0.4
O B:THR228 4.0 56.3 1.0
OG A:SER219 4.1 57.9 1.0
CG A:ASP221 4.1 69.7 0.4
OE1 B:GLU230 4.2 37.7 1.0
O A:PHE220 4.3 56.7 1.0
OD1 A:ASP221 4.4 65.5 0.4
O A:PRO229 4.5 43.5 1.0
O A:ILE196 4.6 48.5 1.0
CB B:GLU230 4.6 40.6 1.0
OG1 B:THR228 4.8 75.2 1.0
CB A:SER219 4.8 54.2 1.0
OD1 A:ASP221 4.9 64.6 0.6

Calcium binding site 2 out of 8 in 6ew9

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Calcium binding site 2 out of 8 in the Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide


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 Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:73.9
occ:1.00
 OG A:SER201 2.8 47.4 1.0
O A:ASN197 3.0 43.4 1.0
CA A:HIS198 3.4 47.5 1.0
N A:GLY199 3.4 46.8 1.0
C A:ASN197 3.6 45.4 1.0
N A:HIS198 3.8 47.6 1.0
N A:SER201 3.8 35.4 1.0
C A:HIS198 3.9 49.0 1.0
N A:ASN200 3.9 35.0 1.0
CB A:SER201 4.1 33.8 1.0
CA A:SER201 4.4 35.6 1.0
CA A:GLY199 4.5 38.5 1.0
CB A:HIS198 4.5 54.0 1.0
C A:GLY199 4.6 41.9 1.0
CA A:ASN200 4.6 32.0 1.0
C A:ASN200 4.7 33.1 1.0
CB A:ASN200 4.7 34.9 1.0
CG2 A:ILE196 4.7 46.5 1.0
O A:THR217 4.9 41.0 1.0
CA A:ASN197 4.9 42.1 1.0
CG A:HIS198 4.9 66.0 1.0

Calcium binding site 3 out of 8 in 6ew9

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Calcium binding site 3 out of 8 in the Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide


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 Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:80.1
occ:1.00
 O A:HOH528 2.5 42.7 1.0
O A:HOH535 2.5 50.1 1.0
O C:HOH517 2.6 51.2 1.0
CA C:CA401 2.7 72.2 1.0
O C:HOH521 3.3 45.6 1.0
O B:HOH512 3.7 48.4 1.0
OG A:SER195 3.8 45.4 1.0
O A:ASP193 3.9 37.8 1.0
O A:GLN170 4.0 35.3 1.0
O A:HOH511 4.3 40.5 1.0
O B:ASP193 4.3 42.3 1.0
O B:HOH507 4.4 45.6 1.0
O B:HOH511 4.5 43.1 1.0
OD2 B:ASP193 4.8 39.4 1.0
O B:HOH501 4.8 44.5 1.0
N A:SER195 4.9 34.7 1.0
OE2 B:GLU230 4.9 45.1 1.0

Calcium binding site 4 out of 8 in 6ew9

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Calcium binding site 4 out of 8 in the Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide


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 Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:80.2
occ:1.00
 O A:THR228 2.9 47.6 1.0
OD1 C:ASP221 3.5 72.9 1.0
C A:THR228 4.1 55.5 1.0
CG C:ASP221 4.2 76.8 1.0
OG C:SER219 4.2 49.6 1.0
OE1 A:GLU230 4.2 48.9 1.0
O C:PHE220 4.3 62.7 1.0
CB A:GLU230 4.3 42.5 1.0
OD1 C:ASN197 4.4 39.2 1.0
O C:ILE196 4.5 38.8 1.0
O C:HOH525 4.5 47.8 1.0
OD2 C:ASP221 4.7 75.6 1.0
O C:PRO229 4.7 50.2 1.0
C A:PRO229 4.8 48.1 1.0
N A:GLU230 4.8 44.7 1.0
CA A:PRO229 4.9 43.6 1.0
N A:THR228 4.9 68.6 1.0
CA A:THR228 5.0 62.0 1.0

Calcium binding site 5 out of 8 in 6ew9

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Calcium binding site 5 out of 8 in the Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide


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 Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:70.6
occ:1.00
 OG B:SER201 2.8 45.5 1.0
O B:ASN197 2.9 44.1 1.0
N B:SER201 3.5 44.5 1.0
N B:GLY199 3.5 48.9 1.0
CA B:HIS198 3.5 51.1 1.0
C B:ASN197 3.6 47.0 1.0
N B:ASN200 3.8 47.5 1.0
CB B:SER201 3.8 37.0 1.0
N B:HIS198 3.8 47.1 1.0
C B:HIS198 4.0 49.4 1.0
CA B:SER201 4.1 45.1 1.0
C B:ASN200 4.3 46.8 1.0
CA B:ASN200 4.4 47.2 1.0
CG2 B:ILE196 4.4 50.2 1.0
CB B:ASN200 4.5 42.4 1.0
C B:GLY199 4.5 42.5 1.0
CA B:GLY199 4.5 45.0 1.0
O B:THR217 4.6 46.6 1.0
CB B:HIS198 4.7 52.5 1.0
CA B:ASN197 4.8 43.3 1.0
N B:ASN197 5.0 39.4 1.0

Calcium binding site 6 out of 8 in 6ew9

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Calcium binding site 6 out of 8 in the Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide


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 Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:70.6
occ:1.00
 O C:HOH514 2.5 53.5 1.0
O C:THR228 2.7 59.6 1.0
OD2 B:ASP221 2.8 70.8 1.0
CG B:ASP221 3.2 73.5 1.0
OD1 B:ASP221 3.7 79.6 1.0
C C:THR228 3.9 62.7 1.0
CB B:ASP221 4.0 68.1 1.0
N C:THR228 4.1 74.4 1.0
OG1 C:THR228 4.3 72.0 1.0
CA B:ASP221 4.4 64.0 1.0
CA C:THR228 4.5 69.7 1.0
CB C:GLU227 4.7 80.4 1.0
OG B:SER219 4.7 62.7 1.0
O B:PRO229 4.8 50.8 1.0
N C:PRO229 4.9 59.3 1.0
CB C:GLU230 4.9 46.8 1.0
OD1 B:ASN197 4.9 37.9 1.0
C C:GLU227 4.9 79.2 1.0
O B:ILE196 5.0 44.9 1.0
CA C:PRO229 5.0 56.1 1.0

Calcium binding site 7 out of 8 in 6ew9

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Calcium binding site 7 out of 8 in the Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide


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 Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:72.2
occ:1.00
 CA A:CA404 2.7 80.1 1.0
O C:HOH521 2.7 45.6 1.0
O C:HOH517 2.7 51.2 1.0
O B:HOH512 2.9 48.4 1.0
O C:ASP193 3.2 35.9 1.0
O B:HOH507 3.3 45.6 1.0
O A:HOH511 3.6 40.5 1.0
OE2 A:GLU230 3.8 46.9 1.0
OG B:SER195 3.8 38.4 1.0
OG C:SER195 3.9 34.8 1.0
O A:HOH535 4.2 50.1 1.0
C C:ASP193 4.4 35.8 1.0
O B:HOH501 4.6 44.5 1.0
OE1 C:GLU230 4.7 46.2 1.0
OD2 C:ASP193 4.7 40.5 1.0
CA C:GLY231 4.8 41.2 1.0
CB C:ASP193 4.8 35.5 1.0
CD A:GLU230 4.9 46.6 1.0
CG C:ASP193 4.9 38.1 1.0
N C:SER195 5.0 31.1 1.0

Calcium binding site 8 out of 8 in 6ew9

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Calcium binding site 8 out of 8 in the Crystal Structure of Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide


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 Degs Stress Sensor Protease in Complex with Activating Dnrlglvyqf Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:68.5
occ:1.00
 O C:ASN197 3.0 28.0 1.0
OG C:SER201 3.1 38.1 1.0
CA C:HIS198 3.3 37.6 1.0
O C:HOH526 3.5 55.9 1.0
N C:GLY199 3.6 36.1 1.0
C C:ASN197 3.7 37.4 1.0
N C:HIS198 3.8 38.1 1.0
N C:SER201 3.8 30.3 1.0
CB C:SER201 3.9 36.1 1.0
C C:HIS198 4.0 40.3 1.0
N C:ASN200 4.2 33.4 1.0
CB C:HIS198 4.3 40.6 1.0
CA C:SER201 4.4 32.9 1.0
CD2 C:HIS198 4.7 49.8 1.0
CA C:GLY199 4.7 29.1 1.0
C C:ASN200 4.8 29.2 1.0
CG C:HIS198 4.8 51.4 1.0
O C:THR217 4.8 41.1 1.0
C C:GLY199 4.9 32.0 1.0
CA C:ASN200 4.9 32.2 1.0
CA C:ASN197 5.0 32.1 1.0
CG2 C:ILE196 5.0 40.0 1.0

Reference:

J.Bongard, M.Lorenz, I.R.Vetter, P.Stege, A.T.Porfetye, A.L.Schmitz, F.Kaschani, A.Wolf, U.Koch, P.Nussbaumer, B.Klebl, M.Kaiser, M.Ehrmann. Identification of Noncatalytic Lysine Residues From Allosteric Circuits Via Covalent Probes. Acs Chem. Biol. V. 13 1307 2018.
ISSN: ESSN 1554-8937
PubMed: 29658704
DOI: 10.1021/ACSCHEMBIO.8B00101
Page generated: Mon Jul 15 18:40:03 2024

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