Calcium in PDB 7jms: Structure of the Hazara Virus Otu Bound to Ubiquitin

Enzymatic activity of Structure of the Hazara Virus Otu Bound to Ubiquitin

All present enzymatic activity of Structure of the Hazara Virus Otu Bound to Ubiquitin:
2.7.7.48; 3.4.19.12;

Protein crystallography data

The structure of Structure of the Hazara Virus Otu Bound to Ubiquitin, PDB code: 7jms was solved by J.V.Dzimianski, S.D.Pegan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.59 / 2.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.850, 55.595, 97.434, 90.00, 97.20, 90.00
R / Rfree (%) 23.5 / 27.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Hazara Virus Otu Bound to Ubiquitin (pdb code 7jms). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Structure of the Hazara Virus Otu Bound to Ubiquitin, PDB code: 7jms:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 7jms

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Calcium binding site 1 out of 9 in the Structure of the Hazara Virus Otu Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Hazara Virus Otu Bound to Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:50.3
occ:1.00
 OD1 A:ASN20 2.2 45.7 1.0
O A:VAL128 2.4 41.4 1.0
O B:THR9 2.7 41.5 1.0
C A:VAL128 3.1 37.2 1.0
CG A:ASN20 3.3 36.7 1.0
CA A:VAL128 3.4 37.1 1.0
C B:THR9 3.7 44.0 1.0
ND2 A:ASN20 3.8 45.4 1.0
N A:GLY129 4.1 40.0 1.0
O A:VAL127 4.2 32.9 1.0
NH1 A:ARG126 4.3 46.3 1.0
CB A:VAL128 4.3 38.5 1.0
CA B:THR9 4.3 40.1 1.0
O A:PRO21 4.3 47.4 1.0
NH2 A:ARG126 4.4 41.1 1.0
N A:VAL128 4.6 36.1 1.0
CB A:ASN20 4.6 29.4 1.0
N B:GLY10 4.6 48.3 1.0
CA A:GLY129 4.7 35.9 1.0
C A:VAL127 4.8 35.0 1.0
CA A:ASN20 4.8 42.7 1.0
CZ A:ARG126 4.8 45.6 1.0
CA B:GLY10 4.9 43.5 1.0
CB B:THR9 5.0 43.6 1.0
C A:ASN20 5.0 44.3 1.0

Calcium binding site 2 out of 9 in 7jms

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Calcium binding site 2 out of 9 in the Structure of the Hazara Virus Otu Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Hazara Virus Otu Bound to Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:58.7
occ:1.00
 OE1 A:GLN34 2.5 58.5 1.0
O A:HOH307 2.5 34.8 1.0
OE1 A:GLU47 2.8 55.5 1.0
CD A:GLN34 3.5 56.7 1.0
O A:SER54 3.5 46.2 1.0
NE2 A:GLN34 3.8 50.4 1.0
O A:HOH314 3.9 30.9 1.0
CD A:GLU47 4.0 53.5 1.0
CD2 A:HIS43 4.3 43.3 1.0
C A:SER54 4.3 46.6 1.0
OE2 A:GLU47 4.5 58.4 1.0
OD1 A:ASP55 4.7 53.3 1.0
O A:HIS43 4.7 42.5 1.0
N A:SER54 4.8 40.6 1.0
CG A:GLN34 4.8 41.6 1.0
N A:ASP55 4.9 46.2 1.0
CA A:ASP55 5.0 47.0 1.0

Calcium binding site 3 out of 9 in 7jms

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Calcium binding site 3 out of 9 in the Structure of the Hazara Virus Otu Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Hazara Virus Otu Bound to Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:79.3
occ:1.00
 O A:HOH326 2.3 59.5 1.0
OE2 A:GLU64 2.7 56.6 1.0
O A:HOH315 3.0 36.8 1.0
CD A:GLU64 3.7 49.1 1.0
OE1 A:GLU64 4.2 46.8 1.0
CD2 A:LEU112 4.5 31.6 1.0
CG A:GLU64 4.8 44.9 1.0
NE2 A:HIS111 4.9 42.8 1.0

Calcium binding site 4 out of 9 in 7jms

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Calcium binding site 4 out of 9 in the Structure of the Hazara Virus Otu Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Hazara Virus Otu Bound to Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:39.1
occ:1.00
 O C:HOH311 2.5 26.2 1.0
OE1 C:GLN34 2.8 25.4 1.0
CD2 C:HIS43 3.3 40.0 1.0
CD C:GLN34 3.9 22.7 1.0
NE2 C:HIS43 4.0 46.1 1.0
CD C:PRO35 4.1 31.9 1.0
CG C:HIS43 4.2 38.1 1.0
NE2 C:GLN34 4.4 20.6 1.0
CG C:PRO35 4.5 34.6 1.0
CB C:HIS43 4.6 32.3 1.0
O C:SER54 4.7 47.1 1.0

Calcium binding site 5 out of 9 in 7jms

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Calcium binding site 5 out of 9 in the Structure of the Hazara Virus Otu Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Hazara Virus Otu Bound to Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:66.3
occ:1.00
 O C:HOH318 3.6 45.6 1.0
OG C:SER11 4.0 56.9 1.0
N C:SER11 4.0 40.0 1.0
O C:TRP9 4.2 57.6 1.0
O A:HOH320 4.2 32.7 1.0
O D:HOH211 4.3 68.9 1.0
CA C:ASP10 4.4 37.8 1.0
CB C:SER11 4.6 37.7 1.0
C C:ASP10 4.8 42.7 1.0
O D:HOH214 4.9 37.4 1.0
CA C:SER11 4.9 35.8 1.0

Calcium binding site 6 out of 9 in 7jms

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Calcium binding site 6 out of 9 in the Structure of the Hazara Virus Otu Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Hazara Virus Otu Bound to Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:63.9
occ:1.00
 OD2 D:ASP32 2.6 30.6 1.0
OD1 D:ASP32 2.6 49.4 1.0
CG D:ASP32 2.9 42.7 1.0
O D:HOH207 3.0 21.0 1.0
O D:HOH201 4.1 45.1 1.0
O D:HOH203 4.2 47.7 1.0
CB D:ASP32 4.3 49.3 1.0

Calcium binding site 7 out of 9 in 7jms

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Calcium binding site 7 out of 9 in the Structure of the Hazara Virus Otu Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Hazara Virus Otu Bound to Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:44.2
occ:1.00
 O E:HOH314 2.1 56.5 1.0
O E:HOH323 2.1 47.0 1.0
OE1 E:GLN34 2.6 41.1 1.0
CD E:GLN34 3.6 39.4 1.0
CD E:PRO35 3.9 38.8 1.0
NE2 E:GLN34 4.0 47.8 1.0
ND1 E:HIS43 4.3 54.5 1.0
CG E:PRO35 4.4 39.6 1.0
OE1 E:GLU47 4.5 53.2 1.0
O E:HOH306 4.6 51.1 1.0
CA E:GLN34 4.8 36.5 1.0
CG E:GLN34 4.8 35.2 1.0
CG E:HIS43 4.9 44.6 1.0
O E:ARG33 4.9 36.9 1.0
CE1 E:HIS43 4.9 54.6 1.0
CB E:GLN34 5.0 36.8 1.0

Calcium binding site 8 out of 9 in 7jms

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Calcium binding site 8 out of 9 in the Structure of the Hazara Virus Otu Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Hazara Virus Otu Bound to Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca101

b:54.6
occ:1.00
 O A:PRO74 2.4 43.6 1.0
OD1 F:ASP32 2.9 39.1 1.0
OD2 F:ASP32 3.2 48.1 1.0
CG F:ASP32 3.3 44.8 1.0
C A:PRO74 3.5 38.3 1.0
O F:HOH209 3.6 48.2 1.0
CA A:PRO74 4.2 39.0 1.0
N A:THR75 4.5 36.1 1.0
CB A:PRO74 4.6 39.2 1.0
CA A:THR75 4.7 37.0 1.0
CB F:ASP32 4.8 42.2 1.0

Calcium binding site 9 out of 9 in 7jms

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Calcium binding site 9 out of 9 in the Structure of the Hazara Virus Otu Bound to Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the Hazara Virus Otu Bound to Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:42.3
occ:1.00
 O G:HOH317 2.4 46.6 1.0
O G:HOH345 2.5 41.4 1.0
OE1 G:GLN34 2.8 42.6 1.0
CD G:GLN34 3.7 37.3 1.0
NE2 G:GLN34 3.8 34.3 1.0
CE G:LYS53 4.1 42.6 1.0
CD G:PRO35 4.8 45.5 1.0
O G:SER54 4.8 42.5 1.0
OD1 G:ASP55 4.8 43.9 1.0
O G:HIS43 5.0 29.4 1.0
NZ G:LYS53 5.0 46.2 1.0
ND1 G:HIS43 5.0 34.0 1.0

Reference:

J.V.Dzimianski, S.L.Mace, I.L.Williams, B.T.Freitas, S.D.Pegan. Flipping the Substrate Preference of Hazara Virus Ovarian Tumour Domain Protease Through Structure-Based Mutagenesis. Acta Crystallogr D Struct V. 76 1114 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 33135682
DOI: 10.1107/S2059798320012875
Page generated: Sat Dec 12 08:06:29 2020

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