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Calcium in PDB 5j2z: Prv UL37 N-Terminal Half (R2 Mutant)

Protein crystallography data

The structure of Prv UL37 N-Terminal Half (R2 Mutant), PDB code: 5j2z was solved by E.E.Heldwein, J.D.Pitts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.72 / 2.50
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 51.281, 68.696, 156.226, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 23.7

Other elements in 5j2z:

The structure of Prv UL37 N-Terminal Half (R2 Mutant) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Prv UL37 N-Terminal Half (R2 Mutant) (pdb code 5j2z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Prv UL37 N-Terminal Half (R2 Mutant), PDB code: 5j2z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5j2z

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Calcium binding site 1 out of 10 in the Prv UL37 N-Terminal Half (R2 Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Prv UL37 N-Terminal Half (R2 Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:22.2
occ:1.00
 OE1 A:GLU82 2.3 56.5 1.0
O A:HOH656 2.4 20.5 1.0
OD2 A:ASP79 2.5 30.2 1.0
CD A:GLU82 3.2 47.5 1.0
CG A:ASP79 3.5 38.6 1.0
OE2 A:GLU82 3.8 50.7 1.0
CA A:CA509 4.0 51.2 1.0
CA A:CA502 4.1 25.0 1.0
CB A:ASP79 4.2 26.3 1.0
CG A:GLU82 4.3 38.3 1.0
OD1 A:ASP79 4.3 44.8 1.0

Calcium binding site 2 out of 10 in 5j2z

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Calcium binding site 2 out of 10 in the Prv UL37 N-Terminal Half (R2 Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Prv UL37 N-Terminal Half (R2 Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:25.0
occ:1.00
 OD2 A:ASP81 2.2 54.4 1.0
OD2 A:ASP79 2.6 30.2 1.0
OD1 A:ASP79 2.8 44.8 1.0
CG A:ASP79 3.0 38.6 1.0
CG A:ASP81 3.3 46.4 1.0
CB A:ASP81 3.8 39.3 1.0
CA A:CA501 4.1 22.2 1.0
OD1 A:ASP81 4.4 41.5 1.0
CB A:ASP79 4.5 26.3 1.0
CH3 A:ACT518 4.7 15.1 1.0
N A:ASP81 5.0 26.9 1.0

Calcium binding site 3 out of 10 in 5j2z

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Calcium binding site 3 out of 10 in the Prv UL37 N-Terminal Half (R2 Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Prv UL37 N-Terminal Half (R2 Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:50.0
occ:1.00
 OD1 A:ASP308 2.4 34.4 1.0
OD1 A:ASP310 2.7 46.9 1.0
OD2 A:ASP310 2.8 42.5 1.0
CL A:CL516 3.0 64.1 1.0
CG A:ASP310 3.0 46.0 1.0
CL A:CL517 3.4 0.9 1.0
CG A:ASP308 3.7 33.0 1.0
CA A:CA504 3.8 41.7 1.0
O A:HOH645 4.2 43.7 1.0
OD2 A:ASP308 4.3 41.8 1.0
ND1 A:HIS311 4.3 35.2 1.0
CB A:ASP310 4.4 36.1 1.0
CA A:ASP308 4.7 27.0 1.0
N A:ASP310 4.7 31.5 1.0
CB A:ASP308 4.8 27.8 1.0
CE1 A:HIS311 4.9 41.3 1.0
C A:ASP308 4.9 33.9 1.0

Calcium binding site 4 out of 10 in 5j2z

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Calcium binding site 4 out of 10 in the Prv UL37 N-Terminal Half (R2 Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Prv UL37 N-Terminal Half (R2 Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:41.7
occ:1.00
 O A:HOH645 2.2 43.7 1.0
OD2 A:ASP310 2.4 42.5 1.0
CG A:ASP310 3.6 46.0 1.0
CA A:CA503 3.8 50.0 1.0
CB A:ASP310 4.4 36.1 1.0
OD1 A:ASP310 4.5 46.9 1.0
CL A:CL516 4.8 64.1 1.0

Calcium binding site 5 out of 10 in 5j2z

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Calcium binding site 5 out of 10 in the Prv UL37 N-Terminal Half (R2 Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Prv UL37 N-Terminal Half (R2 Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:70.9
occ:1.00
 OD2 A:ASP355 2.5 64.4 1.0
OD1 A:ASP355 2.8 61.5 1.0
CG A:ASP355 3.0 53.4 1.0
O A:HOH668 3.2 30.6 1.0
O A:HOH659 3.6 41.3 1.0
CB A:ASP355 4.5 35.9 1.0

Calcium binding site 6 out of 10 in 5j2z

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Calcium binding site 6 out of 10 in the Prv UL37 N-Terminal Half (R2 Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Prv UL37 N-Terminal Half (R2 Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:40.7
occ:1.00
 OD2 A:ASP175 2.3 43.2 1.0
O A:HIS78 2.5 31.7 1.0
O A:ACT518 2.6 42.6 1.0
OXT A:ACT518 2.7 40.9 1.0
O A:ACT521 2.7 59.5 1.0
OXT A:ACT521 3.0 71.4 1.0
O A:HOH666 3.0 42.2 1.0
C A:ACT518 3.1 29.9 1.0
C A:ACT521 3.2 68.7 1.0
CG A:ASP175 3.5 37.9 1.0
C A:HIS78 3.5 25.0 1.0
CA A:ASP79 4.0 24.1 1.0
OD1 A:ASP175 4.1 39.4 1.0
N A:ASP79 4.1 29.0 1.0
N A:HIS78 4.5 29.4 1.0
N A:TRP80 4.5 23.8 1.0
CB A:ASP175 4.6 30.1 1.0
CH3 A:ACT518 4.6 15.1 1.0
CA A:HIS78 4.6 27.3 1.0
CH3 A:ACT521 4.6 69.7 1.0
CG A:ARG77 4.7 54.1 1.0
C A:ASP79 4.8 26.3 1.0
CD1 A:TRP80 4.8 20.7 1.0
H3 A:ACT521 4.9 83.7 1.0
CL A:CL515 4.9 79.0 1.0

Calcium binding site 7 out of 10 in 5j2z

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Calcium binding site 7 out of 10 in the Prv UL37 N-Terminal Half (R2 Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Prv UL37 N-Terminal Half (R2 Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:61.8
occ:1.00
 O A:HOH606 2.4 36.2 1.0
OXT A:ACT519 2.5 49.0 1.0
O A:ACT519 2.5 39.5 1.0
C A:ACT519 2.9 42.3 1.0
O A:HOH665 3.6 56.6 1.0
NH2 A:ARG178 3.9 92.8 1.0
OD1 A:ASP383 4.0 30.7 1.0
CH3 A:ACT519 4.4 20.6 1.0
OD1 A:ASP389 4.6 57.2 1.0
OD2 A:ASP389 4.8 56.0 1.0
CZ A:ARG178 4.9 79.7 1.0

Calcium binding site 8 out of 10 in 5j2z

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Calcium binding site 8 out of 10 in the Prv UL37 N-Terminal Half (R2 Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Prv UL37 N-Terminal Half (R2 Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca508

b:80.1
occ:1.00
 OD1 A:ASP347 2.2 63.7 1.0
O A:HOH658 2.8 39.0 1.0
O A:HOH614 2.9 50.6 1.0
O A:HOH641 3.3 49.8 1.0
CG A:ASP347 3.4 50.7 1.0
CB A:ASP347 4.1 36.1 1.0
OD2 A:ASP347 4.3 44.2 1.0
CA A:ASP347 4.5 25.6 1.0
OE1 A:GLU350 4.6 59.5 1.0

Calcium binding site 9 out of 10 in 5j2z

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Calcium binding site 9 out of 10 in the Prv UL37 N-Terminal Half (R2 Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Prv UL37 N-Terminal Half (R2 Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca509

b:51.2
occ:1.00
 OE2 A:GLU82 2.7 50.7 1.0
CD A:GLU82 3.6 47.5 1.0
OE1 A:GLU82 3.8 56.5 1.0
CA A:CA501 4.0 22.2 1.0
CG A:GLU82 4.9 38.3 1.0

Calcium binding site 10 out of 10 in 5j2z

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Calcium binding site 10 out of 10 in the Prv UL37 N-Terminal Half (R2 Mutant)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Prv UL37 N-Terminal Half (R2 Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca510

b:0.3
occ:1.00
 OE1 A:GLU321 2.4 71.1 1.0
CD A:GLU321 3.4 68.7 1.0
OE2 A:GLU321 3.7 80.4 1.0
CG A:GLU321 4.7 52.8 1.0

Reference:

A.L.Richards, P.J.Sollars, J.D.Pitts, A.M.Stults, E.E.Heldwein, G.E.Pickard, G.A.Smith. The PUL37 Tegument Protein Guides Alpha-Herpesvirus Retrograde Axonal Transport to Promote Neuroinvasion. Plos Pathog. V. 13 06741 2017.
ISSN: ESSN 1553-7374
PubMed: 29216315
DOI: 10.1371/JOURNAL.PPAT.1006741
Page generated: Sun Jul 14 20:49:49 2024

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