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Calcium in PDB 4esv: A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates

Enzymatic activity of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates

All present enzymatic activity of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates:
3.6.4.12;

Protein crystallography data

The structure of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates, PDB code: 4esv was solved by O.Itsathitphaisarn, R.A.Wing, W.K.Eliason, J.Wang, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.92 / 3.20
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 149.124, 180.321, 279.128, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 28.9

Other elements in 4esv:

The structure of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates also contains other interesting chemical elements:

Fluorine (F) 40 atoms
Aluminium (Al) 10 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates (pdb code 4esv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates, PDB code: 4esv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in 4esv

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Calcium binding site 1 out of 14 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:0.3
occ:1.00
OE1 A:GLN388 3.9 86.1 0.5
OD1 A:ASP389 4.0 0.5 1.0
OD2 A:ASP389 4.2 0.1 1.0
CD A:ARG344 4.2 29.8 0.0
O A:SER340 4.5 82.4 1.0
CG A:ASP389 4.5 0.4 1.0
NH1 A:ARG344 4.6 39.2 0.0
CB A:SER385 4.6 89.2 1.0
CB A:ARG344 4.8 72.5 0.5
OE1 B:GLU135 4.8 0.4 1.0
NE A:ARG344 4.9 38.4 0.0
CB A:ARG344 4.9 2.0 0.0
CD A:GLN388 4.9 84.9 0.5

Calcium binding site 2 out of 14 in 4esv

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Calcium binding site 2 out of 14 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:0.0
occ:1.00
O1B A:GDP502 2.1 70.6 1.0
OG1 A:THR217 2.2 87.1 1.0
F2 A:ALF504 3.0 93.2 1.0
F3 A:ALF504 3.1 97.1 1.0
PB A:GDP502 3.3 81.8 1.0
OE1 A:GLU241 3.4 0.1 1.0
OD1 A:ASP320 3.5 0.3 1.0
OD2 A:ASP320 3.5 94.7 1.0
CB A:THR217 3.6 77.1 1.0
O3A A:GDP502 3.7 85.9 1.0
AL A:ALF504 3.7 84.5 1.0
CE A:MET242 3.7 98.5 1.0
CG A:ASP320 4.0 98.6 1.0
O3B A:GDP502 4.1 83.1 1.0
N A:THR217 4.4 77.3 1.0
CG2 A:THR217 4.4 73.3 1.0
CA A:THR217 4.5 77.3 1.0
O2B A:GDP502 4.6 69.5 1.0
CD A:GLU241 4.6 0.9 1.0
O1A A:GDP502 4.7 78.1 1.0
NZ A:LYS216 4.9 80.1 1.0
PA A:GDP502 4.9 81.6 1.0
O A:ASP320 4.9 92.2 1.0
F4 A:ALF504 4.9 97.9 1.0
F1 A:ALF504 4.9 89.6 1.0
NH2 F:ARG420 4.9 85.0 1.0
NE F:ARG420 5.0 76.6 1.0

Calcium binding site 3 out of 14 in 4esv

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Calcium binding site 3 out of 14 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:0.1
occ:1.00
O A:SER378 3.2 89.8 1.0
OP2 V:DT3 4.0 86.5 1.0
C A:SER378 4.2 84.2 1.0
CA A:SER378 4.7 85.6 1.0
CB A:SER378 4.8 86.1 1.0

Calcium binding site 4 out of 14 in 4esv

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Calcium binding site 4 out of 14 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:0.7
occ:1.00
OG A:SER213 2.8 95.6 1.0
CG2 F:VAL424 3.0 82.2 1.0
O2' A:GDP502 3.1 68.5 1.0
O3' A:GDP502 3.5 68.2 1.0
CB A:SER213 3.6 88.3 1.0
N F:GLN419 3.8 80.1 1.0
O F:ALA417 3.9 73.4 1.0
CA F:LYS418 3.9 76.1 1.0
C2' A:GDP502 4.1 68.2 1.0
C3' A:GDP502 4.1 68.0 1.0
O F:GLN419 4.2 95.6 1.0
CB F:VAL424 4.2 76.1 1.0
O A:SER213 4.2 93.2 1.0
C F:LYS418 4.4 78.7 1.0
CG F:LYS418 4.5 69.9 1.0
C F:ALA417 4.7 73.5 1.0
N F:LYS418 4.7 75.5 1.0
CB F:LYS418 4.8 71.1 1.0
C F:GLN419 4.8 85.7 1.0
CA A:SER213 4.8 86.3 1.0
CA F:GLN419 4.9 84.0 1.0
C A:SER213 5.0 86.5 1.0
O F:GLY422 5.0 93.2 1.0

Calcium binding site 5 out of 14 in 4esv

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Calcium binding site 5 out of 14 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:0.9
occ:1.00
OD2 A:ASP391 3.1 98.9 1.0
OE2 A:GLU111 3.5 0.4 1.0
CG A:ASP391 4.2 96.9 1.0
CD A:ARG420 4.2 87.0 1.0
OD1 A:ASP204 4.2 0.9 1.0
OE1 A:GLU111 4.3 0.6 1.0
CD A:GLU111 4.3 0.2 1.0
NZ A:LYS347 4.4 85.1 1.0
NH1 A:ARG420 4.7 90.7 1.0
OD1 A:ASP391 4.8 0.6 1.0

Calcium binding site 6 out of 14 in 4esv

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Calcium binding site 6 out of 14 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:0.9
occ:1.00
O B:GLU241 4.1 0.5 1.0
CG B:PRO294 4.4 0.2 1.0
CB B:PRO294 4.8 0.2 1.0
C B:GLU241 4.9 0.7 1.0

Calcium binding site 7 out of 14 in 4esv

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Calcium binding site 7 out of 14 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:0.2
occ:1.00
O1B C:GDP501 2.0 66.6 1.0
OG1 C:THR217 2.1 84.6 1.0
F2 C:ALF503 2.2 88.6 1.0
PB C:GDP501 3.4 73.4 1.0
CB C:THR217 3.5 77.7 1.0
OE1 C:GLU241 3.5 0.7 1.0
OD2 C:ASP320 3.6 0.7 1.0
AL C:ALF503 3.8 70.4 1.0
OD1 C:ASP320 3.8 0.9 1.0
CE C:MET242 3.9 97.9 1.0
O3A C:GDP501 3.9 78.0 1.0
O3B C:GDP501 4.1 67.3 1.0
CG C:ASP320 4.1 0.2 1.0
F3 C:ALF503 4.1 86.8 1.0
N C:THR217 4.2 74.1 1.0
F4 C:ALF503 4.3 66.7 1.0
CA C:THR217 4.3 74.2 1.0
CG2 C:THR217 4.4 69.2 1.0
O C:ASP320 4.4 93.1 1.0
O2B C:GDP501 4.5 66.6 1.0
CD C:GLU241 4.8 0.7 1.0
O1A C:GDP501 4.8 70.8 1.0
CD2 C:TYR321 4.9 67.5 1.0
NZ C:LYS216 4.9 74.3 1.0
CB C:LYS216 4.9 71.9 1.0

Calcium binding site 8 out of 14 in 4esv

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Calcium binding site 8 out of 14 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:90.6
occ:1.00
OG1 D:THR217 2.1 84.4 1.0
F2 C:ALF504 2.2 92.7 1.0
O1B D:GDP501 2.3 65.2 1.0
F4 C:ALF504 2.5 94.9 1.0
AL C:ALF504 3.2 77.9 1.0
OE1 D:GLU241 3.4 95.7 1.0
CB D:THR217 3.4 76.1 1.0
CE D:MET242 3.5 97.6 1.0
PB D:GDP501 3.7 80.0 1.0
OD2 D:ASP320 3.7 99.4 1.0
OD1 D:ASP320 3.8 0.1 1.0
O3B D:GDP501 4.0 65.8 1.0
CG D:ASP320 4.2 96.8 1.0
CG2 D:THR217 4.2 69.5 1.0
N D:THR217 4.3 76.8 1.0
O1A D:GDP501 4.4 76.9 1.0
CA D:THR217 4.4 76.2 1.0
O3A D:GDP501 4.5 81.8 1.0
F3 C:ALF504 4.5 74.6 1.0
CD D:GLU241 4.6 98.1 1.0
F1 C:ALF504 4.6 67.4 1.0
NH2 C:ARG420 4.7 83.4 1.0
NE C:ARG420 4.7 81.1 1.0
O2A D:GDP501 4.8 78.1 1.0
PA D:GDP501 4.8 80.5 1.0
O2B D:GDP501 4.9 65.6 1.0

Calcium binding site 9 out of 14 in 4esv

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Calcium binding site 9 out of 14 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca504

b:0.5
occ:1.00
O D:ASN285 2.3 0.3 1.0
C D:ASN285 3.5 0.5 1.0
OD1 D:ASN232 3.7 0.5 1.0
CB D:ASN285 3.8 0.2 1.0
CA D:ASN285 4.1 0.4 1.0
N D:ALA286 4.6 0.4 1.0
CA D:ALA286 4.9 0.6 1.0
CG D:ASN232 4.9 0.7 1.0

Calcium binding site 10 out of 14 in 4esv

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Calcium binding site 10 out of 14 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:0.1
occ:1.00
OG1 E:THR217 2.1 85.4 1.0
F2 D:ALF503 2.2 0.2 1.0
O1B E:GDP501 2.2 81.1 1.0
F3 D:ALF503 2.3 88.5 1.0
AL D:ALF503 3.1 93.3 1.0
OD1 E:ASP320 3.4 0.9 1.0
CB E:THR217 3.4 81.4 1.0
PB E:GDP501 3.5 92.0 1.0
OE1 E:GLU241 3.5 0.2 1.0
OD2 E:ASP320 3.6 90.2 1.0
CE E:MET242 3.6 99.5 1.0
O3B E:GDP501 3.8 86.0 1.0
CG E:ASP320 3.9 99.3 1.0
N E:THR217 4.2 77.7 1.0
O3A E:GDP501 4.3 88.0 1.0
O1A E:GDP501 4.3 93.5 1.0
CG2 E:THR217 4.3 78.4 1.0
CA E:THR217 4.4 79.1 1.0
F4 D:ALF503 4.5 80.6 1.0
F1 D:ALF503 4.5 97.4 1.0
PA E:GDP501 4.7 91.5 1.0
O2B E:GDP501 4.7 72.4 1.0
CD E:GLU241 4.8 0.7 1.0
NE D:ARG420 4.9 87.2 1.0
NZ E:LYS216 5.0 80.6 1.0
O2A E:GDP501 5.0 82.2 1.0
NH2 D:ARG420 5.0 89.1 1.0

Reference:

O.Itsathitphaisarn, R.A.Wing, W.K.Eliason, J.Wang, T.A.Steitz. The Hexameric Helicase Dnab Adopts A Nonplanar Conformation During Translocation. Cell(Cambridge,Mass.) V. 151 267 2012.
ISSN: ISSN 0092-8674
PubMed: 23022319
DOI: 10.1016/J.CELL.2012.09.014
Page generated: Sat Dec 12 04:45:39 2020

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