Calcium in PDB 6fi8: Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex

Protein crystallography data

The structure of Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex, PDB code: 6fi8 was solved by N.R.Morero, O.Barabas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 89.84 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 138.640, 138.640, 117.950, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.8

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex (pdb code 6fi8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex, PDB code: 6fi8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 6fi8

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Calcium binding site 1 out of 16 in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex


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 the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:40.4
occ:1.00
 NE2 A:HIS64 2.5 25.1 1.0
O A:HOH307 2.6 36.4 1.0
OD2 A:ASP61 2.7 30.8 1.0
OE1 B:GLN131 2.7 48.4 1.0
NE2 A:HIS66 2.8 26.7 1.0
O A:HOH341 3.0 27.1 1.0
O3' E:DC-1 3.0 52.1 1.0
OP1 E:DC0 3.0 55.7 1.0
CD B:GLN131 3.3 46.2 1.0
CE1 A:HIS64 3.4 25.0 1.0
NE2 B:GLN131 3.5 45.7 1.0
CE1 A:HIS66 3.5 26.3 1.0
P E:DC0 3.5 56.8 1.0
CD2 A:HIS64 3.6 24.7 1.0
CG A:ASP61 3.6 29.2 1.0
CD2 A:HIS66 3.8 26.2 1.0
CB A:ASP61 3.8 27.4 1.0
C4' E:DC-1 3.9 29.4 1.0
C3' E:DC-1 4.0 49.9 1.0
OP2 E:DC0 4.2 55.4 1.0
ND1 A:HIS64 4.6 24.8 1.0
C2' E:DC-1 4.6 49.9 1.0
CG B:GLN131 4.6 43.9 1.0
OH B:TYR127 4.6 46.2 1.0
CG A:HIS64 4.7 24.4 1.0
ND1 A:HIS66 4.7 26.5 1.0
C5' E:DC-1 4.7 28.9 1.0
O B:HOH202 4.8 48.7 1.0
OD1 A:ASP61 4.8 29.8 1.0
CG A:HIS66 4.9 26.7 1.0
O5' E:DC0 4.9 65.2 1.0
O4' E:DC-1 5.0 28.0 1.0

Calcium binding site 2 out of 16 in 6fi8

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Calcium binding site 2 out of 16 in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex


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 the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:54.8
occ:1.00
 O A:ILE128 2.4 64.3 1.0
O A:LYS125 2.4 50.6 1.0
OE1 B:GLU57 2.6 41.1 1.0
OE2 B:GLU57 2.9 41.3 1.0
CD B:GLU57 3.1 39.5 1.0
C A:LYS125 3.5 50.7 1.0
C A:ILE128 3.6 61.7 1.0
N A:ASN130 4.1 60.0 1.0
CB A:LYS125 4.2 46.9 1.0
CA A:LYS125 4.2 46.7 1.0
N A:GLN126 4.4 54.2 1.0
CA A:GLU129 4.5 65.3 1.0
N A:GLU129 4.5 60.7 1.0
CA A:GLN126 4.6 58.7 1.0
CG B:GLU57 4.6 35.4 1.0
CA A:ILE128 4.6 54.5 1.0
CB A:ASN130 4.7 56.8 1.0
N A:ILE128 4.7 56.0 1.0
OE1 A:GLU129 4.8 77.4 1.0
CB A:ILE128 4.8 50.2 1.0
C A:GLU129 4.8 63.8 1.0

Calcium binding site 3 out of 16 in 6fi8

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Calcium binding site 3 out of 16 in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex


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 the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:27.6
occ:1.00
 O C:HOH209 2.4 19.4 1.0
O B:HOH205 2.4 34.9 1.0
O C:HOH226 2.4 20.3 1.0
O B:HOH204 2.4 29.2 1.0
O6 C:DG39 2.5 21.9 1.0
O B:HOH206 2.5 22.6 1.0
N7 C:DG39 2.9 25.6 1.0
C6 C:DG39 3.2 23.9 1.0
C5 C:DG39 3.4 25.9 1.0
O6 C:DG38 3.6 24.7 1.0
C8 C:DG39 4.1 27.2 1.0
O6 C:DG40 4.3 30.2 1.0
O B:HIS11 4.3 22.9 1.0
OP1 C:DG19 4.3 22.8 1.0
C6 C:DG38 4.3 25.2 1.0
OD1 B:ASN12 4.4 26.2 1.0
O C:HOH223 4.4 28.5 1.0
ND1 B:HIS11 4.4 24.6 1.0
O C:HOH208 4.4 22.7 1.0
O C:HOH205 4.5 14.1 1.0
O B:HOH213 4.5 26.2 1.0
N1 C:DG39 4.6 25.4 1.0
N4 C:DC22 4.6 19.7 1.0
N7 C:DG38 4.7 25.4 1.0
C4 C:DG39 4.7 27.8 1.0
CB B:HIS11 4.7 22.9 1.0
C5 C:DG38 4.8 26.1 1.0
ND2 A:ASN109 4.9 16.4 1.0
N7 C:DG40 4.9 34.5 1.0

Calcium binding site 4 out of 16 in 6fi8

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Calcium binding site 4 out of 16 in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex


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 the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca102

b:39.8
occ:1.00
 O C:HOH243 2.4 33.6 1.0
O C:HOH234 2.4 43.5 1.0
O E:HOH106 2.4 42.6 1.0
O C:HOH219 2.5 24.8 1.0
O C:HOH244 2.5 46.8 1.0
O C:HOH215 2.5 43.9 1.0
O C:HOH206 4.2 35.2 1.0
O E:HOH111 4.2 40.8 1.0
N7 C:DG19 4.4 19.9 1.0
O6 C:DG19 4.6 22.9 1.0
O4' C:DA17 4.7 26.1 1.0
N7 E:DA-2 4.8 30.9 1.0
N3 C:DA16 4.8 24.9 1.0
C4' C:DA17 5.0 26.0 1.0

Calcium binding site 5 out of 16 in 6fi8

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Calcium binding site 5 out of 16 in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex


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 the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:36.0
occ:1.00
 O6 D:DG39 2.3 36.9 1.0
O D:HOH202 2.5 49.0 1.0
O A:HOH305 2.5 38.2 1.0
O D:HOH211 2.6 23.2 1.0
O D:HOH219 2.6 31.5 1.0
N7 D:DG39 3.0 36.1 1.0
C6 D:DG39 3.1 36.7 1.0
C5 D:DG39 3.4 36.2 1.0
O6 D:DG38 4.0 36.3 1.0
O D:HOH213 4.2 23.4 1.0
C8 D:DG39 4.3 36.6 1.0
OP1 D:DG19 4.3 30.2 1.0
O6 D:DG40 4.3 30.6 1.0
OD1 A:ASN12 4.4 36.1 1.0
O A:HIS11 4.4 31.0 1.0
N1 D:DG39 4.5 37.6 1.0
ND1 A:HIS11 4.6 33.3 1.0
O A:HOH333 4.6 36.4 1.0
CB A:HIS11 4.6 32.0 1.0
C6 D:DG38 4.6 36.4 1.0
N4 D:DC22 4.7 34.7 1.0
C4 D:DG39 4.8 37.1 1.0
N7 D:DG38 4.8 33.6 1.0
ND2 B:ASN109 4.9 23.3 1.0
N7 D:DG40 5.0 34.4 1.0
CG A:HIS11 5.0 32.0 1.0

Calcium binding site 6 out of 16 in 6fi8

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Calcium binding site 6 out of 16 in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex


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 the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca102

b:55.3
occ:1.00
 O F:HOH203 2.5 42.9 1.0
O D:HOH218 2.5 39.9 1.0
O D:HOH222 2.5 39.2 1.0
O D:HOH220 2.7 32.9 1.0
O D:HOH232 3.6 41.3 1.0
N7 D:DG19 4.6 25.0 1.0
O D:HOH215 4.7 40.5 1.0
O F:HOH202 4.8 44.1 1.0
N3 D:DA16 4.8 34.7 1.0
O6 D:DG19 4.9 30.4 1.0
N7 F:DA-2 4.9 28.8 1.0

Calcium binding site 7 out of 16 in 6fi8

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Calcium binding site 7 out of 16 in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex


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 the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca101

b:67.3
occ:1.00
 OP1 F:DC0 2.4 49.6 1.0
O B:HOH228 2.5 53.4 1.0
O A:HOH339 2.5 47.3 1.0
O A:HOH302 2.5 43.9 1.0
O F:HOH205 2.5 58.0 1.0
O F:HOH206 2.8 23.9 1.0
P F:DC0 3.8 48.2 1.0
OD2 B:ASP61 4.1 47.0 1.0
O A:TYR127 4.3 58.0 1.0
NE2 B:HIS66 4.4 35.8 1.0
NE2 B:GLN59 4.4 45.2 1.0
OE1 B:GLN59 4.6 46.5 1.0
OP2 F:DC0 4.6 49.4 1.0
O5' F:DC0 4.6 51.6 1.0
NE2 B:HIS64 4.7 25.3 1.0
O3' F:DC-1 4.7 39.2 1.0
OE2 A:GLU129 4.7 77.5 1.0
CD2 B:HIS66 4.8 35.4 1.0
CD B:GLN59 4.8 43.9 1.0
O B:HOH201 4.9 34.2 1.0

Calcium binding site 8 out of 16 in 6fi8

Go back to Calcium Binding Sites List in 6fi8
Calcium binding site 8 out of 16 in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex


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 the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:45.6
occ:1.00
 O G:HOH317 2.5 30.5 1.0
O H:HOH312 2.5 41.9 1.0
OE1 G:GLU57 2.5 47.7 1.0
OE2 G:GLU57 2.6 47.3 1.0
CD G:GLU57 2.8 45.1 1.0
OE1 H:GLU129 4.2 64.8 1.0
CG G:GLU57 4.2 40.0 1.0
NE2 G:GLN59 4.3 31.5 1.0
O G:ILE56 4.4 31.6 1.0
NZ H:LYS125 4.4 36.4 1.0
CA G:GLU57 4.4 31.8 1.0
CB G:GLU57 4.7 35.6 1.0
N G:MET58 4.8 28.5 1.0

Calcium binding site 9 out of 16 in 6fi8

Go back to Calcium Binding Sites List in 6fi8
Calcium binding site 9 out of 16 in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca202

b:74.7
occ:1.00
 O G:LYS125 2.4 60.0 1.0
O G:ILE128 2.4 55.6 1.0
OE1 H:GLU57 2.7 53.2 1.0
OE2 H:GLU57 2.7 54.5 1.0
CD H:GLU57 3.1 51.9 1.0
C G:LYS125 3.5 56.7 1.0
C G:ILE128 3.6 54.3 1.0
N G:ASN130 4.0 59.9 1.0
CA G:LYS125 4.2 49.5 1.0
CB G:LYS125 4.2 48.8 1.0
CA G:GLU129 4.4 59.3 1.0
N G:GLN126 4.4 60.0 1.0
N G:GLU129 4.4 56.0 1.0
CA G:ILE128 4.5 52.6 1.0
CA G:GLN126 4.6 61.8 1.0
N G:ILE128 4.6 53.5 1.0
CG H:GLU57 4.6 45.9 1.0
CB G:ASN130 4.6 60.5 1.0
CB G:ILE128 4.7 51.1 1.0
C G:GLU129 4.7 59.9 1.0
C G:GLN126 4.9 61.1 1.0
CA G:ASN130 4.9 61.5 1.0

Calcium binding site 10 out of 16 in 6fi8

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Calcium binding site 10 out of 16 in the Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of the IS608 Transposase in Complex with Left End 29-Mer Dna Hairpin and A 6-Mer Dna Representing the Intact Target Site: Pre-Cleavage Target Capture Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca201

b:0.5
occ:1.00
 O H:HOH317 2.5 56.1 1.0
OE2 H:GLU129 2.7 66.6 1.0
OE1 H:GLN126 3.3 52.8 1.0
NE2 H:GLN126 3.4 51.9 1.0
CD H:GLU129 3.7 64.2 1.0
CD H:GLN126 3.8 51.4 1.0
OE1 H:GLU129 4.0 64.8 1.0
NZ H:LYS125 4.3 36.4 1.0

Reference:

N.R.Morero, C.Zuliani, B.Kumar, A.Bebel, S.Okamoto, C.Guynet, A.B.Hickman, M.Chandler, F.Dyda, O.Barabas. Targeting IS608 Transposon Integration to Highly Specific Sequences By Structure-Based Transposon Engineering. Nucleic Acids Res. V. 46 4152 2018.
ISSN: ESSN 1362-4962
PubMed: 29635476
DOI: 10.1093/NAR/GKY235
Page generated: Sat Dec 12 06:06:51 2020

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