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Calcium in PDB 4yit: Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna

Protein crystallography data

The structure of Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna, PDB code: 4yit was solved by J.P.Hallinan, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.24
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.960, 61.536, 88.621, 97.18, 99.10, 101.89
R / Rfree (%) 22.5 / 29.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna (pdb code 4yit). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna, PDB code: 4yit:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4yit

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Calcium binding site 1 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna


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 Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:50.3
occ:1.00
O A:GLY12 2.0 37.5 1.0
OP1 B:DA14 2.4 34.9 1.0
OP1 C:DA16 2.6 45.8 1.0
OE2 A:GLU169 2.8 51.2 1.0
C A:GLY12 3.2 37.7 1.0
CD A:GLU169 3.3 49.6 1.0
P C:DA16 3.3 45.4 1.0
O5' C:DA16 3.4 43.9 1.0
OE1 A:GLU169 3.4 49.8 1.0
NE2 A:GLN196 3.6 37.4 1.0
C5' C:DA16 3.6 45.3 1.0
OP2 C:DA16 3.7 47.4 1.0
CA A:GLY12 3.9 36.5 1.0
P B:DA14 3.9 36.7 1.0
NZ A:LYS93 4.0 64.1 1.0
OE1 A:GLN196 4.1 37.7 1.0
N A:GLU13 4.2 38.8 1.0
CD A:GLN196 4.3 37.1 1.0
C4' B:DA14 4.4 36.1 1.0
CG A:GLU169 4.4 48.9 1.0
CA A:GLU13 4.5 40.9 1.0
C5' B:DA14 4.5 35.1 1.0
O A:ASP11 4.7 31.4 1.0
O3' B:DA13 4.7 37.3 1.0
O5' B:DA14 4.7 35.9 1.0
OP2 B:DA14 4.7 34.5 1.0
O3' C:DA15 4.8 40.0 1.0
C4' C:DA16 4.9 48.0 1.0
C3' C:DA16 5.0 49.4 1.0

Calcium binding site 2 out of 5 in 4yit

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Calcium binding site 2 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna


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 Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:43.5
occ:1.00
OP1 C:DA15 2.1 37.6 1.0
OE1 A:GLU13 2.4 41.7 1.0
OP2 B:DA15 2.4 39.1 1.0
O A:ALA168 2.4 55.6 1.0
CD A:GLU13 3.4 42.5 1.0
C A:ALA168 3.4 50.9 1.0
P C:DA15 3.6 37.8 1.0
CA A:ALA168 3.8 49.2 1.0
OE2 A:GLU13 3.8 45.2 1.0
P B:DA15 3.8 40.1 1.0
C5' C:DA15 3.9 38.7 1.0
O5' C:DA15 4.2 38.4 1.0
O3' C:DA14 4.3 38.8 1.0
CB A:ALA168 4.4 49.4 1.0
NZ A:LYS249 4.5 40.0 1.0
OP1 B:DA15 4.6 38.2 1.0
N A:GLU169 4.7 49.8 1.0
OP2 C:DA15 4.7 35.0 1.0
CG A:GLU13 4.7 41.2 1.0
O5' B:DA15 4.7 40.0 1.0
C5' B:DA15 4.7 39.4 1.0
O3' B:DA14 4.8 37.1 1.0
C4' C:DA15 4.8 36.9 1.0
OE1 A:GLU169 4.9 49.8 1.0
O A:SER167 5.0 47.3 1.0

Calcium binding site 3 out of 5 in 4yit

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Calcium binding site 3 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna


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 Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:56.7
occ:1.00
OD2 D:ASP209 2.1 69.5 1.0
OD2 A:ASP209 3.1 68.2 1.0
CG D:ASP209 3.3 67.0 1.0
O A:ASP209 3.5 51.1 1.0
CA A:ASP209 3.5 58.8 1.0
CG A:ASP209 3.6 66.2 1.0
CB A:ASP209 3.6 62.1 1.0
OD1 A:ASN212 3.7 64.7 1.0
CB D:ASP209 3.9 65.2 1.0
C A:ASP209 4.0 55.0 1.0
CG A:ASN212 4.0 63.4 1.0
CA A:ASN212 4.0 59.2 1.0
CB A:ASN212 4.1 61.8 1.0
OD1 D:ASP209 4.3 59.8 1.0
O D:ASP209 4.5 59.7 1.0
OD1 A:ASP209 4.6 67.8 1.0
N A:ASN212 4.6 57.3 1.0
N A:ASP209 4.8 59.3 1.0
C D:ASP209 4.9 59.7 1.0
ND2 A:ASN212 5.0 61.0 1.0

Calcium binding site 4 out of 5 in 4yit

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Calcium binding site 4 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna


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 Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:33.5
occ:1.00
OP1 E:DA14 2.1 32.2 1.0
O D:GLY12 2.5 33.2 1.0
OP1 F:DA16 2.6 42.4 1.0
OE2 D:GLU169 2.7 30.9 1.0
OE1 D:GLU169 3.3 29.6 1.0
P F:DA16 3.3 45.2 1.0
C5' F:DA16 3.4 49.7 1.0
CD D:GLU169 3.4 30.5 1.0
OP2 F:DA16 3.5 46.6 1.0
P E:DA14 3.6 32.6 1.0
C D:GLY12 3.7 31.9 1.0
O5' F:DA16 3.8 45.9 1.0
C4' F:DA16 4.0 52.5 1.0
NZ D:LYS93 4.1 51.5 1.0
OE1 D:GLN196 4.3 46.6 1.0
O3' E:DA13 4.3 33.4 1.0
OP2 E:DA14 4.4 32.1 1.0
C4' E:DA14 4.4 34.0 1.0
NE2 D:GLN196 4.5 50.1 1.0
C5' E:DA14 4.5 34.5 1.0
O D:ASP11 4.5 26.2 1.0
CA D:GLY12 4.5 30.2 1.0
O5' E:DA14 4.6 33.0 1.0
N D:GLU13 4.7 34.1 1.0
CG D:GLU169 4.8 29.4 1.0
CA D:GLU13 4.8 36.3 1.0
CD D:GLN196 4.8 47.2 1.0
O3' F:DA15 4.8 40.4 1.0
C3' F:DA16 4.9 51.4 1.0

Calcium binding site 5 out of 5 in 4yit

Go back to Calcium Binding Sites List in 4yit
Calcium binding site 5 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna


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 Laglidadg Meganuclease I-Aabmi Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:40.8
occ:1.00
OP2 E:DA15 2.2 31.6 1.0
OP1 F:DA15 2.3 37.1 1.0
OE1 D:GLU13 2.4 39.1 1.0
O D:ALA168 2.4 31.7 1.0
CD D:GLU13 3.3 38.7 1.0
OE2 D:GLU13 3.5 36.4 1.0
C D:ALA168 3.5 30.9 1.0
P E:DA15 3.5 31.4 1.0
P F:DA15 3.8 34.5 1.0
CA D:ALA168 4.1 32.8 1.0
NZ D:LYS249 4.1 53.1 1.0
OP1 E:DA15 4.1 31.9 1.0
C5' F:DA15 4.3 36.6 1.0
C5' E:DA15 4.3 38.4 1.0
O5' E:DA15 4.4 34.1 1.0
O3' F:DA14 4.4 32.5 1.0
O5' F:DA15 4.5 34.9 1.0
O D:SER167 4.5 36.2 1.0
CG D:GLU13 4.6 38.8 1.0
N D:GLU169 4.6 29.1 1.0
O3' E:DA14 4.7 31.4 1.0
OP2 F:DA15 4.7 34.4 1.0
CD2 D:LEU39 4.8 54.6 1.0
O E:HOH101 4.8 4.5 1.0
C4' F:DA15 4.8 37.6 1.0
CA D:GLU169 5.0 29.1 1.0
C4' E:DA15 5.0 40.3 1.0

Reference:

A.R.Lambert, J.P.Hallinan, B.W.Shen, J.K.Chik, J.M.Bolduc, N.Kulshina, L.I.Robins, B.K.Kaiser, J.Jarjour, K.Havens, A.M.Scharenberg, B.L.Stoddard. Indirect Dna Sequence Recognition and Its Impact on Nuclease Cleavage Activity. Structure V. 24 862 2016.
ISSN: ISSN 0969-2126
PubMed: 27133026
DOI: 10.1016/J.STR.2016.03.024
Page generated: Sat Dec 12 05:13:32 2020

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