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

Protein crystallography data

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

Resolution Low / High (Å) 50.00 / 2.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.869, 91.799, 139.636, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 27.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Laglidadg Meganuclease I-Cpami Bound to Uncleaved Dna (pdb code 4yis). 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-Cpami Bound to Uncleaved Dna, PDB code: 4yis:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4yis

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Calcium binding site 1 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Cpami 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-Cpami Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:55.5
occ:1.00
O A:HOH406 2.3 57.2 1.0
OD2 A:ASP177 2.3 40.5 1.0
O A:HOH401 2.3 62.3 1.0
O E:HOH204 2.3 54.6 1.0
O A:ALA17 2.3 38.9 1.0
OP1 F:DT17 2.3 39.8 1.0
OD1 A:ASP177 2.9 44.6 1.0
CG A:ASP177 2.9 38.3 1.0
P F:DT17 3.1 35.4 1.0
OP2 F:DT17 3.3 38.1 1.0
C A:ALA17 3.4 35.1 1.0
O5' F:DT17 3.5 33.4 1.0
CA A:ALA17 4.0 35.9 1.0
OE2 A:GLU18 4.3 48.4 1.0
CA A:CA302 4.3 58.4 1.0
CB A:ASP177 4.4 36.0 1.0
O A:ASP16 4.6 39.2 1.0
O3' F:DT16 4.6 38.7 1.0
N A:GLU18 4.6 33.5 1.0
OP1 E:DT15 4.6 52.4 1.0
CB A:ALA17 4.7 35.4 1.0
OP1 E:DT16 4.7 45.3 1.0
C5' F:DT17 4.8 30.2 1.0
NZ A:LYS99 4.9 47.2 1.0

Calcium binding site 2 out of 5 in 4yis

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Calcium binding site 2 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Cpami 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-Cpami Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:58.4
occ:1.00
O F:HOH201 2.3 53.1 1.0
OP2 F:DT17 2.3 38.1 1.0
O A:GLY176 2.3 41.6 1.0
OP1 E:DT16 2.3 45.3 1.0
O A:HOH401 2.3 62.3 1.0
OE2 A:GLU18 2.3 48.4 1.0
OD1 A:ASP177 2.3 44.6 1.0
CD A:GLU18 3.0 44.2 1.0
OE1 A:GLU18 3.1 47.9 1.0
C A:GLY176 3.2 35.0 1.0
CG A:ASP177 3.6 38.3 1.0
P F:DT17 3.7 35.4 1.0
P E:DT16 3.7 49.6 1.0
CA A:GLY176 4.0 33.7 1.0
N A:ASP177 4.0 35.7 1.0
CA A:ASP177 4.0 34.7 1.0
OP1 F:DT16 4.2 58.3 1.0
C3' F:DT16 4.3 41.3 1.0
CA A:CA301 4.3 55.5 1.0
CB A:ASP177 4.4 36.0 1.0
OP1 F:DT17 4.4 39.8 1.0
O A:ALA17 4.4 38.9 1.0
OP2 E:DT16 4.5 54.8 1.0
OD2 A:ASP177 4.5 40.5 1.0
O3' F:DT16 4.5 38.7 1.0
CG A:GLU18 4.5 40.1 1.0
O3' E:DT15 4.6 53.3 1.0
O5' E:DT16 4.6 52.8 1.0
O5' F:DT17 4.6 33.4 1.0
C5' F:DT16 4.8 44.6 1.0
C4' F:DT16 4.8 41.6 1.0
C5' E:DT16 4.9 53.1 1.0
C A:ALA17 4.9 35.1 1.0

Calcium binding site 3 out of 5 in 4yis

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Calcium binding site 3 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Cpami 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-Cpami Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:65.2
occ:1.00
OD2 B:ASP177 2.3 42.1 1.0
OP1 D:DT17 2.3 52.5 1.0
O B:ALA17 2.4 40.3 1.0
P D:DT17 3.2 49.2 1.0
CG B:ASP177 3.4 43.1 1.0
O5' D:DT17 3.5 49.7 1.0
C B:ALA17 3.5 33.5 1.0
OP2 D:DT17 3.7 57.1 1.0
OD1 B:ASP177 3.9 46.4 1.0
CA B:ALA17 4.1 33.6 1.0
OP1 C:DT15 4.3 66.8 1.0
NZ B:LYS99 4.3 46.1 1.0
O B:ASP16 4.4 30.4 1.0
CB B:ASP177 4.6 40.2 1.0
N B:GLU18 4.6 35.8 1.0
O3' D:DT16 4.7 50.1 1.0
C5' D:DT17 4.7 44.6 1.0
C5' C:DT15 4.9 59.1 1.0
C4' D:DT17 5.0 42.3 1.0

Calcium binding site 4 out of 5 in 4yis

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Calcium binding site 4 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Cpami 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-Cpami Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:75.9
occ:1.00
OP1 C:DT16 2.3 59.5 1.0
OE2 B:GLU18 2.3 65.8 1.0
O B:GLY176 2.4 48.0 1.0
OP2 D:DT17 2.4 57.1 1.0
OD1 B:ASP177 2.4 46.4 1.0
OP1 D:DT16 2.5 69.0 1.0
CD B:GLU18 3.0 58.4 1.0
OE1 B:GLU18 3.1 66.0 1.0
C B:GLY176 3.6 40.4 1.0
CG B:ASP177 3.7 43.1 1.0
P C:DT16 3.8 58.0 1.0
C3' D:DT16 3.9 57.0 1.0
P D:DT17 3.9 49.2 1.0
C5' D:DT16 3.9 62.0 1.0
P D:DT16 4.0 65.2 1.0
O5' D:DT16 4.2 61.6 1.0
C4' D:DT16 4.2 61.8 1.0
CG B:GLU18 4.3 51.5 1.0
C5' C:DT16 4.3 61.0 1.0
O5' C:DT16 4.4 57.2 1.0
O3' D:DT16 4.4 50.1 1.0
CA B:GLY176 4.4 39.9 1.0
O3' C:DT15 4.5 60.0 1.0
N B:ASP177 4.5 39.3 1.0
CA B:ASP177 4.5 40.7 1.0
OD2 B:ASP177 4.6 42.1 1.0
CB B:ASP177 4.8 40.2 1.0
OP1 D:DT17 4.8 52.5 1.0
OP2 C:DT16 4.8 65.0 1.0
OP2 D:DT16 4.9 63.2 1.0
O5' D:DT17 4.9 49.7 1.0

Calcium binding site 5 out of 5 in 4yis

Go back to Calcium Binding Sites List in 4yis
Calcium binding site 5 out of 5 in the Crystal Structure of Laglidadg Meganuclease I-Cpami 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-Cpami Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:77.2
occ:1.00
OE1 B:GLU271 2.2 41.6 1.0
OD1 B:ASN268 2.3 40.6 1.0
CD B:GLU271 3.4 41.5 1.0
CG B:ASN268 3.5 37.9 1.0
OE2 B:GLU271 3.8 39.8 1.0
ND2 B:ASN268 4.2 39.4 1.0
CB B:ASN268 4.6 37.0 1.0
CG B:GLU271 4.6 39.7 1.0
CA B:ASN268 4.7 37.7 1.0
CB B:GLU271 4.7 39.8 1.0
CG1 B:ILE293 4.9 42.2 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: Wed Jul 9 03:12:05 2025

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