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

Protein crystallography data

The structure of Crystal Structure of Laglidadg Meganuclease I-Gpemi Bound to Uncleaved Dna, PDB code: 4yhx 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 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 151.985, 39.895, 73.986, 90.00, 90.43, 90.00
R / Rfree (%) 17.8 / 24.4

Calcium Binding Sites:

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

Calcium binding site 1 out of 3 in 4yhx

Go back to Calcium Binding Sites List in 4yhx
Calcium binding site 1 out of 3 in the Crystal Structure of Laglidadg Meganuclease I-Gpemi 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-Gpemi Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:25.2
occ:1.00
OP2 C:DA16 2.2 23.2 1.0
OP1 B:DC15 2.3 21.5 1.0
O C:HOH135 2.3 34.1 1.0
O A:ALA18 2.3 24.0 1.0
OE1 A:GLU183 2.3 30.8 1.0
O A:HOH552 2.4 19.8 1.0
CD A:GLU183 3.4 29.5 1.0
C A:ALA18 3.4 23.7 1.0
P C:DA16 3.5 27.3 1.0
O B:HOH112 3.7 42.5 1.0
OE2 A:GLU183 3.7 26.1 1.0
P B:DC15 3.7 23.0 1.0
CA A:CA402 3.8 42.1 1.0
O5' C:DA16 4.0 28.4 1.0
CA A:ALA18 4.0 21.8 1.0
OE1 A:GLN209 4.3 23.3 1.0
OP1 C:DA16 4.3 28.1 1.0
NE2 A:GLN209 4.4 21.1 1.0
O3' B:DT14 4.4 24.1 1.0
C5' C:DA16 4.4 27.9 1.0
C5' B:DC15 4.5 24.1 1.0
N A:GLU19 4.6 23.9 1.0
O3' C:DT15 4.6 25.1 1.0
O5' B:DC15 4.6 23.9 1.0
O A:ASP17 4.6 22.9 1.0
C4' B:DC15 4.7 25.6 1.0
OP2 B:DC15 4.7 24.0 1.0
CG A:GLU183 4.7 28.6 1.0
CD A:GLN209 4.7 24.3 1.0
OE1 A:GLU19 4.8 41.2 1.0
CB A:ALA18 4.8 24.0 1.0
CA A:GLU19 5.0 25.3 1.0

Calcium binding site 2 out of 3 in 4yhx

Go back to Calcium Binding Sites List in 4yhx
Calcium binding site 2 out of 3 in the Crystal Structure of Laglidadg Meganuclease I-Gpemi 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-Gpemi Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:42.1
occ:1.00
OE2 A:GLU183 2.2 26.1 1.0
O3' B:DC15 2.6 24.3 1.0
OP2 C:DA16 2.6 23.2 1.0
OP2 B:DA16 2.6 23.7 1.0
O3' C:DT15 2.7 25.1 1.0
OE1 A:GLU19 2.8 41.2 1.0
P B:DA16 3.1 27.5 1.0
CD A:GLU183 3.2 29.5 1.0
OE2 A:GLU19 3.3 36.0 1.0
P C:DA16 3.3 27.3 1.0
CD A:GLU19 3.3 37.2 1.0
C3' B:DC15 3.6 24.9 1.0
OE1 A:GLU183 3.6 30.8 1.0
C3' C:DT15 3.7 24.9 1.0
CA A:CA403 3.8 26.7 1.0
CA A:CA401 3.8 25.2 1.0
O A:GLY182 3.9 24.4 1.0
O5' B:DA16 3.9 25.8 1.0
C4' B:DC15 4.0 25.6 1.0
O5' C:DA16 4.1 28.4 1.0
C4' C:DT15 4.1 22.8 1.0
O A:ALA18 4.1 24.0 1.0
OP1 B:DA16 4.4 26.8 1.0
OP1 C:DA16 4.5 28.1 1.0
C A:GLY182 4.5 22.1 1.0
CG A:GLU183 4.5 28.6 1.0
C A:ALA18 4.7 23.7 1.0
CG A:GLU19 4.7 35.0 1.0
C5' B:DC15 4.8 24.1 1.0
OP1 B:DC15 4.8 21.5 1.0
O B:HOH128 4.9 40.5 1.0
CA A:GLU183 4.9 23.2 1.0
C5' C:DT15 4.9 23.4 1.0
C2' B:DC15 5.0 22.1 1.0

Calcium binding site 3 out of 3 in 4yhx

Go back to Calcium Binding Sites List in 4yhx
Calcium binding site 3 out of 3 in the Crystal Structure of Laglidadg Meganuclease I-Gpemi 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-Gpemi Bound to Uncleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:26.7
occ:1.00
OP2 B:DA16 2.2 23.7 1.0
O B:HOH145 2.3 24.1 1.0
O A:HOH555 2.3 28.2 1.0
OP1 C:DT15 2.3 25.1 1.0
O A:GLY182 2.4 24.4 1.0
OE2 A:GLU19 2.4 36.0 1.0
C A:GLY182 3.4 22.1 1.0
O B:HOH117 3.5 41.8 1.0
P B:DA16 3.6 27.5 1.0
CD A:GLU19 3.6 37.2 1.0
P C:DT15 3.7 25.6 1.0
CA A:CA402 3.8 42.1 1.0
CA A:GLY182 3.8 22.4 1.0
O5' B:DA16 4.1 25.8 1.0
OE1 A:GLU19 4.1 41.2 1.0
C5' B:DA16 4.2 26.3 1.0
O3' C:DA14 4.2 25.8 1.0
C5' C:DT15 4.4 23.4 1.0
OP1 B:DA16 4.4 26.8 1.0
O A:SER181 4.4 22.4 1.0
C4' C:DT15 4.5 22.8 1.0
O5' C:DT15 4.6 24.1 1.0
OE2 A:GLU183 4.6 26.1 1.0
N A:GLU183 4.6 23.0 1.0
O3' B:DC15 4.6 24.3 1.0
OP2 C:DT15 4.8 22.0 1.0
CG A:GLU19 4.8 35.0 1.0
C4' B:DA16 5.0 24.3 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: Wed Jul 9 03:10:13 2025

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