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Calcium in PDB 3dvo: Sgrai with Cognate Dna and Calcium Bound

Enzymatic activity of Sgrai with Cognate Dna and Calcium Bound

All present enzymatic activity of Sgrai with Cognate Dna and Calcium Bound:
3.1.21.4;

Protein crystallography data

The structure of Sgrai with Cognate Dna and Calcium Bound, PDB code: 3dvo was solved by P.W.Dunten, N.C.Horton, E.J.Little, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.07 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.136, 119.248, 123.799, 90.00, 95.62, 90.00
R / Rfree (%) 22 / 27.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Sgrai with Cognate Dna and Calcium Bound (pdb code 3dvo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Sgrai with Cognate Dna and Calcium Bound, PDB code: 3dvo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3dvo

Go back to Calcium Binding Sites List in 3dvo
Calcium binding site 1 out of 8 in the Sgrai with Cognate Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Sgrai with Cognate Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca340

b:21.3
occ:1.00
 OD2 A:ASP188 2.4 24.0 1.0
OP1 F:DC8 2.4 21.1 1.0
O A:HOH530 2.4 19.4 1.0
O A:HOH531 2.5 20.1 1.0
O F:HOH746 2.5 17.0 1.0
O A:PHE241 2.5 19.9 1.0
OD1 A:ASP188 3.0 35.7 1.0
CG A:ASP188 3.0 27.4 1.0
P F:DC8 3.5 22.7 1.0
C A:PHE241 3.7 23.1 1.0
N A:PHE241 3.9 24.7 1.0
O5' F:DC8 3.9 19.5 1.0
OP2 F:DC8 4.1 24.7 1.0
C5' F:DC8 4.2 22.3 1.0
CA A:PHE241 4.3 21.4 1.0
O A:HOH409 4.4 21.7 1.0
CB A:ASP188 4.5 28.3 1.0
O A:HOH506 4.5 25.1 1.0
CB A:PHE241 4.5 19.1 1.0
OP2 F:DC9 4.6 20.5 1.0
O A:HOH478 4.6 32.2 1.0
CG A:LYS242 4.7 26.0 1.0
N A:LYS242 4.7 20.4 1.0
C A:ALA240 4.8 23.3 1.0
O3' F:DA7 4.8 24.3 1.0
OE1 A:GLU103 4.8 41.1 1.0
O A:HOH514 4.9 31.6 1.0

Calcium binding site 2 out of 8 in 3dvo

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Calcium binding site 2 out of 8 in the Sgrai with Cognate Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Sgrai with Cognate Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca341

b:43.3
occ:1.00
 O A:LEU150 2.5 27.5 1.0
O A:HOH532 2.6 29.3 1.0
OD1 A:ASN149 2.6 28.8 1.0
OE2 A:GLU103 2.6 37.5 1.0
O A:HOH515 2.7 30.0 1.0
O A:HOH533 2.8 39.5 1.0
O A:HOH442 3.0 30.0 1.0
CD A:GLU103 3.5 37.8 1.0
C A:LEU150 3.5 20.6 1.0
CG A:ASN149 3.6 25.3 1.0
OE1 A:GLU103 3.9 41.1 1.0
ND2 A:ASN149 4.0 28.4 1.0
O A:HOH514 4.2 31.6 1.0
CA A:PRO151 4.2 22.8 1.0
N A:LEU150 4.3 22.5 1.0
N A:PRO151 4.3 26.1 1.0
O A:ASP188 4.4 24.9 1.0
O A:HOH428 4.4 25.1 1.0
CA A:LEU150 4.5 21.2 1.0
C A:PRO151 4.6 23.3 1.0
C A:ASN149 4.6 24.0 1.0
CG A:GLU103 4.8 27.0 1.0
N A:ARG152 4.8 20.1 1.0
CB A:ASN149 4.9 19.2 1.0
O A:ASN149 5.0 20.9 1.0

Calcium binding site 3 out of 8 in 3dvo

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Calcium binding site 3 out of 8 in the Sgrai with Cognate Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Sgrai with Cognate Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca340

b:24.9
occ:1.00
 OD1 B:ASP188 2.4 29.1 1.0
O B:HOH493 2.4 22.1 1.0
OP1 E:DC8 2.4 23.6 1.0
O B:HOH494 2.4 17.5 1.0
O E:HOH46 2.4 20.8 1.0
O B:PHE241 2.5 21.7 1.0
OD2 B:ASP188 3.0 36.5 1.0
CG B:ASP188 3.0 33.5 1.0
P E:DC8 3.5 24.4 1.0
C B:PHE241 3.6 23.7 1.0
O5' E:DC8 3.7 18.0 1.0
N B:PHE241 3.8 19.4 1.0
OP2 E:DC8 4.1 24.6 1.0
C5' E:DC8 4.2 21.4 1.0
CA B:PHE241 4.2 19.5 1.0
O E:HOH20 4.3 23.7 1.0
O B:HOH475 4.4 29.9 1.0
O B:HOH379 4.5 26.6 1.0
CB B:PHE241 4.5 21.0 1.0
CB B:ASP188 4.5 26.5 1.0
OP2 E:DC9 4.5 17.3 1.0
CG B:LYS242 4.7 22.2 1.0
N B:LYS242 4.7 23.9 1.0
O3' E:DA7 4.8 26.1 1.0
C B:ALA240 4.8 23.4 1.0
CA B:LYS242 5.0 18.8 1.0

Calcium binding site 4 out of 8 in 3dvo

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Calcium binding site 4 out of 8 in the Sgrai with Cognate Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Sgrai with Cognate Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca341

b:50.4
occ:1.00
 O B:LEU150 2.4 22.2 1.0
OD1 B:ASN149 2.5 30.4 1.0
O B:HOH496 2.7 38.5 1.0
OE1 B:GLU103 2.7 42.5 1.0
O B:HOH495 2.8 37.4 1.0
O B:HOH478 3.4 33.9 1.0
CD B:GLU103 3.4 36.7 1.0
C B:LEU150 3.5 23.4 1.0
CG B:ASN149 3.6 28.1 1.0
O B:ASP188 3.8 28.6 1.0
OE2 B:GLU103 3.9 39.1 1.0
ND2 B:ASN149 4.1 29.3 1.0
N B:LEU150 4.2 24.3 1.0
CG B:GLU103 4.3 23.3 1.0
N B:PRO151 4.4 25.1 1.0
CA B:PRO151 4.4 23.9 1.0
CA B:LEU150 4.5 21.7 1.0
C B:ASN149 4.5 24.8 1.0
O B:HOH347 4.5 25.2 1.0
C B:ASP188 4.8 26.5 1.0
O B:ASN149 4.8 26.5 1.0
C B:PRO151 4.8 22.6 1.0
CB B:ASN149 4.9 20.5 1.0
CA B:ASP188 4.9 26.2 1.0

Calcium binding site 5 out of 8 in 3dvo

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Calcium binding site 5 out of 8 in the Sgrai with Cognate Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Sgrai with Cognate Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca340

b:26.2
occ:1.00
 O C:HOH499 2.4 26.8 1.0
O C:PHE241 2.4 23.5 1.0
O C:HOH500 2.4 22.7 1.0
OP1 H:DC8 2.5 28.8 1.0
O H:HOH760 2.5 25.8 1.0
OD1 C:ASP188 2.5 33.6 1.0
OD2 C:ASP188 3.1 38.4 1.0
CG C:ASP188 3.1 31.3 1.0
P H:DC8 3.5 24.3 1.0
C C:PHE241 3.5 25.1 1.0
N C:PHE241 3.9 27.7 1.0
O5' H:DC8 3.9 22.0 1.0
C5' H:DC8 3.9 21.3 1.0
OP2 H:DC8 4.1 23.8 1.0
OE1 C:GLU103 4.1 38.7 1.0
CA C:PHE241 4.2 21.6 1.0
O C:HOH342 4.3 23.4 1.0
CB C:PHE241 4.5 21.9 1.0
OP2 H:DC9 4.5 20.8 1.0
CB C:ASP188 4.6 26.6 1.0
CG C:LYS242 4.6 19.9 1.0
N C:LYS242 4.6 22.6 1.0
CD C:GLU103 4.7 40.1 1.0
C C:ALA240 4.8 26.7 1.0
O3' H:DA7 4.8 19.8 1.0
O C:HOH375 4.8 28.0 1.0
CA C:LYS242 4.9 21.1 1.0
O3' H:DC8 5.0 18.1 1.0
OE2 C:GLU103 5.0 43.0 1.0

Calcium binding site 6 out of 8 in 3dvo

Go back to Calcium Binding Sites List in 3dvo
Calcium binding site 6 out of 8 in the Sgrai with Cognate Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Sgrai with Cognate Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca341

b:57.6
occ:1.00
 O C:LEU150 2.6 27.7 1.0
OD1 C:ASN149 2.8 41.0 1.0
OE2 C:GLU103 2.9 43.0 1.0
O C:HOH501 2.9 46.9 1.0
O C:HOH391 3.4 34.9 1.0
CD C:GLU103 3.6 40.1 1.0
CG C:ASN149 3.6 31.8 1.0
C C:LEU150 3.7 24.7 1.0
O C:HOH354 3.8 36.3 1.0
ND2 C:ASN149 3.8 33.0 1.0
OE1 C:GLU103 4.0 38.7 1.0
O C:ASP188 4.1 27.7 1.0
N C:LEU150 4.3 25.7 1.0
O C:HOH462 4.4 35.6 1.0
CA C:PRO151 4.5 28.0 1.0
CG C:GLU103 4.5 29.2 1.0
N C:PRO151 4.5 25.5 1.0
CA C:LEU150 4.6 31.4 1.0
C C:ASN149 4.7 26.4 1.0
O C:HOH347 4.7 25.1 1.0
C C:PRO151 4.8 25.3 1.0
O C:HOH481 4.9 35.7 1.0
CB C:ASN149 5.0 26.8 1.0
OD2 C:ASP188 5.0 38.4 1.0
C C:ASP188 5.0 28.1 1.0
CA C:ASP188 5.0 25.2 1.0
CB C:ASP188 5.0 26.6 1.0

Calcium binding site 7 out of 8 in 3dvo

Go back to Calcium Binding Sites List in 3dvo
Calcium binding site 7 out of 8 in the Sgrai with Cognate Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Sgrai with Cognate Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca340

b:24.5
occ:1.00
 OD2 D:ASP188 2.4 29.2 1.0
O D:HOH496 2.4 25.4 1.0
OP1 G:DC8 2.5 27.3 1.0
O D:PHE241 2.5 23.0 1.0
O G:HOH47 2.6 27.6 1.0
O D:HOH497 2.6 25.1 1.0
OD1 D:ASP188 3.0 38.0 1.0
CG D:ASP188 3.0 29.3 1.0
P G:DC8 3.6 25.5 1.0
C D:PHE241 3.6 24.4 1.0
O5' G:DC8 3.8 22.7 1.0
N D:PHE241 3.9 22.2 1.0
C5' G:DC8 4.1 24.5 1.0
O D:HOH411 4.2 30.5 1.0
CA D:PHE241 4.2 23.2 1.0
OP2 G:DC8 4.3 26.5 1.0
O G:HOH38 4.3 21.8 1.0
O D:HOH478 4.4 34.9 1.0
CB D:ASP188 4.5 30.5 1.0
CG D:LYS242 4.5 21.9 1.0
CB D:PHE241 4.6 27.6 1.0
OP2 G:DC9 4.6 24.1 1.0
O D:HOH476 4.6 27.1 1.0
N D:LYS242 4.7 23.2 1.0
C D:ALA240 4.8 25.3 1.0
O3' G:DA7 4.8 30.6 1.0
O D:HOH391 4.9 38.0 1.0
CA D:LYS242 4.9 23.5 1.0

Calcium binding site 8 out of 8 in 3dvo

Go back to Calcium Binding Sites List in 3dvo
Calcium binding site 8 out of 8 in the Sgrai with Cognate Dna and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Sgrai with Cognate Dna and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca341

b:51.1
occ:1.00
 O D:LEU150 2.5 31.1 1.0
O D:HOH498 2.5 37.1 1.0
OD1 D:ASN149 2.6 35.0 1.0
OE2 D:GLU103 2.7 43.0 1.0
OE1 D:GLU103 2.9 44.3 1.0
CD D:GLU103 3.0 40.8 1.0
O D:HOH391 3.1 38.0 1.0
O D:HOH397 3.1 42.8 1.0
O D:HOH428 3.5 30.2 1.0
CG D:ASN149 3.5 30.2 1.0
C D:LEU150 3.6 26.0 1.0
O D:ASP188 3.6 32.1 1.0
ND2 D:ASN149 3.9 33.5 1.0
O D:HOH382 4.1 39.5 1.0
N D:LEU150 4.1 28.9 1.0
CG D:GLU103 4.2 34.2 1.0
CA D:PRO151 4.4 26.1 1.0
CA D:LEU150 4.4 24.6 1.0
N D:PRO151 4.5 25.1 1.0
C D:ASN149 4.5 25.3 1.0
C D:ASP188 4.5 32.0 1.0
CA D:ASP188 4.7 32.8 1.0
O D:HOH452 4.7 34.3 1.0
CB D:ASN149 4.8 21.8 1.0
C D:PRO151 4.9 26.9 1.0
O D:HOH348 4.9 24.0 1.0
CA D:ASN149 4.9 25.0 1.0
CB D:ASP188 5.0 30.5 1.0
OD1 D:ASP188 5.0 38.0 1.0

Reference:

P.W.Dunten, E.J.Little, M.T.Gregory, V.M.Manohar, M.Dalton, D.Hough, J.Bitinaite, N.C.Horton. The Structure of Sgrai Bound to Dna; Recognition of An 8 Base Pair Target. Nucleic Acids Res. V. 36 5405 2008.
ISSN: ISSN 0305-1048
PubMed: 18701646
DOI: 10.1093/NAR/GKN510
Page generated: Sat Jul 13 09:11:48 2024

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