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Calcium in PDB 1ene: 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium.

Protein crystallography data

The structure of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium., PDB code: 1ene was solved by T.K.Chiu, R.E.Dickerson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 0.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 31.750, 25.725, 34.088, 90.00, 116.88, 90.00
R / Rfree (%) 12.1 / 14.8

Calcium Binding Sites:

The binding sites of Calcium atom in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium. (pdb code 1ene). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium., PDB code: 1ene:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 1ene

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Calcium binding site 1 out of 7 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca111

b:5.0
occ:0.50
 O A:HOH1360 2.4 5.3 0.5
O A:HOH1364 2.4 5.8 0.5
O A:HOH1359 2.4 5.9 0.5
O A:HOH1362 2.4 5.1 0.5
O A:HOH1361 2.4 4.8 0.5
O A:EOH1114 2.4 5.4 0.5
O A:HOH1363 2.5 6.3 0.5
O A:HOH1356 2.6 8.5 0.5
O A:HOH1301 2.7 11.5 0.5
C1 A:EOH1114 2.9 6.1 0.5
O A:HOH249 3.2 6.4 0.4
H5' A:DC2 3.4 6.4 0.6
H4' A:DC2 3.8 6.1 0.4
H4' A:DC2 3.8 6.0 0.6
C5' A:DC2 4.1 5.3 0.6
H5'' A:DC2 4.1 6.4 0.6
H5' A:DC2 4.1 6.7 0.4
C2 A:EOH1114 4.3 4.2 0.5
C4' A:DC2 4.4 5.0 0.6
C4' A:DC2 4.4 5.1 0.4
O4' A:DC2 4.5 4.5 1.0
O A:HOH202 4.7 6.2 1.0
C5' A:DC2 4.7 5.6 0.4
O2 A:DC1 4.8 7.1 1.0
H1' A:DC1 5.0 8.8 1.0
H5'' A:DC2 5.0 6.7 0.4

Calcium binding site 2 out of 7 in 1ene

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Calcium binding site 2 out of 7 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca112

b:6.1
occ:0.58
 CA A:CA112 0.0 6.1 0.6
CA A:CA112 1.2 9.7 0.4
O A:HOH1371 1.6 9.7 0.4
O A:HOH1366 1.8 11.2 0.4
O A:HOH1366 2.4 7.5 0.6
O A:HOH1371 2.4 7.1 0.6
O A:HOH1370 2.4 8.8 0.6
O A:HOH1369 2.4 10.2 0.6
O A:HOH1367 2.4 8.5 0.6
O A:HOH1365 2.5 7.9 0.6
O A:HOH1368 2.5 6.6 0.6
O A:HOH1365 2.7 8.8 0.4
O A:HOH1370 2.9 10.7 0.4
O A:HOH222 3.0 9.9 0.4
O A:HOH1369 3.1 11.8 0.4
O A:HOH1367 3.2 10.8 0.4
O A:HOH1368 3.6 10.6 0.4
H21 A:DG4 3.7 7.7 1.0
O A:HOH206 3.7 11.9 0.4
H5' A:DG6 3.9 8.3 0.4
O A:HOH230 3.9 17.4 0.4
N2 A:DG4 4.4 6.4 1.0
H22 A:DG4 4.4 7.7 1.0
O A:HOH230 4.4 10.3 0.6
O A:HOH208 4.5 11.3 1.0
O A:HOH206 4.5 5.0 0.6
O A:HOH222 4.6 8.4 0.6
H5'' A:DG6 4.7 8.3 0.4
C5' A:DG6 4.7 6.9 0.4
H4' A:DG6 4.8 13.5 0.6
H5' A:DG6 4.9 11.6 0.6
H4' A:DG6 4.9 12.3 0.4

Calcium binding site 3 out of 7 in 1ene

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Calcium binding site 3 out of 7 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca112

b:9.7
occ:0.42
 CA A:CA112 0.0 9.7 0.4
CA A:CA112 1.2 6.1 0.6
O A:HOH1369 1.6 10.2 0.6
O A:HOH1370 1.8 8.8 0.6
O A:HOH1365 2.3 7.9 0.6
O A:HOH1370 2.4 10.7 0.4
O A:HOH1369 2.4 11.8 0.4
O A:HOH1366 2.4 11.2 0.4
O A:HOH1368 2.4 10.6 0.4
O A:HOH1367 2.4 10.8 0.4
O A:HOH1371 2.4 9.7 0.4
O A:HOH1365 2.5 8.8 0.4
O A:HOH1367 2.8 8.5 0.6
H5' A:DG6 3.1 8.3 0.4
O A:HOH1366 3.2 7.5 0.6
O A:HOH1371 3.4 7.1 0.6
O A:HOH1368 3.5 6.6 0.6
H4' A:DG6 3.7 13.5 0.6
H4' A:DG6 3.8 12.3 0.4
C5' A:DG6 3.8 6.9 0.4
H5'' A:DG6 3.9 8.3 0.4
H21 A:DG4 3.9 7.7 1.0
H5' A:DG6 4.1 11.6 0.6
O A:HOH222 4.1 9.9 0.4
C4' A:DG6 4.2 10.3 0.4
O4' A:DG6 4.4 10.0 1.0
C4' A:DG6 4.4 11.2 0.6
H22 A:DG4 4.5 7.7 1.0
O A:HOH208 4.5 11.3 1.0
N2 A:DG4 4.5 6.4 1.0
O2 A:DC5 4.6 8.6 1.0
O A:HOH206 4.6 11.9 0.4
C5' A:DG6 4.8 9.7 0.6
H1' A:DC5 4.9 10.4 1.0

Calcium binding site 4 out of 7 in 1ene

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Calcium binding site 4 out of 7 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca113

b:5.5
occ:0.38
 O A:HOH1377 0.5 9.5 0.3
O A:HOH259 1.0 10.7 0.3
O A:HOH1373 2.4 7.2 0.4
O A:HOH1376 2.4 7.5 0.4
O A:HOH1374 2.4 8.0 0.4
O A:HOH1372 2.5 7.1 0.4
O A:HOH1375 2.5 6.7 0.4
O A:HOH1379 2.6 11.5 0.3
CA A:CA1113 2.6 7.4 0.3
O A:HOH1379 2.7 9.6 0.3
O A:HOH1381 2.9 8.1 0.3
O A:HOH1380 3.1 5.6 0.3
O A:HOH259 3.2 6.8 0.3
O A:HOH1381 3.2 13.3 0.3
H41 A:DC1 3.4 6.5 1.0
O A:HOH215 3.4 12.8 0.3
N4 A:DC1 4.1 5.4 1.0
H42 A:DC1 4.1 6.5 1.0
O A:HOH252 4.5 8.9 0.2
O A:HOH1378 4.6 8.7 0.3
CA A:CA1113 4.9 9.1 0.3
O A:HOH1382 4.9 9.6 0.3
O A:HOH203 4.9 7.5 1.0

Calcium binding site 5 out of 7 in 1ene

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Calcium binding site 5 out of 7 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1113

b:9.1
occ:0.31
 O A:HOH252 1.8 8.9 0.2
O A:HOH215 2.1 12.8 0.3
O A:HOH1377 2.4 8.9 0.3
O A:HOH1378 2.5 9.1 0.3
O A:HOH1380 2.5 10.3 0.3
O A:HOH1382 2.5 9.1 0.3
O A:HOH1381 2.5 13.3 0.3
O A:HOH1379 2.5 11.5 0.3
O A:HOH252 2.6 10.2 0.8
O A:HOH1375 2.7 6.7 0.4
O A:HOH287 3.7 9.9 0.3
O A:HOH1376 4.4 7.5 0.4
O A:HOH1379 4.8 9.6 0.3
CA A:CA113 4.9 5.5 0.4
O A:HOH1377 4.9 9.5 0.3
O A:HOH259 5.0 10.7 0.3

Calcium binding site 6 out of 7 in 1ene

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Calcium binding site 6 out of 7 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1113

b:7.4
occ:0.31
 O A:HOH1374 1.4 8.0 0.4
O A:HOH259 2.1 10.7 0.3
O A:HOH1372 2.4 7.1 0.4
O A:HOH1377 2.4 9.5 0.3
O A:HOH1382 2.4 9.6 0.3
O A:HOH1378 2.4 8.7 0.3
O A:HOH1380 2.4 5.6 0.3
O A:HOH1379 2.4 9.6 0.3
O A:HOH1381 2.5 8.1 0.3
O A:HOH259 2.6 6.8 0.3
CA A:CA113 2.6 5.5 0.4
O A:HOH1376 2.8 7.5 0.4
O A:HOH253 3.4 10.7 0.4
O A:HOH1373 3.7 7.2 0.4
O A:HOH201 4.2 7.8 1.0
O A:HOH1381 4.2 13.3 0.3
O A:HOH203 4.2 7.5 1.0
O A:HOH214 4.3 13.4 0.8
H42 A:DC1 4.5 6.5 1.0
O A:HOH1375 4.7 6.7 0.4
H41 A:DC1 4.7 6.5 1.0
O A:HOH1379 4.8 11.5 0.3
O A:HOH253 4.8 16.2 0.6
N4 A:DC1 4.9 5.4 1.0

Calcium binding site 7 out of 7 in 1ene

Go back to Calcium Binding Sites List in 1ene
Calcium binding site 7 out of 7 in the 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of 1A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca114

b:14.2
occ:0.50
 O A:HOH260 1.6 16.7 0.5
O A:HOH1383 2.4 9.0 0.5
O A:HOH1385 2.4 11.4 0.5
O A:HOH1384 2.4 14.5 0.5

Reference:

T.K.Chiu, R.E.Dickerson. 1 A Crystal Structures of B-Dna Reveal Sequence-Specific Binding and Groove-Specific Bending of Dna By Magnesium and Calcium. J.Mol.Biol. V. 301 915 2000.
ISSN: ISSN 0022-2836
PubMed: 10966796
DOI: 10.1006/JMBI.2000.4012
Page generated: Mon Jul 7 14:40:58 2025

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