Atomistry » Calcium » PDB 1edm-1evu » 1ene
Atomistry »
  Calcium »
    PDB 1edm-1evu »
      1ene »

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

Go back to Calcium Binding Sites List in 1ene
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

Go back to Calcium Binding Sites List in 1ene
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

Go back to Calcium Binding Sites List in 1ene
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

Go back to Calcium Binding Sites List in 1ene
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

Go back to Calcium Binding Sites List in 1ene
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

Go back to Calcium Binding Sites List in 1ene
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: Thu Jul 11 07:54:08 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy