Atomistry » Magnesium » PDB 1e9a-1en9 » 1en3
Atomistry »
  Magnesium »
    PDB 1e9a-1en9 »
      1en3 »

Magnesium in PDB 1en3: 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: 1en3 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 (°) 32.001, 25.369, 33.633, 90.00, 112.98, 90.00
R / Rfree (%) 14.1 / 15.9

Magnesium Binding Sites:

The binding sites of Magnesium 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 1en3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium 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: 1en3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1en3

Go back to Magnesium Binding Sites List in 1en3
Magnesium binding site 1 out of 5 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 Magnesium with other atoms in the Mg 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:Mg111

b:10.2
occ:0.50
O A:HOH1318 2.0 13.2 1.0
O A:HOH1319 2.1 13.6 1.0
O A:HOH1320 2.1 13.9 1.0
H5' A:DC2 3.5 9.8 1.0
O A:HOH216 4.0 13.3 1.0
O A:HOH206 4.0 12.7 1.0
H1' A:DC1 4.1 8.8 1.0
O A:HOH214 4.2 15.9 1.0
O A:HOH231 4.3 16.9 1.0
O2 A:DC1 4.4 6.8 1.0
H4' A:DC2 4.4 9.1 1.0
C5' A:DC2 4.4 8.2 1.0
O4' A:DC2 4.6 6.7 1.0
H5'' A:DC2 4.6 9.8 1.0
C4' A:DC2 4.7 7.6 1.0

Magnesium binding site 2 out of 5 in 1en3

Go back to Magnesium Binding Sites List in 1en3
Magnesium binding site 2 out of 5 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 Magnesium with other atoms in the Mg 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:Mg112

b:11.7
occ:0.66
O A:HOH1323 2.1 10.5 0.7
O A:HOH1324 2.1 17.0 0.7
O A:HOH1326 2.1 10.3 0.7
O A:HOH1321 2.1 14.1 0.7
O A:HOH1322 2.1 12.9 0.7
O A:HOH1325 2.1 16.3 0.7
H5' A:DG6 3.8 15.7 1.0
O A:HOH235 3.9 9.2 0.3
H4' A:DG6 4.0 13.5 1.0
O A:HOH247 4.0 14.8 0.3
O A:HOH245 4.1 19.4 0.5
O A:HOH205 4.2 14.4 1.0
O A:HOH232 4.2 15.5 1.0
O4' A:DG6 4.3 11.2 1.0
O2 A:DC5 4.3 12.1 1.0
O A:HOH238 4.4 17.5 1.0
O A:HOH208 4.4 18.5 1.0
H2 A:DA4 4.4 13.1 1.0
C4' A:DG6 4.5 11.3 1.0
H1' A:DC5 4.5 16.5 1.0
C5' A:DG6 4.5 13.1 1.0
H4' A:DC5 4.6 16.4 1.0
H5'' A:DG6 4.8 15.7 1.0

Magnesium binding site 3 out of 5 in 1en3

Go back to Magnesium Binding Sites List in 1en3
Magnesium binding site 3 out of 5 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 Magnesium with other atoms in the Mg 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:Mg114

b:18.4
occ:1.00
O A:HOH1328 2.1 18.7 1.0
O A:HOH1329 2.1 25.9 1.0
O A:HOH1327 2.1 24.8 1.0
O A:HOH1330 2.1 25.0 1.0
O A:HOH1331 2.1 16.1 1.0
O A:HOH1332 2.1 29.3 1.0
O A:HOH210 3.9 22.9 0.5

Magnesium binding site 4 out of 5 in 1en3

Go back to Magnesium Binding Sites List in 1en3
Magnesium binding site 4 out of 5 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 Magnesium with other atoms in the Mg 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:Mg113

b:11.2
occ:0.61
MG A:MG113 0.0 11.2 0.6
O A:HOH1334 1.5 14.7 0.4
O A:HOH1337 1.8 11.1 0.4
O A:HOH1335 2.1 14.6 0.6
O A:HOH1334 2.1 13.4 0.6
O A:HOH1336 2.1 11.6 0.6
O A:HOH1333 2.1 18.4 0.6
O A:HOH1338 2.1 16.6 0.6
O A:HOH1337 2.1 8.3 0.6
MG A:MG113 2.3 9.3 0.4
O A:HOH1335 3.0 12.1 0.4
O A:HOH1336 3.2 16.7 0.4
O A:HOH201 3.9 8.5 1.0
O A:HOH1338 4.0 12.8 0.4
H42 A:DC1 4.0 7.6 1.0
O A:HOH234 4.1 25.4 1.0
O A:HOH1333 4.1 13.1 0.4
H41 A:DC1 4.3 7.6 1.0
O A:HOH202 4.3 10.7 1.0
N4 A:DC1 4.5 6.3 1.0
O A:HOH233 4.5 14.5 0.6

Magnesium binding site 5 out of 5 in 1en3

Go back to Magnesium Binding Sites List in 1en3
Magnesium binding site 5 out of 5 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 Magnesium with other atoms in the Mg 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:Mg113

b:9.3
occ:0.39
MG A:MG113 0.0 9.3 0.4
O A:HOH1338 1.9 16.6 0.6
O A:HOH1333 2.0 18.4 0.6
O A:HOH1333 2.1 13.1 0.4
O A:HOH1338 2.1 12.8 0.4
O A:HOH1337 2.1 11.1 0.4
O A:HOH1336 2.1 16.7 0.4
O A:HOH1334 2.1 14.7 0.4
O A:HOH1335 2.1 12.1 0.4
O A:HOH1335 2.3 14.6 0.6
MG A:MG113 2.3 11.2 0.6
O A:HOH1336 3.8 11.6 0.6
O A:HOH1334 3.9 13.4 0.6
O A:HOH1337 4.0 8.3 0.6
O A:HOH234 5.0 25.4 1.0

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 Dec 14 05:52:31 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy