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Magnesium in PDB 4fs5: Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2

Protein crystallography data

The structure of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2, PDB code: 4fs5 was solved by T.Chatake, T.Sunami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.68 / 1.30
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 18.593, 18.593, 72.700, 90.00, 90.00, 120.00
R / Rfree (%) 21.1 / 26.4

Other elements in 4fs5:

The structure of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 (pdb code 4fs5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2, PDB code: 4fs5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 4fs5

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Magnesium binding site 1 out of 10 in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:14.7
occ:1.00
 O A:HOH203 1.9 18.5 1.0
O A:HOH202 1.9 23.3 1.0
O A:HOH201 2.2 23.0 1.0
O A:HOH204 2.2 19.2 1.0
OP1 A:DG2 2.2 17.2 1.0
P A:DG2 3.4 15.1 1.0
O5' A:DG2 3.6 15.6 1.0
O A:HOH207 4.0 16.1 1.0
OP2 A:DG2 4.3 17.5 1.0
O3' A:DC1 4.6 15.8 1.0
C3' A:DC1 4.8 14.7 1.0
MG A:MG102 5.0 18.1 1.0
C5' A:DG2 5.0 15.4 1.0

Magnesium binding site 2 out of 10 in 4fs5

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Magnesium binding site 2 out of 10 in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:18.1
occ:1.00
 OP2 A:DG2 1.9 17.5 1.0
O A:HOH206 2.0 26.7 1.0
O A:HOH207 2.1 16.1 1.0
O A:HOH205 2.2 22.9 1.0
O A:HOH208 2.2 22.5 1.0
P A:DG2 3.2 15.1 1.0
OP1 A:DG2 3.8 17.2 1.0
O5' A:DG2 3.9 15.6 1.0
C5' A:DG2 4.2 15.4 1.0
O3' A:DC1 4.4 15.8 1.0
CL A:CL110 4.9 22.6 1.0
MG A:MG101 5.0 14.7 1.0

Magnesium binding site 3 out of 10 in 4fs5

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Magnesium binding site 3 out of 10 in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:15.1
occ:1.00
 O A:HOH210 1.9 21.6 1.0
O A:HOH211 2.1 18.6 1.0
O A:HOH209 2.2 22.6 1.0
OP1 A:DC5 2.2 14.7 1.0
O A:HOH212 2.2 19.3 1.0
P A:DC5 3.7 14.6 1.0
O A:HOH215 4.1 15.5 1.0
N7 A:DG6 4.3 14.6 1.0
C2' A:DG4 4.3 12.4 1.0
O3' A:DG4 4.4 14.7 1.0
O A:HOH240 4.5 14.6 1.0
OP2 A:DC5 4.5 17.3 1.0
O5' A:DC5 4.6 12.7 1.0
O6 A:DG6 4.8 12.2 1.0
C3' A:DG4 4.9 12.6 1.0
C5' A:DC5 5.0 11.5 1.0

Magnesium binding site 4 out of 10 in 4fs5

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Magnesium binding site 4 out of 10 in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:18.7
occ:1.00
 O A:HOH214 1.8 26.9 1.0
O A:HOH215 2.0 15.5 1.0
O A:HOH216 2.1 22.6 1.0
O A:HOH213 2.1 23.7 1.0
OP2 A:DC5 2.2 17.3 1.0
P A:DC5 3.4 14.6 1.0
OP1 A:DC5 3.8 14.7 1.0
O A:HOH249 4.3 24.3 1.0
O5' A:DC5 4.4 12.7 1.0
C5' A:DC5 4.4 11.5 1.0
O3' A:DG4 4.5 14.7 1.0
O A:HOH247 4.5 21.8 1.0

Magnesium binding site 5 out of 10 in 4fs5

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Magnesium binding site 5 out of 10 in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:13.3
occ:1.00
 OP1 A:DC3 1.9 14.4 1.0
O A:HOH220 2.0 15.9 1.0
O A:HOH218 2.1 14.8 1.0
O A:HOH219 2.1 21.0 1.0
O A:HOH217 2.2 16.6 1.0
P A:DC3 3.4 14.5 1.0
OP2 A:DC3 4.1 15.4 1.0
C2' A:DG2 4.2 15.3 1.0
O3' A:DG2 4.2 14.6 1.0
O A:HOH224 4.3 20.0 1.0
O5' A:DC3 4.3 12.1 1.0
N7 A:DG4 4.3 11.1 1.0
O A:HOH238 4.5 10.3 1.0
C5' A:DC3 4.6 11.5 1.0
O6 A:DG4 4.6 10.2 1.0
MG A:MG106 4.8 16.2 1.0
C3' A:DG2 4.8 14.4 1.0

Magnesium binding site 6 out of 10 in 4fs5

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Magnesium binding site 6 out of 10 in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:16.2
occ:1.00
 OP2 A:DC3 1.9 15.4 1.0
O A:HOH223 2.0 16.9 1.0
O A:HOH221 2.0 30.0 1.0
O A:HOH224 2.2 20.0 1.0
O A:HOH222 2.3 26.6 1.0
P A:DC3 3.2 14.5 1.0
OP1 A:DC3 3.9 14.4 1.0
O A:HOH250 4.0 24.1 1.0
O3' A:DG2 4.1 14.6 1.0
O5' A:DC3 4.2 12.1 1.0
C5' A:DC3 4.4 11.5 1.0
O A:HOH220 4.6 15.9 1.0
MG A:MG105 4.8 13.3 1.0
O A:HOH241 4.9 15.4 1.0
O A:HOH227 4.9 17.2 1.0

Magnesium binding site 7 out of 10 in 4fs5

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Magnesium binding site 7 out of 10 in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:12.1
occ:1.00
 O A:HOH227 2.0 17.2 1.0
OP1 A:DG4 2.1 14.4 1.0
O A:HOH228 2.2 16.0 1.0
O A:HOH226 2.2 14.6 1.0
O A:HOH225 2.2 24.4 1.0
P A:DG4 3.3 12.1 1.0
O5' A:DG4 3.7 10.5 1.0
O A:HOH248 3.9 26.6 1.0
OP2 A:DG4 4.0 13.6 1.0
O A:HOH232 4.3 19.3 1.0
O3' A:DC3 4.6 11.5 1.0
O A:HOH250 4.6 24.1 1.0
O A:HOH221 4.7 30.0 1.0
MG A:MG108 4.9 17.1 1.0
C3' A:DC3 4.9 10.5 1.0
C5' A:DG4 5.0 13.3 1.0

Magnesium binding site 8 out of 10 in 4fs5

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Magnesium binding site 8 out of 10 in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:17.1
occ:1.00
 O A:HOH229 2.0 17.2 1.0
OP2 A:DG4 2.1 13.6 1.0
O A:HOH230 2.1 18.7 1.0
O A:HOH231 2.1 18.4 1.0
O A:HOH232 2.2 19.3 1.0
P A:DG4 3.4 12.1 1.0
O5' A:DG4 4.0 10.5 1.0
C5' A:DG4 4.0 13.3 1.0
O A:HOH235 4.1 19.6 1.0
OP1 A:DG4 4.1 14.4 1.0
O B:HOH202 4.2 25.5 1.0
O3' A:DC3 4.5 11.5 1.0
O A:HOH228 4.6 16.0 1.0
CL A:CL111 4.8 17.2 1.0
MG A:MG107 4.9 12.1 1.0

Magnesium binding site 9 out of 10 in 4fs5

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Magnesium binding site 9 out of 10 in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg109

b:17.2
occ:1.00
 O B:HOH207 1.9 20.5 1.0
O B:HOH204 2.1 13.3 1.0
O B:HOH205 2.1 30.1 1.0
O A:HOH237 2.1 30.0 1.0
O A:HOH236 2.2 21.6 1.0
O B:HOH206 2.2 20.2 1.0
O B:HOH220 3.9 26.3 1.0
O3' A:DC5 4.0 15.4 1.0
OP2 A:DG6 4.2 22.1 1.0
O3' B:DC9 4.3 12.0 1.0
O2 A:DC5 4.4 12.0 1.0
C2' A:DC5 4.4 11.2 1.0
OP2 B:DG10 4.5 13.1 1.0
C2' B:DC9 4.5 8.2 1.0
O B:HOH213 4.6 17.5 1.0
O2 B:DC9 4.6 8.9 1.0
P A:DG6 4.6 18.2 1.0
C3' A:DC5 4.7 13.2 1.0
P B:DG10 4.9 12.0 1.0
C3' B:DC9 5.0 9.8 1.0

Magnesium binding site 10 out of 10 in 4fs5

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Magnesium binding site 10 out of 10 in the Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Z-Dna Hexamer Cgcgcg at 500 Mm MGCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:18.8
occ:1.00
 O A:HOH235 2.0 19.6 1.0
O A:HOH233 2.1 12.5 1.0
O A:HOH234 2.1 17.2 1.0
O B:HOH202 2.1 25.5 1.0
O B:HOH203 2.1 25.2 1.0
O B:HOH201 2.1 25.5 1.0
O3' B:DC11 4.0 14.0 1.0
O A:HOH230 4.1 18.7 1.0
OP2 B:DG12 4.1 22.9 1.0
O3' A:DC3 4.3 11.5 1.0
O2 B:DC11 4.3 12.4 1.0
C2' B:DC11 4.4 10.7 1.0
OP2 A:DG4 4.5 13.6 1.0
C2' A:DC3 4.5 9.1 1.0
O A:HOH244 4.5 18.9 1.0
O2 A:DC3 4.6 9.2 1.0
P B:DG12 4.6 17.6 1.0
O A:HOH248 4.7 26.6 1.0
C3' B:DC11 4.8 12.4 1.0
OP1 B:DG12 4.9 21.1 1.0
C3' A:DC3 4.9 10.5 1.0
P A:DG4 5.0 12.1 1.0
C1' B:DC11 5.0 9.9 1.0

Reference:

T.Chatake, T.Sunami. Direct Interactions Between Z-Dna and Alkaline Earth Cations, Discovered in the Presence of High Concentrations of MGCL2 and CACL2 J.Inorg.Biochem. V. 124 15 2013.
ISSN: ISSN 0162-0134
PubMed: 23578858
DOI: 10.1016/J.JINORGBIO.2013.03.004
Page generated: Fri Aug 16 15:18:09 2024

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