Atomistry » Magnesium » PDB 4fs5-4g7f » 4fs5
Atomistry »
  Magnesium »
    PDB 4fs5-4g7f »
      4fs5 »

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

Go back to Magnesium Binding Sites List in 4fs5
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

Go back to Magnesium Binding Sites List in 4fs5
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

Go back to Magnesium Binding Sites List in 4fs5
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

Go back to Magnesium Binding Sites List in 4fs5
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

Go back to Magnesium Binding Sites List in 4fs5
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

Go back to Magnesium Binding Sites List in 4fs5
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

Go back to Magnesium Binding Sites List in 4fs5
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

Go back to Magnesium Binding Sites List in 4fs5
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

Go back to Magnesium Binding Sites List in 4fs5
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

Go back to Magnesium Binding Sites List in 4fs5
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

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