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Magnesium in PDB 2ply: Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna.

Protein crystallography data

The structure of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna., PDB code: 2ply was solved by N.Soler, D.Fourmy, S.Yoshizawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.35 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.640, 120.838, 50.865, 90.00, 100.18, 90.00
R / Rfree (%) 22.7 / 28.7

Other elements in 2ply:

The structure of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. (pdb code 2ply). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 17 binding sites of Magnesium where determined in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna., PDB code: 2ply:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in 2ply

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Magnesium binding site 1 out of 17 in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg140

b:42.0
occ:1.00
O A:HOH130 2.2 37.5 1.0
O A:HOH51 2.3 20.7 1.0
NH1 A:ARG461 3.6 2.3 1.0
OH A:TYR458 3.7 14.1 1.0
OP1 C:G28 3.8 20.9 1.0
OE2 A:GLU468 4.1 44.5 1.0
CZ A:TYR458 4.2 12.7 1.0
CE1 A:TYR458 4.4 7.6 1.0
O A:HOH67 4.5 7.5 1.0
OE1 A:GLU468 4.6 44.1 1.0
O A:HOH68 4.7 18.9 1.0
CZ A:ARG461 4.7 8.1 1.0
CD A:GLU468 4.8 44.1 1.0
CE1 A:PHE454 5.0 14.8 1.0

Magnesium binding site 2 out of 17 in 2ply

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Magnesium binding site 2 out of 17 in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg141

b:41.0
occ:1.00
O E:HOH164 2.5 12.0 1.0
O2' E:G14 2.8 15.5 1.0
N3 E:G14 3.0 8.9 1.0
C2' E:G14 3.3 16.4 1.0
CD1 B:LEU460 3.3 18.2 1.0
O4' E:C15 3.3 16.2 1.0
C1' E:G14 3.6 12.9 1.0
N2 E:G14 3.7 8.5 1.0
C2 E:G14 3.8 10.4 1.0
C4 E:G14 4.0 5.8 1.0
C1' E:C15 4.1 14.5 1.0
N9 E:G14 4.2 8.0 1.0
O2 E:C35 4.3 20.6 1.0
C4' E:C15 4.4 17.0 1.0
O E:HOH163 4.4 17.9 1.0
CG B:LEU460 4.5 20.9 1.0
N2 E:G13 4.5 12.7 1.0
N1 E:C15 4.5 14.5 1.0
C6 E:C15 4.7 13.2 1.0
C5' E:C15 4.7 14.4 1.0
C3' E:G14 4.8 15.5 1.0
O4' E:G14 4.8 17.7 1.0

Magnesium binding site 3 out of 17 in 2ply

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Magnesium binding site 3 out of 17 in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg142

b:18.1
occ:1.00
O A:HOH59 2.6 9.1 1.0
O A:HOH60 3.0 31.0 1.0
OD2 A:ASP617 3.0 10.7 1.0
CB A:ASP617 3.7 8.1 1.0
CG A:ASP617 3.8 9.2 1.0
CA A:GLU614 4.5 4.5 1.0
CG A:GLU614 4.5 5.2 1.0
NH2 A:ARG629 4.5 4.5 1.0
O A:GLU614 4.6 6.2 1.0
CB A:GLU614 4.7 3.2 1.0
CB A:ARG624 4.9 9.5 1.0
CG A:ARG624 4.9 13.4 1.0

Magnesium binding site 4 out of 17 in 2ply

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Magnesium binding site 4 out of 17 in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg144

b:32.5
occ:1.00
N7 E:G14 3.1 10.9 1.0
N7 E:G13 3.4 12.2 1.0
C8 E:G13 3.5 10.6 1.0
C8 E:G14 3.6 9.3 1.0
OP2 E:G14 3.9 22.2 1.0
C5 E:G13 3.9 8.0 1.0
N9 E:G13 4.1 12.2 1.0
C4 E:G13 4.3 11.3 1.0
C3' E:G13 4.3 22.0 1.0
C5 E:G14 4.4 6.9 1.0
C6 E:G13 4.6 12.0 1.0
C5' E:G13 4.6 24.8 1.0
O6 E:G14 4.7 13.9 1.0
P E:G14 4.9 20.8 1.0
O6 E:G13 5.0 16.4 1.0

Magnesium binding site 5 out of 17 in 2ply

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Magnesium binding site 5 out of 17 in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg145

b:53.0
occ:1.00
OH A:TYR458 2.9 14.1 1.0
OP1 C:G14 3.0 15.8 1.0
CE2 A:TYR458 3.6 6.4 1.0
CZ A:TYR458 3.7 12.7 1.0
NH2 A:ARG457 4.0 35.0 1.0
O A:HOH51 4.1 20.7 1.0
P C:G14 4.1 16.1 1.0
NH2 A:ARG461 4.2 3.5 1.0
CZ A:ARG457 4.4 35.2 1.0
NE A:ARG457 4.5 34.0 1.0
OP2 C:C15 4.6 7.2 1.0
C5' C:G14 4.6 12.9 1.0
OP2 C:G14 4.6 22.1 1.0
O5' C:G14 4.7 13.8 1.0
OP1 C:G28 4.8 20.9 1.0
CD2 A:TYR458 4.9 4.5 1.0
CZ A:ARG461 5.0 8.1 1.0

Magnesium binding site 6 out of 17 in 2ply

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Magnesium binding site 6 out of 17 in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg146

b:61.9
occ:1.00
OE1 B:GLU468 4.1 52.9 1.0
O B:HOH35 4.3 22.9 1.0
OH B:TYR458 4.5 18.5 1.0
NH1 B:ARG461 4.5 20.4 1.0
CE1 B:TYR458 4.8 15.2 1.0
CE1 B:PHE454 4.8 15.8 1.0
CZ B:TYR458 4.9 16.3 1.0

Magnesium binding site 7 out of 17 in 2ply

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Magnesium binding site 7 out of 17 in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg147

b:24.8
occ:1.00
OP2 C:C20 2.7 13.9 1.0
O C:HOH64 2.8 8.8 1.0
N B:LYS607 2.9 8.8 1.0
OP2 C:C21 3.0 15.7 1.0
CB B:LYS607 3.1 9.4 1.0
O5' C:C20 3.3 10.9 1.0
P C:C20 3.5 12.2 1.0
CA B:LYS607 3.6 9.1 1.0
N B:ARG606 3.6 10.3 1.0
CB B:SER605 3.6 10.8 1.0
C B:ARG606 3.9 9.0 1.0
OG B:SER605 3.9 14.3 1.0
CA B:ARG606 4.0 9.9 1.0
OP1 C:C20 4.1 15.6 1.0
C B:SER605 4.1 9.6 1.0
CB B:ARG606 4.2 8.9 1.0
C6 C:C20 4.2 14.1 1.0
C5 C:C20 4.2 13.7 1.0
P C:C21 4.4 15.0 1.0
C3' C:C20 4.4 13.1 1.0
C5 C:C21 4.4 10.2 1.0
CA B:SER605 4.5 10.5 1.0
CG B:LYS607 4.5 10.5 1.0
O3' C:C20 4.7 14.4 1.0
C5' C:C20 4.7 7.8 1.0
O B:SER605 4.7 9.7 1.0
CD B:LYS607 4.8 10.2 1.0
CG B:ARG606 4.9 9.6 1.0
C B:LYS607 4.9 9.6 1.0
O3' C:G19 4.9 13.8 1.0

Magnesium binding site 8 out of 17 in 2ply

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Magnesium binding site 8 out of 17 in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg148

b:38.5
occ:1.00
O C:HOH65 2.5 18.4 1.0
OP2 C:U18 3.0 13.8 1.0
OP2 C:G19 3.9 12.4 1.0
O5' C:U18 4.0 17.1 1.0
P C:U18 4.0 17.4 1.0
C5 C:U18 4.2 4.7 1.0
C6 C:U18 4.3 8.5 1.0
OP1 C:U18 4.8 15.3 1.0
O C:HOH66 4.9 22.1 1.0
C3' C:U18 4.9 14.7 1.0

Magnesium binding site 9 out of 17 in 2ply

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Magnesium binding site 9 out of 17 in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg149

b:32.5
occ:1.00
CE1 A:HIS555 3.2 3.7 1.0
NH2 A:ARG559 3.5 14.2 1.0
O C:HOH3 3.8 2.2 1.0
NE2 A:HIS555 4.1 5.0 1.0
OP2 C:G16 4.1 9.2 1.0
ND1 A:HIS555 4.1 4.8 1.0
OP2 C:G27 4.3 15.3 1.0
CZ A:ARG559 4.4 16.2 1.0
NH1 A:ARG559 4.7 15.1 1.0
C5' C:G27 4.8 14.5 1.0
OP1 C:G27 4.9 18.8 1.0
OP2 C:G28 4.9 14.0 1.0
P C:G27 5.0 17.6 1.0
O C:HOH93 5.0 35.8 1.0

Magnesium binding site 10 out of 17 in 2ply

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Magnesium binding site 10 out of 17 in the Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Mrna Binding Fragment of Elongation Factor Selb in Complex with Secis Rna. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg151

b:58.0
occ:1.00
OP1 C:C32 2.5 32.1 1.0
P C:C32 3.5 29.7 1.0
OP2 C:C32 3.7 27.3 1.0
O5' C:C32 4.3 24.2 1.0
C5' C:C32 4.6 21.7 1.0
O3' C:A31 4.8 25.9 1.0
OP2 C:G33 5.0 16.0 1.0

Reference:

N.Soler, D.Fourmy, S.Yoshizawa. Structural Insight Into A Molecular Switch in Tandem Winged-Helix Motifs From Elongation Factor Selb. J.Mol.Biol. V. 370 728 2007.
ISSN: ISSN 0022-2836
PubMed: 17537456
DOI: 10.1016/J.JMB.2007.05.001
Page generated: Mon Dec 14 07:34:42 2020

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