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Magnesium in PDB 2pjp: Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna

Protein crystallography data

The structure of Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna, PDB code: 2pjp 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) 51.50 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.498, 56.515, 48.414, 90.00, 95.60, 90.00
R / Rfree (%) 20 / 25.1

Other elements in 2pjp:

The structure of Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 4 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna (pdb code 2pjp). 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna, PDB code: 2pjp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in 2pjp

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Magnesium binding site 1 out of 17 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg99

b:43.8
occ:1.00
OP2 B:C28 3.2 25.8 1.0
OP2 B:A29 3.4 28.8 1.0
C5 B:C28 3.6 10.4 1.0
C6 B:C28 3.8 17.7 1.0
O5' B:C28 3.9 23.6 1.0
P B:C28 4.1 22.2 1.0
N7 B:A29 4.3 26.6 1.0
C4 B:C28 4.5 15.1 1.0
C3' B:C28 4.6 23.4 1.0
C8 B:A29 4.7 25.0 1.0
P B:A29 4.7 26.5 1.0
OP1 B:C28 4.8 21.3 1.0
N1 B:C28 4.9 20.1 1.0

Magnesium binding site 2 out of 17 in 2pjp

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Magnesium binding site 2 out of 17 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg100

b:60.9
occ:1.00
O B:HOH184 2.2 25.3 1.0
O A:HOH126 2.5 44.4 1.0
CG2 A:VAL578 4.1 27.5 1.0
OP1 B:C20 4.4 27.9 1.0
O B:HOH159 4.4 18.6 1.0
CD1 A:LEU582 4.5 20.0 1.0
O A:HOH32 4.8 18.4 1.0
CG A:LEU582 4.9 21.4 1.0
N A:GLY579 4.9 23.2 1.0
MG B:MG106 5.0 63.6 1.0

Magnesium binding site 3 out of 17 in 2pjp

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Magnesium binding site 3 out of 17 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:59.6
occ:1.00
O A:HOH67 2.3 40.0 1.0
O A:HOH68 2.4 32.2 1.0
NH2 A:ARG598 3.8 16.5 1.0
N A:GLY600 3.8 27.2 1.0
NE A:ARG598 3.8 19.2 1.0
CZ A:ARG598 3.9 18.7 1.0
CA A:GLY600 4.0 26.5 1.0
O A:GLY600 4.1 24.9 1.0
O A:HOH69 4.1 35.4 1.0
C A:GLY600 4.5 25.6 1.0
NH1 A:ARG598 4.6 15.7 1.0
CD A:ARG598 4.6 20.8 1.0
CG A:ARG598 4.9 24.6 1.0
C A:ARG599 5.0 27.5 1.0

Magnesium binding site 4 out of 17 in 2pjp

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Magnesium binding site 4 out of 17 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg104

b:52.6
occ:1.00
O B:HOH183 2.4 32.5 1.0
O B:HOH201 2.6 43.7 1.0
O2' B:U24 3.9 24.0 1.0
C3' B:U24 3.9 26.5 1.0
OP1 B:C25 4.1 30.2 1.0
C2' B:U24 4.2 23.5 1.0
O A:HOH68 4.2 32.2 1.0
OP2 B:U24 4.3 18.9 1.0
O3' B:U24 4.5 31.3 1.0
O B:HOH191 4.6 37.8 1.0
O2' B:G23 4.7 24.2 1.0
NH1 A:ARG598 4.8 15.7 1.0
P B:C25 4.9 30.6 1.0
O5' B:U24 4.9 24.0 1.0

Magnesium binding site 5 out of 17 in 2pjp

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Magnesium binding site 5 out of 17 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg105

b:58.4
occ:1.00
OP1 B:A21 2.7 21.6 1.0
C5' B:A21 3.7 18.4 1.0
P B:A21 3.7 17.6 1.0
NE A:ARG573 3.7 35.5 1.0
O3' B:C20 3.8 16.0 1.0
O A:HOH59 4.0 40.3 1.0
O5' B:A21 4.1 19.0 1.0
NH2 A:ARG573 4.1 28.2 1.0
CZ A:ARG573 4.2 30.0 1.0
CD A:ARG573 4.5 24.6 1.0

Magnesium binding site 6 out of 17 in 2pjp

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Magnesium binding site 6 out of 17 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg106

b:63.6
occ:1.00
OP1 B:C20 3.4 27.9 1.0
O3' B:G19 3.4 22.9 1.0
P B:C20 3.9 26.5 1.0
C5' B:C20 4.2 18.1 1.0
O2' B:G19 4.3 27.0 1.0
O5' B:C20 4.4 21.5 1.0
C3' B:G19 4.6 23.0 1.0
O B:HOH184 4.6 25.3 1.0
C4' B:G19 4.8 24.0 1.0
MG A:MG100 5.0 60.9 1.0

Magnesium binding site 7 out of 17 in 2pjp

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Magnesium binding site 7 out of 17 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg150

b:42.9
occ:1.00
O B:HOH170 2.3 35.2 1.0
O B:HOH199 2.4 50.0 1.0
N7 B:G16 3.0 24.8 1.0
N7 B:G15 3.5 26.9 1.0
C8 B:G16 3.7 24.2 1.0
C5 B:G15 3.9 28.8 1.0
C8 B:G15 3.9 30.4 1.0
C5 B:G16 4.2 24.6 1.0
C6 B:G15 4.3 30.8 1.0
O6 B:G16 4.5 28.3 1.0
C4 B:G15 4.5 29.2 1.0
N9 B:G15 4.5 32.3 1.0
O6 B:G15 4.5 31.3 1.0
C6 B:G16 4.7 24.5 1.0
OP2 B:G16 4.7 39.1 1.0
C3' B:G15 4.9 42.7 1.0
N9 B:G16 5.0 27.0 1.0

Magnesium binding site 8 out of 17 in 2pjp

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Magnesium binding site 8 out of 17 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg151

b:52.5
occ:1.00
C3' B:C25 3.6 29.0 1.0
C2' B:C25 3.7 29.2 1.0
O2' B:C25 4.1 27.6 1.0
OP2 B:U26 4.2 34.0 1.0
O B:HOH182 4.4 35.1 1.0
O5' B:C25 4.5 30.1 1.0
O3' B:C25 4.5 30.8 1.0
C4' B:C25 4.6 29.2 1.0
C5' B:C25 4.7 29.4 1.0
P B:U26 4.7 31.9 1.0
OP1 B:U26 4.8 34.3 1.0

Magnesium binding site 9 out of 17 in 2pjp

Go back to Magnesium Binding Sites List in 2pjp
Magnesium binding site 9 out of 17 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg152

b:71.4
occ:1.00
OP1 B:C30 3.5 40.2 1.0
OP2 B:C31 4.1 40.5 1.0
O5' B:C30 4.1 35.5 1.0
P B:C30 4.1 38.9 1.0
OP2 B:C30 4.5 36.3 1.0
OP1 B:C31 4.6 46.8 1.0
C5' B:C30 4.6 36.2 1.0
P B:C31 4.7 42.2 1.0

Magnesium binding site 10 out of 17 in 2pjp

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Magnesium binding site 10 out of 17 in the Structure of the Mrna-Binding Domain of Elongation Factor Selb From E.Coli 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 Domain of Elongation Factor Selb From E.Coli in Complex with Secis Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg140

b:66.5
occ:1.00
OP1 B:C31 3.1 46.8 1.0
P B:C31 4.1 42.2 1.0
OP2 B:C31 4.4 40.5 1.0
O5' B:C31 4.5 44.2 1.0
OP2 B:G32 4.9 45.3 1.0
C5' B:C31 5.0 42.9 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 07:34:36 2020

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