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Magnesium in PDB 3pen: Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form.

Protein crystallography data

The structure of Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form., PDB code: 3pen was solved by V.I.Arkhipova, A.M.Lazopulo, S.M.Lazopulo, M.B.Garber, O.S.Nikonov, S.V.Nikonov, A.G.Gabdoulkhakov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.10 / 2.30
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 187.120, 187.120, 187.120, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form. (pdb code 3pen). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form., PDB code: 3pen:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3pen

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Magnesium binding site 1 out of 5 in the Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg417

b:35.4
occ:1.00
 O A:HOH594 2.5 41.2 1.0
OG1 A:THR54 2.5 28.1 1.0
O A:THR70 2.6 34.3 1.0
O A:HOH603 2.6 30.7 1.0
O A:HOH611 2.6 28.3 1.0
O A:HOH591 2.6 29.0 1.0
CB A:THR54 3.5 30.0 1.0
C A:THR70 3.7 34.6 1.0
CB A:THR70 3.8 33.6 1.0
OG1 A:THR70 3.9 31.7 1.0
CA A:THR54 4.1 30.9 1.0
O A:THR30 4.2 30.4 1.0
N A:ASN55 4.3 29.3 1.0
CA A:THR70 4.3 31.4 1.0
O A:ASN55 4.5 31.8 1.0
O A:HOH598 4.6 41.2 1.0
O A:HOH650 4.6 47.5 1.0
C A:THR54 4.7 30.2 1.0
O A:HOH547 4.8 30.5 1.0
O A:HOH577 4.8 41.4 1.0
C A:THR30 4.8 30.6 1.0
N A:GLU71 4.8 38.8 1.0
O A:ILE29 4.8 27.2 1.0
CG2 A:THR54 4.8 24.5 1.0
CA A:THR30 4.8 28.2 1.0
O A:GLU53 5.0 27.5 1.0

Magnesium binding site 2 out of 5 in 3pen

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Magnesium binding site 2 out of 5 in the Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg418

b:28.1
occ:1.00
 O A:HOH596 2.4 28.7 1.0
O A:VAL154 2.4 26.9 1.0
O A:VAL151 2.5 25.6 1.0
C A:VAL151 3.5 25.0 1.0
C A:VAL154 3.6 27.3 1.0
O A:HOH585 4.0 28.5 1.0
C A:SER155 4.0 31.9 1.0
N A:LYS156 4.1 29.5 1.0
CB A:VAL151 4.1 23.1 1.0
CA A:SER155 4.3 30.1 1.0
CA A:VAL151 4.3 23.3 1.0
O A:SER155 4.3 29.7 1.0
N A:SER155 4.4 24.4 1.0
N A:ASP152 4.4 25.0 1.0
N A:VAL154 4.5 26.8 1.0
CA A:ASP152 4.5 25.8 1.0
CG2 A:VAL151 4.5 19.7 1.0
CA A:LYS156 4.6 28.7 1.0
CG2 A:VAL154 4.6 22.0 1.0
CA A:VAL154 4.6 25.7 1.0
C A:ASP152 4.7 28.7 1.0
O A:ASP152 5.0 28.0 1.0
O A:HOH718 5.0 34.6 1.0

Magnesium binding site 3 out of 5 in 3pen

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Magnesium binding site 3 out of 5 in the Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg419

b:44.3
occ:1.00
 O1B A:GDP416 2.5 23.6 1.0
OG1 A:THR23 2.6 33.9 1.0
O A:HOH589 2.6 38.5 1.0
O A:HOH574 2.7 42.0 1.0
O3B A:GDP416 3.5 28.0 1.0
NZ A:LYS48 3.6 45.9 1.0
PB A:GDP416 3.6 24.6 1.0
CB A:THR23 3.8 28.8 1.0
O A:HOH580 4.0 28.6 1.0
OD1 A:ASP93 4.1 38.0 1.0
CE A:LYS48 4.3 48.8 1.0
N A:THR23 4.3 23.2 1.0
O A:HOH593 4.3 50.3 1.0
O2B A:GDP416 4.4 25.0 1.0
CE A:LYS22 4.5 24.8 1.0
CA A:THR23 4.6 25.6 1.0
O2A A:GDP416 4.6 28.2 1.0
O A:HOH622 4.7 39.9 1.0
CB A:LYS22 4.8 21.4 1.0
O3A A:GDP416 4.8 27.0 1.0
CG2 A:THR23 4.8 27.7 1.0
O A:ALA94 5.0 25.8 1.0

Magnesium binding site 4 out of 5 in 3pen

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Magnesium binding site 4 out of 5 in the Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg420

b:37.8
occ:1.00
 O A:TYR68 2.3 35.4 1.0
OD2 A:ASP192 2.4 33.9 1.0
O A:GLU66 2.4 31.2 1.0
O A:HOH581 2.6 40.3 1.0
O A:HOH617 2.7 36.6 1.0
C A:GLU66 3.3 34.1 1.0
C A:TYR68 3.5 33.3 1.0
CG A:ASP192 3.6 39.0 1.0
CA A:GLU66 3.7 33.3 1.0
CG1 A:VAL69 3.8 35.0 1.0
N A:TYR68 4.2 30.9 1.0
CB A:GLU66 4.3 32.9 1.0
CA A:VAL69 4.3 31.5 1.0
N A:VAL69 4.3 29.2 1.0
C A:ALA67 4.4 36.3 1.0
N A:ALA67 4.4 32.1 1.0
CA A:TYR68 4.4 30.1 1.0
CB A:ASP192 4.5 31.9 1.0
OD1 A:ASP192 4.5 35.6 1.0
O A:HOH423 4.6 36.1 1.0
O A:PRO65 4.6 29.4 1.0
CB A:VAL69 4.7 36.6 1.0
O A:ALA67 4.7 36.7 1.0
OG A:SER76 4.8 51.1 1.0
CA A:ALA67 4.9 37.8 1.0

Magnesium binding site 5 out of 5 in 3pen

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Magnesium binding site 5 out of 5 in the Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Archaeal Initiation Factor AIF2GAMMA Subunit Delta 37-47 From Sulfolobus Solfataricus in the Gdp-Bound Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg421

b:44.5
occ:1.00
 O A:HOH616 2.4 30.1 1.0
O A:MET111 2.4 29.2 1.0
O A:HOH610 2.6 33.9 1.0
O A:HOH615 2.6 46.2 1.0
O A:HOH601 2.7 39.5 1.0
O A:HOH588 2.7 42.4 1.0
O A:HOH692 3.2 48.9 1.0
C A:MET111 3.6 27.0 1.0
CA A:ASP112 4.3 26.8 1.0
N A:ASP112 4.4 24.5 1.0
N A:MET111 4.5 28.8 1.0
O A:ALA109 4.5 27.2 1.0
CA A:MET111 4.6 29.6 1.0
OD2 A:ASP112 4.6 29.6 1.0
O A:ALA108 4.8 26.9 1.0
O A:HOH573 4.8 33.1 1.0
O A:HOH584 4.8 29.8 1.0
O A:HOH42 4.9 28.0 1.0
O A:HOH693 5.0 46.0 1.0

Reference:

V.I.Arkhipova, A.M.Lazopulo, S.M.Lazopulo, M.B.Garber, O.S.Nikonov, S.V.Nikonov, A.G.Gabdoulkhakov. Structure of Archaeal Initiation Factor AIF2GAMMA Subunit From Sulfolobus Solfataricus in the Gdp-Bound Form. To Be Published.
Page generated: Mon Aug 11 01:49:27 2025

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