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Magnesium in PDB 5bn3: Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans

Enzymatic activity of Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans

All present enzymatic activity of Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans:
3.6.3.14;

Protein crystallography data

The structure of Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans, PDB code: 5bn3 was solved by S.Mohanty, C.Jobichen, V.P.R.Chichili, J.Sivaraman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.65 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 192.459, 192.459, 110.241, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 21

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans (pdb code 5bn3). 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 A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans, PDB code: 5bn3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5bn3

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Magnesium binding site 1 out of 5 in the Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg609

b:30.3
occ:1.00
 OG1 A:THR230 2.1 27.0 1.0
O A:HOH849 2.1 34.4 1.0
O2B A:ADP601 2.1 25.8 1.0
O A:HOH753 2.1 28.3 1.0
O A:HOH741 2.1 27.7 1.0
O A:HOH727 2.1 32.2 1.0
CB A:THR230 3.1 33.5 1.0
PB A:ADP601 3.3 30.0 1.0
O3B A:ADP601 3.5 29.9 1.0
NH1 A:ARG253 3.7 39.8 1.0
OE2 A:GLU256 3.9 43.5 1.0
OE1 A:GLU252 3.9 46.2 1.0
O A:HOH724 4.0 33.5 1.0
N A:THR230 4.0 28.2 1.0
O A:HOH792 4.0 38.5 1.0
O2A A:ADP601 4.1 31.1 1.0
CA A:THR230 4.1 33.6 1.0
CG2 A:THR230 4.2 31.5 1.0
OD2 A:ASP320 4.2 41.6 1.0
O3A A:ADP601 4.3 29.8 1.0
OE1 A:GLU256 4.3 43.6 1.0
O1B A:ADP601 4.4 28.4 1.0
OD1 A:ASP320 4.4 35.5 1.0
CD A:GLU256 4.5 38.5 1.0
PA A:ADP601 4.5 31.3 1.0
O1A A:ADP601 4.5 33.4 1.0
NH1 B:ARG326 4.7 39.3 1.0
CD A:GLU252 4.7 46.7 1.0
CG A:ASP320 4.8 42.2 1.0
NZ A:LYS229 4.8 28.7 1.0
CZ A:ARG253 4.9 39.5 1.0
CB A:LYS229 5.0 31.7 1.0

Magnesium binding site 2 out of 5 in 5bn3

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Magnesium binding site 2 out of 5 in the Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg610

b:41.9
occ:1.00
 OG A:SER372 2.3 44.0 1.0
OG1 A:THR374 2.4 31.6 1.0
O A:VAL315 2.7 30.6 1.0
N A:THR374 3.4 32.8 1.0
CB A:THR374 3.4 34.3 1.0
O A:SER372 3.4 29.5 1.0
N A:VAL315 3.5 33.1 1.0
CB A:SER372 3.5 31.7 1.0
C A:SER372 3.6 33.4 1.0
C A:VAL315 3.6 31.5 1.0
N A:GLY216 3.8 34.3 1.0
C A:LEU373 4.0 33.4 1.0
N A:LEU373 4.0 31.8 1.0
CA A:THR374 4.0 30.8 1.0
CB A:SER314 4.1 38.9 1.0
CA A:LEU373 4.1 33.3 1.0
C A:SER314 4.2 35.3 1.0
CA A:VAL315 4.2 28.4 1.0
CA A:SER372 4.2 35.8 1.0
CA A:SER314 4.2 37.9 1.0
CB A:LYS215 4.4 40.1 1.0
C A:LYS215 4.4 33.6 1.0
CA A:LYS215 4.4 33.5 1.0
CA A:GLY216 4.5 33.0 1.0
CG A:LYS215 4.5 52.3 1.0
N A:VAL316 4.6 32.3 1.0
CD A:LYS215 4.7 61.2 1.0
CG2 A:THR374 4.7 37.0 1.0
O A:LEU373 4.9 30.5 1.0
CA A:VAL316 5.0 32.5 1.0

Magnesium binding site 3 out of 5 in 5bn3

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Magnesium binding site 3 out of 5 in the Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg509

b:85.0
occ:1.00
 N B:ASP90 4.0 63.6 1.0
CA B:ASP90 4.2 68.2 1.0
N B:TYR91 4.3 47.7 1.0
CD2 B:TYR91 4.3 74.3 1.0
C B:ASP90 4.8 55.7 1.0

Magnesium binding site 4 out of 5 in 5bn3

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Magnesium binding site 4 out of 5 in the Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg510

b:74.7
occ:1.00
 OH B:TYR102 3.4 54.8 1.0
O A:HOH945 3.7 65.2 1.0
CE1 B:TYR102 4.2 43.8 1.0
O A:HOH940 4.2 54.5 1.0
CZ B:TYR102 4.3 48.9 1.0
CE A:LYS88 4.3 70.7 1.0
CD A:LYS88 4.5 55.0 1.0
O A:HOH839 4.8 55.1 1.0

Magnesium binding site 5 out of 5 in 5bn3

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Magnesium binding site 5 out of 5 in the Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Unique Atp Synthase Neqa-Neqb in Complex with Adp From Nanoarcheaum Equitans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg511

b:66.7
occ:1.00
 N B:ASP93 3.2 47.3 1.0
CB B:ASP93 3.8 46.6 1.0
CA B:ARG92 3.9 45.0 1.0
C B:ARG92 4.0 49.0 1.0
CA B:ASP93 4.1 47.5 1.0
O B:TYR91 4.2 50.6 1.0
CD B:ARG92 4.5 66.8 1.0
CE B:LYS62 4.6 58.7 1.0
CB B:ARG92 4.7 44.9 1.0
NZ B:LYS62 4.7 76.8 1.0
O B:HOH652 4.7 55.2 1.0
N B:ARG92 4.9 46.9 1.0
C B:TYR91 5.0 58.1 1.0

Reference:

S.Mohanty, C.Jobichen, V.P.R.Chichili, A.Velazquez-Campoy, B.C.Low, C.W.V.Hogue, J.Sivaraman. Structural Basis For A Unique Atp Synthase Core Complex From Nanoarcheaum Equitans J.Biol.Chem. V. 290 27280 2015.
ISSN: ESSN 1083-351X
PubMed: 26370083
DOI: 10.1074/JBC.M115.677492
Page generated: Sun Sep 29 01:11:59 2024

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