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Magnesium in PDB 3bb1: Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp

Protein crystallography data

The structure of Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp, PDB code: 3bb1 was solved by P.Koenig, I.Sinning, E.Schleiff, I.Tews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.88 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 178.776, 180.061, 90.948, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 28.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp (pdb code 3bb1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp, PDB code: 3bb1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3bb1

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Magnesium binding site 1 out of 8 in the Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp


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 TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg282

b:65.2
occ:1.00
 OG A:SER53 1.9 62.9 1.0
O2G A:GNP281 2.0 64.9 1.0
O2B A:GNP281 2.0 64.5 1.0
O A:HOH293 2.1 61.9 1.0
O A:HOH292 2.1 64.2 1.0
O A:HOH294 2.1 63.7 1.0
CB A:SER53 3.0 62.2 1.0
PB A:GNP281 3.3 63.3 1.0
PG A:GNP281 3.3 66.4 1.0
N3B A:GNP281 3.5 63.4 1.0
N A:SER53 3.7 62.5 1.0
OD2 A:ASP93 3.8 65.4 1.0
CA A:SER53 3.9 61.8 1.0
O2A A:GNP281 3.9 60.3 1.0
O A:HOH302 4.0 55.4 1.0
OD1 A:ASP93 4.1 66.7 1.0
O A:SER66 4.2 68.7 1.0
O1G A:GNP281 4.2 65.1 1.0
O3G A:GNP281 4.2 63.4 1.0
O1B A:GNP281 4.3 61.2 1.0
O3A A:GNP281 4.3 62.0 1.0
O A:HOH303 4.4 56.0 1.0
PA A:GNP281 4.4 60.8 1.0
CG A:ASP93 4.4 65.0 1.0
O1A A:GNP281 4.4 63.2 1.0
CB A:LYS52 4.6 63.9 1.0
O A:THR94 4.6 64.5 1.0
CE A:LYS52 4.6 63.4 1.0
C A:LYS52 4.8 63.5 1.0
NZ A:LYS52 4.8 67.2 1.0
O A:SER72 4.8 97.8 1.0

Magnesium binding site 2 out of 8 in 3bb1

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Magnesium binding site 2 out of 8 in the Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp


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 TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg282

b:66.8
occ:1.00
 O2G B:GNP281 2.0 68.0 1.0
O2B B:GNP281 2.0 67.8 1.0
O B:HOH283 2.1 64.9 1.0
O B:HOH284 2.1 65.2 1.0
O B:HOH285 2.1 67.2 1.0
OG B:SER53 2.2 69.2 1.0
CB B:SER53 3.1 69.8 1.0
PG B:GNP281 3.2 69.6 1.0
PB B:GNP281 3.2 71.5 1.0
N3B B:GNP281 3.5 68.6 1.0
OD2 B:ASP93 3.8 80.6 1.0
N B:SER53 3.8 70.0 1.0
O3G B:GNP281 3.9 70.6 1.0
CA B:SER53 4.0 69.9 1.0
O2A B:GNP281 4.0 73.9 1.0
OD1 B:ASP93 4.2 82.1 1.0
O B:SER66 4.3 85.0 1.0
O1B B:GNP281 4.3 70.6 1.0
O3A B:GNP281 4.3 70.8 1.0
PA B:GNP281 4.4 74.4 1.0
CG B:ASP93 4.4 78.7 1.0
O1A B:GNP281 4.5 77.2 1.0
O1G B:GNP281 4.5 69.8 1.0
CB B:LYS52 4.6 70.5 1.0
NZ B:LYS52 4.8 67.5 1.0
O B:SER72 4.9 0.8 1.0
C B:LYS52 4.9 70.0 1.0
CE B:LYS52 4.9 68.7 1.0

Magnesium binding site 3 out of 8 in 3bb1

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Magnesium binding site 3 out of 8 in the Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp


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 TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg282

b:63.4
occ:1.00
 O2G C:GNP281 2.0 64.5 1.0
O2B C:GNP281 2.0 65.1 1.0
O C:HOH292 2.0 65.5 1.0
O C:HOH293 2.1 62.9 1.0
O C:HOH294 2.1 64.0 1.0
OG C:SER53 2.1 61.1 1.0
CB C:SER53 3.1 60.5 1.0
PB C:GNP281 3.3 66.4 1.0
PG C:GNP281 3.3 65.7 1.0
N3B C:GNP281 3.6 65.5 1.0
N C:SER53 3.8 60.6 1.0
OD2 C:ASP93 3.8 62.9 1.0
CA C:SER53 4.0 60.6 1.0
OD1 C:ASP93 4.0 65.2 1.0
O1B C:GNP281 4.2 67.9 1.0
O1G C:GNP281 4.2 62.0 1.0
NH1 C:ARG76 4.3 95.8 1.0
O3G C:GNP281 4.3 65.9 1.0
CD C:ARG76 4.3 90.7 1.0
O2A C:GNP281 4.4 60.8 1.0
CG C:ASP93 4.4 62.3 1.0
O C:THR94 4.4 63.2 1.0
O3A C:GNP281 4.4 65.5 1.0
O C:SER66 4.4 78.2 1.0
CE C:LYS52 4.4 59.9 1.0
NE C:ARG76 4.6 93.2 1.0
CZ C:ARG76 4.6 94.9 1.0
CB C:LYS52 4.6 61.7 1.0
PA C:GNP281 4.7 63.3 1.0
O1A C:GNP281 4.8 63.0 1.0
C C:LYS52 4.9 60.7 1.0
NZ C:LYS52 4.9 57.2 1.0

Magnesium binding site 4 out of 8 in 3bb1

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Magnesium binding site 4 out of 8 in the Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp


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 TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg282

b:58.8
occ:1.00
 O2G D:GNP281 2.0 61.5 1.0
O2B D:GNP281 2.0 61.3 1.0
O D:HOH283 2.1 58.9 1.0
O D:HOH285 2.1 57.8 1.0
O D:HOH284 2.1 59.3 1.0
OG D:SER53 2.1 66.6 1.0
CB D:SER53 3.2 67.3 1.0
PB D:GNP281 3.2 61.0 1.0
PG D:GNP281 3.2 64.2 1.0
N3B D:GNP281 3.4 61.9 1.0
N D:SER53 3.8 68.2 1.0
OD2 D:ASP93 4.0 71.5 1.0
CA D:SER53 4.0 68.0 1.0
O1G D:GNP281 4.1 64.5 1.0
O1B D:GNP281 4.2 64.1 1.0
O3G D:GNP281 4.2 64.3 1.0
O3A D:GNP281 4.3 64.8 1.0
OD1 D:ASP93 4.3 72.4 1.0
O2A D:GNP281 4.3 68.5 1.0
PA D:GNP281 4.5 67.1 1.0
CG D:ASP93 4.6 69.7 1.0
O1A D:GNP281 4.6 69.7 1.0
CB D:LYS52 4.7 68.2 1.0
O D:SER66 4.7 80.8 1.0
O D:SER72 4.8 94.0 1.0
C D:LYS52 4.9 68.4 1.0
O D:THR94 4.9 62.5 1.0
NZ D:LYS52 5.0 64.5 1.0

Magnesium binding site 5 out of 8 in 3bb1

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Magnesium binding site 5 out of 8 in the Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp


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 TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg282

b:64.6
occ:1.00
 O2G E:GNP281 2.0 67.2 1.0
O2B E:GNP281 2.0 64.5 1.0
O E:HOH292 2.1 60.6 1.0
O E:HOH291 2.1 62.6 1.0
OG E:SER53 2.1 61.9 1.0
O E:HOH293 2.1 60.7 1.0
PB E:GNP281 3.2 65.0 1.0
PG E:GNP281 3.3 68.7 1.0
CB E:SER53 3.3 60.3 1.0
N3B E:GNP281 3.4 65.4 1.0
O3G E:GNP281 4.0 72.9 1.0
N E:SER53 4.1 59.0 1.0
OD2 E:ASP93 4.1 61.2 1.0
O2A E:GNP281 4.1 60.2 1.0
OD1 E:ASP93 4.2 60.2 1.0
O1B E:GNP281 4.2 61.9 1.0
O E:SER66 4.2 81.9 1.0
CA E:SER53 4.3 59.9 1.0
O3A E:GNP281 4.4 65.7 1.0
O1G E:GNP281 4.5 66.2 1.0
CG E:ASP93 4.5 61.5 1.0
PA E:GNP281 4.6 66.4 1.0
O E:THR94 4.6 62.8 1.0
CE E:LYS52 4.7 56.0 1.0
O1A E:GNP281 4.8 67.2 1.0
O E:HOH327 4.9 73.4 1.0

Magnesium binding site 6 out of 8 in 3bb1

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Magnesium binding site 6 out of 8 in the Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp


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 TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg282

b:63.5
occ:1.00
 O2G F:GNP281 2.0 62.0 1.0
O F:HOH292 2.0 63.9 1.0
OG F:SER53 2.0 63.6 1.0
O2B F:GNP281 2.0 64.1 1.0
O F:HOH293 2.1 66.5 1.0
O F:HOH294 2.1 61.9 1.0
CB F:SER53 3.0 65.3 1.0
PB F:GNP281 3.2 63.7 1.0
PG F:GNP281 3.2 63.6 1.0
N3B F:GNP281 3.3 61.3 1.0
N F:SER53 3.7 65.1 1.0
CA F:SER53 4.0 65.8 1.0
O1G F:GNP281 4.1 56.5 1.0
O2A F:GNP281 4.1 65.5 1.0
OD2 F:ASP93 4.1 62.5 1.0
O3G F:GNP281 4.2 64.2 1.0
O3A F:GNP281 4.2 65.7 1.0
O1B F:GNP281 4.2 64.0 1.0
OD1 F:ASP93 4.3 64.4 1.0
PA F:GNP281 4.5 65.1 1.0
O F:SER66 4.5 81.0 1.0
O1A F:GNP281 4.6 65.8 1.0
CG F:ASP93 4.7 64.5 1.0
NZ F:LYS52 4.7 64.6 1.0
CB F:LYS52 4.8 65.0 1.0
O F:THR94 4.8 65.1 1.0
C F:LYS52 4.9 65.1 1.0

Magnesium binding site 7 out of 8 in 3bb1

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Magnesium binding site 7 out of 8 in the Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp


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 TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg282

b:64.0
occ:1.00
 O2B G:GNP281 2.0 64.0 1.0
OG G:SER53 2.0 60.9 1.0
O2G G:GNP281 2.0 65.5 1.0
O G:HOH293 2.1 65.1 1.0
O G:HOH292 2.1 60.8 1.0
O G:HOH294 2.1 61.8 1.0
CB G:SER53 3.1 60.0 1.0
PB G:GNP281 3.2 65.2 1.0
PG G:GNP281 3.3 66.0 1.0
N3B G:GNP281 3.5 65.4 1.0
N G:SER53 3.9 60.5 1.0
O2A G:GNP281 4.0 59.1 1.0
OD2 G:ASP93 4.0 62.4 1.0
O G:SER66 4.0 72.7 1.0
O3G G:GNP281 4.1 64.2 1.0
OD1 G:ASP93 4.1 61.0 1.0
CA G:SER53 4.1 60.1 1.0
O1B G:GNP281 4.2 66.8 1.0
O3A G:GNP281 4.3 63.3 1.0
O1G G:GNP281 4.4 62.4 1.0
PA G:GNP281 4.4 62.8 1.0
CG G:ASP93 4.5 62.7 1.0
CB G:LYS52 4.6 60.9 1.0
O1A G:GNP281 4.6 62.8 1.0
CE G:LYS52 4.7 61.1 1.0
O G:HOH322 4.8 79.1 1.0
OG G:SER68 4.8 84.7 1.0
NZ G:LYS52 4.8 63.3 1.0
O G:THR94 4.8 64.8 1.0
C G:LYS52 4.9 60.9 1.0

Magnesium binding site 8 out of 8 in 3bb1

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Magnesium binding site 8 out of 8 in the Crystal Structure of TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp


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 TOC34 From Pisum Sativum in Complex with MG2+ and Gmppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg282

b:71.2
occ:1.00
 O2G H:GNP281 2.0 74.5 1.0
O2B H:GNP281 2.0 74.2 1.0
O H:HOH284 2.0 74.1 1.0
OG H:SER53 2.1 73.3 1.0
O H:HOH283 2.1 74.9 1.0
O H:HOH285 2.1 72.6 1.0
CB H:SER53 3.0 73.8 1.0
PB H:GNP281 3.2 74.7 1.0
PG H:GNP281 3.2 75.9 1.0
N3B H:GNP281 3.4 75.7 1.0
OD2 H:ASP93 3.5 80.9 1.0
N H:SER53 3.9 74.0 1.0
CA H:SER53 4.0 73.7 1.0
OD1 H:ASP93 4.1 78.8 1.0
O1G H:GNP281 4.2 75.8 1.0
CG H:ASP93 4.2 78.1 1.0
O3G H:GNP281 4.3 72.5 1.0
O3A H:GNP281 4.3 76.3 1.0
O2A H:GNP281 4.3 74.1 1.0
O1B H:GNP281 4.3 74.3 1.0
O H:SER66 4.4 88.1 1.0
NZ H:LYS52 4.6 74.0 1.0
PA H:GNP281 4.6 74.8 1.0
O1A H:GNP281 4.6 74.7 1.0
CB H:LYS52 4.9 75.6 1.0
O H:THR94 4.9 75.2 1.0
CE H:LYS52 5.0 75.1 1.0

Reference:

P.Koenig, M.Oreb, A.Hofle, S.Kaltofen, K.Rippe, I.Sinning, E.Schleiff, I.Tews. The Gtpase Cycle of the Chloroplast Import Receptors TOC33/TOC34: Implications From Monomeric and Dimeric Structures. Structure V. 16 585 2008.
ISSN: ISSN 0969-2126
PubMed: 18400179
DOI: 10.1016/J.STR.2008.01.008
Page generated: Mon Dec 14 07:55:05 2020

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