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Magnesium in PDB 4qqf: Crystal Structure of Mitochondrial Import Inner Membrane Translocase Subunit TIM50

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Import Inner Membrane Translocase Subunit TIM50, PDB code: 4qqf was solved by J.Z.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.52 / 2.67
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 164.287, 164.287, 150.532, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mitochondrial Import Inner Membrane Translocase Subunit TIM50 (pdb code 4qqf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Mitochondrial Import Inner Membrane Translocase Subunit TIM50, PDB code: 4qqf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4qqf

Go back to Magnesium Binding Sites List in 4qqf
Magnesium binding site 1 out of 6 in the Crystal Structure of Mitochondrial Import Inner Membrane Translocase Subunit TIM50


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 Mitochondrial Import Inner Membrane Translocase Subunit TIM50 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:68.0
occ:1.00
 O D:HOH508 2.8 30.0 1.0
O D:HOH507 3.8 30.0 1.0
N D:GLY220 3.9 65.8 1.0
O D:ARG218 3.9 72.2 1.0
CE D:LYS217 4.1 69.5 1.0
O D:HOH505 4.2 73.1 1.0
OD2 D:ASP222 4.4 86.9 1.0
CG D:ASP222 4.4 76.6 1.0
N D:ALA221 4.5 70.0 1.0
NZ D:LYS217 4.6 63.7 1.0
CA D:PRO219 4.6 70.2 1.0
N D:ASP222 4.6 60.6 1.0
CB F:ASN262 4.7 76.2 1.0
CA D:GLY220 4.7 66.5 1.0
C D:PRO219 4.7 66.7 1.0
CB D:ASP222 4.8 63.5 1.0
OD1 D:ASP222 4.8 80.7 1.0
ND2 F:ASN262 4.8 80.2 1.0
CD D:LYS217 4.8 69.5 1.0
C D:ARG218 4.9 71.2 1.0
C D:GLY220 4.9 71.5 1.0
CG D:LYS217 5.0 68.1 1.0

Magnesium binding site 2 out of 6 in 4qqf

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Magnesium binding site 2 out of 6 in the Crystal Structure of Mitochondrial Import Inner Membrane Translocase Subunit TIM50


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 Mitochondrial Import Inner Membrane Translocase Subunit TIM50 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:41.2
occ:1.00
 N A:GLY220 3.6 75.0 1.0
NE1 E:TRP207 3.7 59.7 1.0
N E:TRP213 3.9 67.8 1.0
CA A:GLY220 3.9 73.0 1.0
N A:ASP222 3.9 60.9 1.0
CB A:ASP222 3.9 62.9 1.0
CB E:TRP213 4.1 66.7 1.0
N A:TYR223 4.1 62.4 1.0
CD1 E:TRP207 4.2 53.2 1.0
C A:GLY220 4.2 66.6 1.0
N A:ALA221 4.2 58.0 1.0
CG A:ASP222 4.4 68.3 1.0
CA A:ASP222 4.4 62.9 1.0
CA E:GLY212 4.5 71.0 1.0
CB A:TYR223 4.6 60.6 1.0
C E:GLY212 4.6 72.6 1.0
CA E:TRP213 4.6 64.2 1.0
OD2 A:ASP222 4.6 80.5 1.0
C A:ASP222 4.8 65.9 1.0
C A:ALA221 4.8 56.6 1.0
C A:PRO219 4.9 66.5 1.0
CE2 E:TRP207 4.9 56.3 1.0
O A:GLY220 4.9 62.7 1.0
OD1 A:ASP222 5.0 66.4 1.0
CA A:TYR223 5.0 59.7 1.0

Magnesium binding site 3 out of 6 in 4qqf

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Magnesium binding site 3 out of 6 in the Crystal Structure of Mitochondrial Import Inner Membrane Translocase Subunit TIM50


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 Mitochondrial Import Inner Membrane Translocase Subunit TIM50 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:47.6
occ:1.00
 N B:GLY220 3.7 57.2 1.0
O B:ARG218 3.9 58.2 1.0
CA B:PRO219 4.3 69.7 1.0
N B:ALA221 4.4 47.1 1.0
C B:PRO219 4.5 64.9 1.0
OD2 B:ASP222 4.6 0.2 1.0
CA B:GLY220 4.6 54.8 1.0
N B:ASP222 4.6 53.6 1.0
CG B:ASP222 4.7 0.9 1.0
C B:ARG218 4.8 61.5 1.0
CE B:LYS217 4.8 66.5 1.0
C B:GLY220 4.8 55.2 1.0
CB B:LYS217 4.8 54.8 1.0
NZ B:LYS217 4.9 75.6 1.0
CB B:ASP222 4.9 63.4 1.0
CD B:LYS217 5.0 67.4 1.0

Magnesium binding site 4 out of 6 in 4qqf

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Magnesium binding site 4 out of 6 in the Crystal Structure of Mitochondrial Import Inner Membrane Translocase Subunit TIM50


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 Mitochondrial Import Inner Membrane Translocase Subunit TIM50 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:41.8
occ:1.00
 N C:GLY220 3.6 67.4 1.0
CB C:ASP222 3.7 64.3 1.0
CA C:GLY220 3.8 62.3 1.0
N C:ASP222 3.8 59.3 1.0
N C:TYR223 4.0 62.2 1.0
C C:GLY220 4.1 58.5 1.0
N C:ALA221 4.2 64.1 1.0
CA C:ASP222 4.2 60.1 1.0
CG C:ASP222 4.3 65.5 1.0
OD2 C:ASP222 4.5 67.5 1.0
C C:ASP222 4.7 58.2 1.0
O C:GLY220 4.7 59.3 1.0
CB C:TYR223 4.7 62.1 1.0
C C:ALA221 4.8 60.3 1.0
C C:PRO219 4.9 66.5 1.0

Magnesium binding site 5 out of 6 in 4qqf

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Magnesium binding site 5 out of 6 in the Crystal Structure of Mitochondrial Import Inner Membrane Translocase Subunit TIM50


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 Mitochondrial Import Inner Membrane Translocase Subunit TIM50 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:39.4
occ:1.00
 N E:GLY220 3.6 50.3 1.0
CA E:GLY220 3.8 49.0 1.0
N E:ASP222 3.9 58.0 1.0
CB E:ASP222 3.9 65.9 1.0
N E:TYR223 4.0 58.5 1.0
C E:GLY220 4.1 54.1 1.0
N E:ALA221 4.2 51.1 1.0
CA E:ASP222 4.4 56.8 1.0
CG E:ASP222 4.5 65.7 1.0
CB E:TYR223 4.5 62.8 1.0
C E:ASP222 4.7 61.6 1.0
OD2 E:ASP222 4.7 66.0 1.0
O E:GLY220 4.7 51.0 1.0
C E:PRO219 4.8 54.0 1.0
C E:ALA221 4.8 54.1 1.0
CA E:TYR223 4.9 54.4 1.0

Magnesium binding site 6 out of 6 in 4qqf

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Magnesium binding site 6 out of 6 in the Crystal Structure of Mitochondrial Import Inner Membrane Translocase Subunit TIM50


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 Mitochondrial Import Inner Membrane Translocase Subunit TIM50 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:55.1
occ:1.00
 OD1 F:ASP222 1.9 98.3 1.0
OD2 F:ASP222 2.5 0.2 1.0
CG F:ASP222 2.5 0.0 1.0
N F:GLY220 3.5 81.4 1.0
NE1 C:TRP207 3.5 96.3 1.0
N C:TRP213 3.6 84.1 1.0
CA F:GLY220 3.7 76.6 1.0
CB C:TRP213 3.7 86.2 1.0
CB F:ASP222 4.0 96.7 1.0
CD1 C:TRP207 4.1 0.9 1.0
N F:TYR223 4.2 80.8 1.0
CA C:GLY212 4.2 87.3 1.0
C F:GLY220 4.3 73.1 1.0
N F:ASP222 4.3 100.0 1.0
CA C:TRP213 4.3 83.4 1.0
C C:GLY212 4.4 87.5 1.0
N F:ALA221 4.5 74.5 1.0
CB F:TYR223 4.5 82.6 1.0
CA F:ASP222 4.6 95.4 1.0
C F:PRO219 4.7 97.8 1.0
CE2 C:TRP207 4.8 95.7 1.0
CG C:TRP213 4.8 76.4 1.0
C F:ASP222 4.9 90.8 1.0
O F:GLY220 4.9 69.1 1.0

Reference:

J.Li, B.Sha. The Structure of TIM50(164-361) Suggests the Mechanism By Which TIM50 Receives Mitochondrial Presequences. Acta Crystallogr F Struct V. 71 1146 2015BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 26323300
DOI: 10.1107/S2053230X15013102
Page generated: Tue Aug 20 02:08:40 2024

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