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Magnesium in PDB 8jyu: Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp (pdb code 8jyu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp, PDB code: 8jyu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8jyu

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Magnesium binding site 1 out of 6 in the Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:66.9
occ:1.00
 O1P A:AMP602 2.2 51.4 1.0
OE1 A:GLU322 2.8 51.2 1.0
OE2 A:GLU322 3.5 53.1 1.0
CD A:GLU322 3.5 47.3 1.0
CB A:MET320 3.5 39.1 1.0
P A:AMP602 3.6 64.0 1.0
OG1 A:THR175 3.7 55.6 1.0
C5' A:AMP602 3.8 36.8 1.0
N A:SER321 3.9 31.0 1.0
O5' A:AMP602 4.0 51.2 1.0
CE A:MET320 4.2 41.7 1.0
CB A:SER321 4.3 37.0 1.0
CG A:MET320 4.3 38.4 1.0
CA A:MET320 4.4 31.2 1.0
OG A:SER321 4.5 47.6 1.0
CB A:THR175 4.5 48.1 1.0
CG2 A:THR175 4.6 45.8 1.0
C A:MET320 4.6 39.0 1.0
O1 A:DKA603 4.6 62.5 1.0
CA A:SER321 4.6 26.8 1.0
O2P A:AMP602 4.7 45.3 1.0
N A:GLU322 4.8 37.2 1.0
C4' A:AMP602 4.8 40.2 1.0
O3' A:AMP602 4.8 53.3 1.0
SD A:MET320 4.9 61.8 1.0
CG A:GLU322 5.0 37.9 1.0

Magnesium binding site 2 out of 6 in 8jyu

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Magnesium binding site 2 out of 6 in the Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:66.9
occ:1.00
 O2P D:AMP602 2.2 51.4 1.0
OE1 D:GLU322 2.8 51.2 1.0
OE2 D:GLU322 3.5 53.1 1.0
CD D:GLU322 3.5 47.3 1.0
CB D:MET320 3.5 39.1 1.0
P D:AMP602 3.6 64.0 1.0
OG1 D:THR175 3.7 55.6 1.0
C5' D:AMP602 3.8 36.8 1.0
N D:SER321 3.9 31.0 1.0
O5' D:AMP602 4.0 51.2 1.0
CE D:MET320 4.2 41.7 1.0
CB D:SER321 4.3 37.0 1.0
CG D:MET320 4.3 38.4 1.0
CA D:MET320 4.4 31.2 1.0
OG D:SER321 4.5 47.6 1.0
CB D:THR175 4.5 48.1 1.0
CG2 D:THR175 4.6 45.8 1.0
C D:MET320 4.6 39.0 1.0
O2 D:DKA603 4.6 62.5 1.0
CA D:SER321 4.6 26.8 1.0
O1P D:AMP602 4.7 45.3 1.0
N D:GLU322 4.8 37.2 1.0
C4' D:AMP602 4.8 40.2 1.0
O3' D:AMP602 4.8 53.3 1.0
SD D:MET320 4.9 61.8 1.0
CG D:GLU322 5.0 37.9 1.0

Magnesium binding site 3 out of 6 in 8jyu

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Magnesium binding site 3 out of 6 in the Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:66.9
occ:1.00
 O2P B:AMP602 2.2 51.4 1.0
OE1 B:GLU322 2.8 51.2 1.0
OE2 B:GLU322 3.5 53.1 1.0
CD B:GLU322 3.5 47.3 1.0
CB B:MET320 3.5 39.1 1.0
P B:AMP602 3.6 64.0 1.0
OG1 B:THR175 3.7 55.6 1.0
C5' B:AMP602 3.8 36.8 1.0
N B:SER321 3.9 31.0 1.0
O5' B:AMP602 4.0 51.2 1.0
CE B:MET320 4.2 41.7 1.0
CB B:SER321 4.3 37.0 1.0
CG B:MET320 4.3 38.4 1.0
CA B:MET320 4.4 31.2 1.0
OG B:SER321 4.5 47.6 1.0
CB B:THR175 4.5 48.1 1.0
CG2 B:THR175 4.6 45.8 1.0
C B:MET320 4.6 39.0 1.0
O2 B:DKA603 4.6 62.5 1.0
CA B:SER321 4.6 26.8 1.0
O1P B:AMP602 4.7 45.3 1.0
N B:GLU322 4.8 37.2 1.0
C4' B:AMP602 4.8 40.2 1.0
O3' B:AMP602 4.8 53.3 1.0
SD B:MET320 4.9 61.8 1.0
CG B:GLU322 5.0 37.9 1.0

Magnesium binding site 4 out of 6 in 8jyu

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Magnesium binding site 4 out of 6 in the Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:66.9
occ:1.00
 O1P C:AMP602 2.2 51.4 1.0
OE1 C:GLU322 2.8 51.2 1.0
OE2 C:GLU322 3.5 53.1 1.0
CD C:GLU322 3.5 47.3 1.0
CB C:MET320 3.5 39.1 1.0
P C:AMP602 3.6 64.0 1.0
OG1 C:THR175 3.7 55.6 1.0
C5' C:AMP602 3.8 36.8 1.0
N C:SER321 3.9 31.0 1.0
O5' C:AMP602 4.0 51.2 1.0
CE C:MET320 4.2 41.7 1.0
CB C:SER321 4.3 37.0 1.0
CG C:MET320 4.3 38.4 1.0
CA C:MET320 4.4 31.2 1.0
OG C:SER321 4.5 47.6 1.0
CB C:THR175 4.5 48.1 1.0
CG2 C:THR175 4.6 45.8 1.0
C C:MET320 4.6 39.0 1.0
O1 C:DKA603 4.6 62.5 1.0
CA C:SER321 4.6 26.8 1.0
O2P C:AMP602 4.7 45.3 1.0
N C:GLU322 4.8 37.2 1.0
C4' C:AMP602 4.8 40.2 1.0
O3' C:AMP602 4.8 53.3 1.0
SD C:MET320 4.9 61.8 1.0
CG C:GLU322 5.0 37.9 1.0

Magnesium binding site 5 out of 6 in 8jyu

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Magnesium binding site 5 out of 6 in the Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:66.9
occ:1.00
 O1P E:AMP602 2.2 51.4 1.0
OE1 E:GLU322 2.8 51.2 1.0
OE2 E:GLU322 3.5 53.1 1.0
CD E:GLU322 3.5 47.3 1.0
CB E:MET320 3.5 39.1 1.0
P E:AMP602 3.6 64.0 1.0
OG1 E:THR175 3.7 55.6 1.0
C5' E:AMP602 3.8 36.8 1.0
N E:SER321 3.9 31.0 1.0
O5' E:AMP602 4.0 51.2 1.0
CE E:MET320 4.2 41.7 1.0
CB E:SER321 4.3 37.0 1.0
CG E:MET320 4.3 38.4 1.0
CA E:MET320 4.4 31.2 1.0
OG E:SER321 4.5 47.6 1.0
CB E:THR175 4.5 48.1 1.0
CG2 E:THR175 4.6 45.8 1.0
C E:MET320 4.6 39.0 1.0
O1 E:DKA603 4.6 62.5 1.0
CA E:SER321 4.6 26.8 1.0
O2P E:AMP602 4.7 45.3 1.0
N E:GLU322 4.8 37.2 1.0
C4' E:AMP602 4.8 40.2 1.0
O3' E:AMP602 4.8 53.3 1.0
SD E:MET320 4.9 61.8 1.0
CG E:GLU322 5.0 37.9 1.0

Magnesium binding site 6 out of 6 in 8jyu

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Magnesium binding site 6 out of 6 in the Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:66.9
occ:1.00
 O2P F:AMP602 2.2 51.4 1.0
OE1 F:GLU322 2.8 51.2 1.0
OE2 F:GLU322 3.5 53.1 1.0
CD F:GLU322 3.5 47.3 1.0
CB F:MET320 3.5 39.1 1.0
P F:AMP602 3.6 64.0 1.0
OG1 F:THR175 3.7 55.6 1.0
C5' F:AMP602 3.8 36.8 1.0
N F:SER321 3.9 31.0 1.0
O5' F:AMP602 4.0 51.2 1.0
CE F:MET320 4.2 41.7 1.0
CB F:SER321 4.3 37.0 1.0
CG F:MET320 4.3 38.4 1.0
CA F:MET320 4.4 31.2 1.0
OG F:SER321 4.5 47.6 1.0
CB F:THR175 4.5 48.1 1.0
CG2 F:THR175 4.6 45.8 1.0
C F:MET320 4.6 39.0 1.0
O2 F:DKA603 4.6 62.5 1.0
CA F:SER321 4.6 26.8 1.0
O1P F:AMP602 4.7 45.3 1.0
N F:GLU322 4.8 37.2 1.0
C4' F:AMP602 4.8 40.2 1.0
O3' F:AMP602 4.8 53.3 1.0
SD F:MET320 4.9 61.8 1.0
CG F:GLU322 5.0 37.9 1.0

Reference:

H.Huang, S.Chang, M.Huang, H.Zhang, C.Zhou, X.Zhang, Y.Feng. Acyl-Acp Synthetase Structure Bound to Decanoyl-Amp To Be Published.
Page generated: Fri Oct 4 13:41:29 2024

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