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Magnesium in PDB 5k8f: Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99

Enzymatic activity of Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99

All present enzymatic activity of Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99:
6.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99, PDB code: 5k8f was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), D.Fox Iii, S.L.Delker, K.T.Potts, D.D.Lorimer, T.E.Edwards, M.W.Mutz, Ssgcid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.62 / 2.45
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.370, 83.920, 101.570, 110.06, 105.24, 87.65
R / Rfree (%) 17.8 / 22.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99 (pdb code 5k8f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99, PDB code: 5k8f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5k8f

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Magnesium binding site 1 out of 7 in the Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99


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 Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:41.2
occ:0.70
 O2B A:ATP703 2.4 46.5 0.6
MG A:MG702 2.7 49.1 0.7
O2A A:ATP703 2.8 35.0 0.6
O07 A:6R9704 2.9 36.0 0.4
O3G A:ATP703 3.0 49.5 0.6
OE1 A:GLU442 3.0 30.5 1.0
O A:HOH802 3.1 48.4 1.0
O3A A:ATP703 3.2 39.4 0.6
PB A:ATP703 3.2 43.5 0.6
OE2 A:GLU442 3.3 32.5 1.0
PA A:ATP703 3.4 35.2 0.6
O3B A:ATP703 3.5 50.5 0.6
CD A:GLU442 3.6 32.3 1.0
O5' A:ATP703 3.7 35.3 0.6
C5' A:ATP703 3.8 33.7 0.6
PG A:ATP703 4.0 52.5 0.6
C09 A:6R9704 4.0 33.9 0.4
P05 A:6R9704 4.2 34.1 0.4
O08 A:6R9704 4.2 34.9 0.4
CB A:MET440 4.3 31.4 1.0
CG2 A:THR289 4.3 56.0 0.5
CG2 A:THR289 4.4 56.2 0.5
SD A:MET440 4.4 39.0 1.0
N A:THR441 4.6 26.2 1.0
C4' A:ATP703 4.6 33.9 0.6
CG A:MET440 4.6 36.2 1.0
O1B A:ATP703 4.7 42.3 0.6
OG1 A:THR441 4.7 30.1 1.0
O1G A:ATP703 4.8 50.7 0.6
CB A:THR441 4.8 30.0 1.0
O3' A:ATP703 4.8 33.1 0.6
O1A A:ATP703 4.9 35.5 0.6
C10 A:6R9704 4.9 34.1 0.4
CB A:THR289 5.0 59.1 0.5
O26 A:6R9704 5.0 32.6 0.4

Magnesium binding site 2 out of 7 in 5k8f

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Magnesium binding site 2 out of 7 in the Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99


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 Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:49.1
occ:0.71
 O3G A:ATP703 1.9 49.5 0.6
O2B A:ATP703 2.1 46.5 0.6
O A:HOH802 2.4 48.4 1.0
MG A:MG701 2.7 41.2 0.7
NH2 A:ARG542 3.0 65.4 1.0
PG A:ATP703 3.1 52.5 0.6
CZ A:ARG542 3.1 61.2 1.0
NH1 A:ARG542 3.1 59.2 1.0
PB A:ATP703 3.3 43.5 0.6
O3B A:ATP703 3.5 50.5 0.6
O2G A:ATP703 3.6 55.9 0.6
NE A:ARG542 4.0 57.0 1.0
O3' A:ATP703 4.2 33.1 0.6
O1B A:ATP703 4.4 42.3 0.6
O26 A:6R9704 4.4 32.6 0.4
O1G A:ATP703 4.4 50.7 0.6
O3A A:ATP703 4.4 39.4 0.6
O A:HOH965 4.6 39.7 1.0
O5' A:ATP703 4.6 35.3 0.6
C4' A:ATP703 4.6 33.9 0.6
C5' A:ATP703 4.7 33.7 0.6
C09 A:6R9704 4.8 33.9 0.4
OE2 A:GLU442 4.8 32.5 1.0
CD A:ARG542 4.8 51.6 1.0
C10 A:6R9704 4.8 34.1 0.4
SD A:MET440 4.9 39.0 1.0
NZ A:LYS297 5.0 55.1 0.5

Magnesium binding site 3 out of 7 in 5k8f

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Magnesium binding site 3 out of 7 in the Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99


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 Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:34.4
occ:0.50
 O06 B:6R9704 2.4 68.0 0.5
MG B:MG702 2.8 66.4 0.7
O1B B:ATP703 2.8 61.4 0.7
OE1 B:GLU442 2.9 49.6 1.0
O3A B:ATP703 2.9 66.3 0.7
O1A B:ATP703 3.0 67.9 0.7
PA B:ATP703 3.4 68.5 0.7
PB B:ATP703 3.5 61.6 0.7
C09 B:6R9704 3.5 71.5 0.5
O2G B:ATP703 3.5 65.7 0.7
CB B:MET440 3.5 47.5 1.0
OE2 B:GLU442 3.5 50.4 1.0
CD B:GLU442 3.6 48.9 1.0
C5' B:ATP703 3.6 71.5 0.7
P05 B:6R9704 3.7 68.7 0.5
O5' B:ATP703 3.7 70.4 0.7
O08 B:6R9704 3.9 70.3 0.5
N B:THR441 4.1 43.0 1.0
O3B B:ATP703 4.3 63.4 0.7
SD B:MET440 4.3 52.5 1.0
C4' B:ATP703 4.4 72.7 0.7
O3' B:ATP703 4.4 72.6 0.7
C10 B:6R9704 4.5 72.7 0.5
CA B:MET440 4.5 46.6 1.0
O26 B:6R9704 4.5 72.6 0.5
CG B:MET440 4.5 48.8 1.0
PG B:ATP703 4.6 64.3 0.7
CB B:THR441 4.6 42.8 1.0
CG2 B:THR289 4.6 60.4 1.0
O07 B:6R9704 4.7 69.0 0.5
O04 B:6R9704 4.7 68.0 0.5
OG1 B:THR441 4.7 41.6 1.0
O2B B:ATP703 4.8 62.7 0.7
C B:MET440 4.8 43.8 1.0
C3' B:ATP703 4.9 72.7 0.7
O2A B:ATP703 4.9 68.9 0.7
CA B:THR441 4.9 43.8 1.0
N B:GLU442 4.9 40.5 1.0
C11 B:6R9704 5.0 72.7 0.5

Magnesium binding site 4 out of 7 in 5k8f

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Magnesium binding site 4 out of 7 in the Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99


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 Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:66.4
occ:0.73
 O2G B:ATP703 2.0 65.7 0.7
O1B B:ATP703 2.2 61.4 0.7
MG B:MG701 2.8 34.4 0.5
PG B:ATP703 3.3 64.3 0.7
PB B:ATP703 3.5 61.6 0.7
O3B B:ATP703 3.8 63.4 0.7
O3G B:ATP703 3.9 65.1 0.7
NH1 B:ARG542 4.1 62.6 1.0
O3A B:ATP703 4.1 66.3 0.7
OE2 B:GLU442 4.3 50.4 1.0
O1G B:ATP703 4.5 64.0 0.7
O3' B:ATP703 4.5 72.6 0.7
O26 B:6R9704 4.6 72.6 0.5
O2B B:ATP703 4.7 62.7 0.7
O06 B:6R9704 4.8 68.0 0.5
OE1 B:GLU442 4.9 49.6 1.0
OG1 B:THR293 4.9 0.5 1.0
C09 B:6R9704 5.0 71.5 0.5

Magnesium binding site 5 out of 7 in 5k8f

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Magnesium binding site 5 out of 7 in the Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99


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 Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:38.1
occ:0.66
 O2B C:ATP703 2.5 47.2 0.6
MG C:MG702 2.6 48.5 0.7
O07 C:6R9704 2.6 46.5 0.4
O2A C:ATP703 2.8 46.0 0.6
O3G C:ATP703 3.0 55.1 0.6
O3A C:ATP703 3.1 47.3 0.6
OE1 C:GLU442 3.1 38.0 1.0
PB C:ATP703 3.2 48.8 0.6
PA C:ATP703 3.4 46.8 0.6
OE2 C:GLU442 3.6 38.6 1.0
C09 C:6R9704 3.6 43.6 0.4
O5' C:ATP703 3.7 45.1 0.6
C5' C:ATP703 3.7 43.5 0.6
CD C:GLU442 3.8 38.4 1.0
O3B C:ATP703 3.8 51.9 0.6
P05 C:6R9704 3.8 45.9 0.4
PG C:ATP703 3.9 54.7 0.6
O08 C:6R9704 4.0 45.0 0.4
O1G C:ATP703 4.1 55.8 0.6
CB C:MET440 4.3 45.5 1.0
CG2 C:THR289 4.4 50.6 1.0
C4' C:ATP703 4.5 43.1 0.6
N C:THR441 4.6 34.9 1.0
C10 C:6R9704 4.6 43.0 0.4
O06 C:6R9704 4.6 46.1 0.4
O1B C:ATP703 4.7 52.2 0.6
SD C:MET440 4.7 52.6 1.0
O3' C:ATP703 4.7 41.3 0.6
OG1 C:THR441 4.7 39.4 1.0
CB C:THR441 4.7 37.0 1.0
NH1 C:ARG542 4.8 43.0 0.5
O1A C:ATP703 4.9 45.5 0.6
O26 C:6R9704 4.9 41.1 0.4
CG C:MET440 4.9 50.5 1.0

Magnesium binding site 6 out of 7 in 5k8f

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Magnesium binding site 6 out of 7 in the Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99


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 Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:48.5
occ:0.72
 O2B C:ATP703 2.2 47.2 0.6
O1G C:ATP703 2.3 55.8 0.6
MG C:MG701 2.6 38.1 0.7
O3G C:ATP703 2.7 55.1 0.6
PG C:ATP703 2.9 54.7 0.6
NH2 C:ARG542 3.2 44.2 0.5
NH1 C:ARG542 3.3 43.0 0.5
CZ C:ARG542 3.4 50.1 0.5
PB C:ATP703 3.4 48.8 0.6
NH2 C:ARG542 3.6 43.1 0.5
O3B C:ATP703 3.6 51.9 0.6
NE C:ARG542 4.2 48.4 0.5
O3A C:ATP703 4.3 47.3 0.6
O2G C:ATP703 4.3 52.4 0.6
O3' C:ATP703 4.6 41.3 0.6
O1B C:ATP703 4.6 52.2 0.6
OE2 C:GLU442 4.6 38.6 1.0
C09 C:6R9704 4.8 43.6 0.4
O26 C:6R9704 4.8 41.1 0.4
O07 C:6R9704 4.8 46.5 0.4
CZ C:ARG542 4.9 42.6 0.5
O5' C:ATP703 4.9 45.1 0.6
C4' C:ATP703 4.9 43.1 0.6
C5' C:ATP703 4.9 43.5 0.6
C10 C:6R9704 5.0 43.0 0.4

Magnesium binding site 7 out of 7 in 5k8f

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Magnesium binding site 7 out of 7 in the Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99


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 Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg705

b:74.2
occ:1.00
 OE1 C:GLU90 2.5 66.0 1.0
O C:HOH813 2.5 59.3 1.0
NE2 C:HIS91 3.1 42.0 1.0
CD C:GLU90 3.2 64.1 1.0
OE2 C:GLU90 3.4 67.2 1.0
OE1 A:GLU138 3.4 53.9 1.0
CD2 C:HIS91 3.7 40.9 1.0
NZ A:LYS118 3.9 48.0 1.0
CD A:GLU138 4.2 52.2 1.0
CE1 C:HIS91 4.3 41.2 1.0
CG C:GLU90 4.4 55.2 1.0
OE2 A:GLU138 4.5 55.3 1.0
CB C:GLU90 4.9 48.4 1.0
CG C:HIS91 5.0 39.7 1.0

Reference:

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), Ssgcid, D.Fox Iii, S.L.Delker, K.T.Potts, M.M.Numa, T.E.Edwards, D.D.Lorimer, M.W.Mutz, D.J.Krysan. Crystal Structure of Acetyl-Coa Synthetase in Complex with Atp and Acetyl-Amp From Cryptococcus Neoformans H99 To Be Published.
Page generated: Tue Aug 12 13:02:01 2025

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