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Magnesium in PDB 3b9t: Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution

Protein crystallography data

The structure of Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution, PDB code: 3b9t was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.81 / 1.58
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 62.165, 82.723, 83.576, 107.82, 105.81, 95.18
R / Rfree (%) 13.8 / 17.7

Other elements in 3b9t:

The structure of Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution (pdb code 3b9t). 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 Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution, PDB code: 3b9t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3b9t

Go back to Magnesium Binding Sites List in 3b9t
Magnesium binding site 1 out of 8 in the Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution


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 Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg484

b:26.0
occ:1.00
 OD1 A:ASP341 2.1 14.2 1.0
NE2 A:HIS343 2.2 15.7 1.0
OE2 A:GLU357 2.3 19.6 1.0
OE1 A:GLU357 2.3 20.8 1.0
C2 A:EDO494 2.4 22.9 1.0
OD2 A:ASP341 2.6 17.9 1.0
CD A:GLU357 2.6 18.5 1.0
CG A:ASP341 2.7 16.9 1.0
CD2 A:HIS343 3.1 13.7 1.0
C1 A:EDO494 3.2 31.8 1.0
CE1 A:HIS343 3.3 13.7 1.0
MG A:MG485 3.3 36.2 1.0
O2 A:EDO494 3.5 35.3 1.0
O1 A:EDO494 3.6 27.3 1.0
OE2 A:GLU350 4.0 24.4 1.0
CE1 A:HIS110 4.0 17.7 1.0
CG A:GLU357 4.1 17.6 1.0
CB A:ASP341 4.1 15.4 1.0
CG A:HIS343 4.2 12.1 1.0
ND1 A:HIS343 4.3 16.2 1.0
O A:HOH501 4.3 13.3 1.0
O A:ASP341 4.4 11.8 1.0
OD1 A:ASP316 4.4 13.4 1.0
NE2 A:HIS110 4.6 15.1 1.0
CD2 A:HIS160 4.6 14.2 1.0
NE2 A:HIS160 4.7 14.7 1.0
N A:ALA355 4.7 15.3 1.0
CA A:ASP341 4.7 13.7 1.0
C A:ASP341 4.8 13.5 1.0
CB A:ALA355 4.9 13.1 1.0
CB A:GLU357 5.0 15.9 1.0

Magnesium binding site 2 out of 8 in 3b9t

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Magnesium binding site 2 out of 8 in the Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution


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 Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg485

b:36.2
occ:1.00
 O1 A:EDO494 1.8 27.3 1.0
OD1 A:ASP316 1.9 13.4 1.0
OD2 A:ASP341 2.0 17.9 1.0
OD1 A:ASN314 2.1 15.9 1.0
OD2 A:ASP316 2.4 14.3 1.0
CG A:ASP316 2.5 14.3 1.0
C1 A:EDO494 2.9 31.8 1.0
CG A:ASN314 3.1 13.6 1.0
CG A:ASP341 3.2 16.9 1.0
ND2 A:ASN314 3.3 16.4 1.0
MG A:MG484 3.3 26.0 1.0
C2 A:EDO494 3.4 22.9 1.0
NE2 A:HIS160 3.7 14.7 1.0
NE2 A:HIS343 3.8 15.7 1.0
CE1 A:HIS343 3.9 13.7 1.0
OD1 A:ASP341 3.9 14.2 1.0
OE2 A:GLU350 4.0 24.4 1.0
CB A:ASP316 4.0 12.1 1.0
CA A:GLY291 4.3 13.5 1.0
CB A:ASP341 4.3 15.4 1.0
OG1 A:THR292 4.3 18.1 1.0
O2 A:EDO494 4.3 35.3 1.0
CD2 A:HIS160 4.4 14.2 1.0
C A:GLY291 4.4 13.1 1.0
CB A:ASN314 4.4 12.2 1.0
O A:GLY291 4.5 15.3 1.0
OD2 A:ASP464 4.5 17.2 1.0
OE1 A:GLU350 4.5 17.2 1.0
CE1 A:HIS160 4.5 19.2 1.0
OD1 A:ASP464 4.6 15.0 1.0
CD A:GLU350 4.7 18.4 1.0
CA A:ASP316 4.7 12.7 1.0
O1 A:EDO490 4.7 28.4 1.0
O A:ASN314 4.8 14.2 1.0
CA A:ASN314 4.8 12.5 1.0
N A:ASP316 4.9 14.0 1.0
C A:ASN314 4.9 14.6 1.0
CG A:ASP464 4.9 16.0 1.0

Magnesium binding site 3 out of 8 in 3b9t

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Magnesium binding site 3 out of 8 in the Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution


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 Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg484

b:21.9
occ:1.00
 OD1 B:ASP341 2.1 15.9 1.0
OE2 B:GLU357 2.2 20.4 1.0
NE2 B:HIS343 2.3 13.4 1.0
C2 B:EDO486 2.3 23.0 1.0
OE1 B:GLU357 2.3 16.4 1.0
OD2 B:ASP341 2.6 18.4 1.0
CD B:GLU357 2.6 18.2 1.0
CG B:ASP341 2.7 14.7 1.0
C1 B:EDO486 3.1 26.8 1.0
CD2 B:HIS343 3.1 15.7 1.0
CE1 B:HIS343 3.3 18.4 1.0
MG B:MG485 3.4 35.8 1.0
O1 B:EDO486 3.4 22.0 1.0
O2 B:EDO486 3.5 28.4 1.0
CE1 B:HIS110 4.0 14.5 1.0
CG B:GLU357 4.1 14.1 1.0
OE2 B:GLU350 4.1 20.4 1.0
CB B:ASP341 4.1 12.1 1.0
CG B:HIS343 4.3 13.9 1.0
O B:HOH500 4.3 13.1 1.0
ND1 B:HIS343 4.3 15.1 1.0
O B:ASP341 4.4 13.3 1.0
OD1 B:ASP316 4.5 14.3 1.0
NE2 B:HIS110 4.5 15.0 1.0
CD2 B:HIS160 4.6 12.3 1.0
NE2 B:HIS160 4.7 16.2 1.0
N B:ALA355 4.7 15.6 1.0
CA B:ASP341 4.8 12.4 1.0
C B:ASP341 4.8 11.6 1.0
CB B:ALA355 4.9 15.2 1.0
CB B:GLU357 4.9 15.4 1.0

Magnesium binding site 4 out of 8 in 3b9t

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Magnesium binding site 4 out of 8 in the Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution


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 Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg485

b:35.8
occ:1.00
 O1 B:EDO486 1.7 22.0 1.0
OD2 B:ASP341 2.0 18.4 1.0
OD1 B:ASP316 2.0 14.3 1.0
OD1 B:ASN314 2.1 15.9 1.0
OD2 B:ASP316 2.5 15.8 1.0
CG B:ASP316 2.6 15.0 1.0
C1 B:EDO486 2.9 26.8 1.0
CG B:ASN314 3.0 15.4 1.0
CG B:ASP341 3.2 14.7 1.0
ND2 B:ASN314 3.3 18.2 1.0
MG B:MG484 3.4 21.9 1.0
C2 B:EDO486 3.5 23.0 1.0
NE2 B:HIS160 3.7 16.2 1.0
NE2 B:HIS343 3.8 13.4 1.0
CE1 B:HIS343 3.9 18.4 1.0
OD1 B:ASP341 3.9 15.9 1.0
CB B:ASP316 4.1 12.1 1.0
CB B:ASP341 4.1 12.1 1.0
OG1 B:THR292 4.1 17.9 1.0
OE2 B:GLU350 4.2 20.4 1.0
CA B:GLY291 4.2 11.7 1.0
CD2 B:HIS160 4.3 12.3 1.0
O2 B:EDO486 4.3 28.4 1.0
O B:GLY291 4.3 14.6 1.0
C B:GLY291 4.4 13.9 1.0
CB B:ASN314 4.4 12.9 1.0
CE1 B:HIS160 4.5 19.6 1.0
OD2 B:ASP464 4.6 16.0 1.0
O2 B:EDO490 4.7 25.1 1.0
OE1 B:GLU350 4.7 16.1 1.0
OD1 B:ASP464 4.7 13.5 1.0
CA B:ASP316 4.7 11.8 1.0
CA B:ASN314 4.7 11.7 1.0
O B:ASN314 4.8 12.5 1.0
CD B:GLU350 4.8 19.8 1.0
C B:ASN314 4.9 13.0 1.0
N B:ASP316 4.9 11.9 1.0
N B:THR292 5.0 13.9 1.0

Magnesium binding site 5 out of 8 in 3b9t

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Magnesium binding site 5 out of 8 in the Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution


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 Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg484

b:20.8
occ:1.00
 OD1 C:ASP341 2.2 13.7 1.0
OE2 C:GLU357 2.2 16.0 1.0
NE2 C:HIS343 2.2 12.8 1.0
OE1 C:GLU357 2.3 17.0 1.0
C2 C:EDO496 2.4 22.4 1.0
CD C:GLU357 2.5 16.8 1.0
OD2 C:ASP341 2.6 15.2 1.0
CG C:ASP341 2.7 10.3 1.0
C1 C:EDO496 2.8 26.6 1.0
CD2 C:HIS343 3.1 11.9 1.0
CE1 C:HIS343 3.3 12.9 1.0
O1 C:EDO496 3.4 21.4 1.0
MG C:MG485 3.4 28.1 1.0
O2 C:EDO496 3.7 33.8 1.0
CG C:GLU357 4.0 13.0 1.0
OE2 C:GLU350 4.1 17.9 1.0
CE1 C:HIS110 4.1 11.5 1.0
CB C:ASP341 4.2 10.2 1.0
CG C:HIS343 4.3 10.5 1.0
ND1 C:HIS343 4.4 12.9 1.0
O C:HOH500 4.4 9.1 1.0
OD1 C:ASP316 4.4 10.5 1.0
O C:ASP341 4.4 12.4 1.0
NE2 C:HIS110 4.6 12.6 1.0
N C:ALA355 4.6 12.7 1.0
CD2 C:HIS160 4.7 16.0 1.0
NE2 C:HIS160 4.8 15.7 1.0
CA C:ASP341 4.9 11.9 1.0
CB C:ALA355 4.9 11.7 1.0
C C:ASP341 4.9 12.7 1.0
CB C:GLU357 4.9 11.4 1.0

Magnesium binding site 6 out of 8 in 3b9t

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Magnesium binding site 6 out of 8 in the Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution


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 Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg485

b:28.1
occ:1.00
 O1 C:EDO496 1.7 21.4 1.0
OD1 C:ASP316 2.0 10.5 1.0
OD1 C:ASN314 2.1 14.7 1.0
OD2 C:ASP341 2.1 15.2 1.0
OD2 C:ASP316 2.5 11.8 1.0
CG C:ASP316 2.6 10.3 1.0
C1 C:EDO496 2.9 26.6 1.0
CG C:ASN314 3.0 13.6 1.0
CG C:ASP341 3.3 10.3 1.0
ND2 C:ASN314 3.3 13.5 1.0
MG C:MG484 3.4 20.8 1.0
C2 C:EDO496 3.6 22.4 1.0
NE2 C:HIS160 3.7 15.7 1.0
NE2 C:HIS343 3.9 12.8 1.0
CE1 C:HIS343 4.0 12.9 1.0
OD1 C:ASP341 4.0 13.7 1.0
CB C:ASP316 4.1 11.0 1.0
OE2 C:GLU350 4.1 17.9 1.0
OG1 C:THR292 4.2 16.1 1.0
CD2 C:HIS160 4.2 16.0 1.0
CB C:ASP341 4.3 10.2 1.0
CA C:GLY291 4.3 10.8 1.0
C C:GLY291 4.4 12.4 1.0
CB C:ASN314 4.4 12.6 1.0
O2 C:EDO496 4.4 33.8 1.0
O2 C:EDO489 4.5 21.2 1.0
O C:GLY291 4.5 12.6 1.0
OD2 C:ASP464 4.5 12.0 1.0
CE1 C:HIS160 4.5 20.7 1.0
OD1 C:ASP464 4.6 12.8 1.0
OE1 C:GLU350 4.6 13.4 1.0
O C:ASN314 4.8 10.9 1.0
CA C:ASP316 4.8 8.9 1.0
CD C:GLU350 4.8 15.6 1.0
CA C:ASN314 4.8 10.9 1.0
C C:ASN314 4.9 10.1 1.0
CG C:ASP464 4.9 12.9 1.0
N C:ASP316 4.9 11.2 1.0
N C:THR292 5.0 11.5 1.0

Magnesium binding site 7 out of 8 in 3b9t

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Magnesium binding site 7 out of 8 in the Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution


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 Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg484

b:20.0
occ:1.00
 OD1 D:ASP341 2.1 16.2 1.0
NE2 D:HIS343 2.2 13.1 1.0
OE2 D:GLU357 2.2 14.3 1.0
OE1 D:GLU357 2.3 15.5 1.0
OD2 D:ASP341 2.5 18.7 1.0
CD D:GLU357 2.6 14.6 1.0
CG D:ASP341 2.6 14.1 1.0
C2 D:EDO488 2.7 28.4 1.0
O2 D:EDO488 2.8 19.8 1.0
C1 D:EDO488 3.1 28.0 1.0
CD2 D:HIS343 3.1 11.4 1.0
CE1 D:HIS343 3.2 12.8 1.0
O1 D:EDO488 3.5 18.3 1.0
MG D:MG485 3.5 28.1 1.0
OE2 D:GLU350 4.0 20.0 1.0
CG D:GLU357 4.1 14.8 1.0
CE1 D:HIS110 4.1 15.2 1.0
CB D:ASP341 4.1 13.0 1.0
CG D:HIS343 4.3 11.7 1.0
ND1 D:HIS343 4.3 13.8 1.0
O D:HOH498 4.4 10.6 1.0
O D:ASP341 4.4 9.8 1.0
OD1 D:ASP316 4.4 11.4 1.0
NE2 D:HIS110 4.6 12.9 1.0
N D:ALA355 4.7 11.6 1.0
CD2 D:HIS160 4.7 18.2 1.0
CA D:ASP341 4.8 11.6 1.0
NE2 D:HIS160 4.8 17.4 1.0
C D:ASP341 4.9 11.6 1.0
CB D:ALA355 4.9 13.1 1.0
CB D:GLU357 5.0 12.7 1.0

Magnesium binding site 8 out of 8 in 3b9t

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Magnesium binding site 8 out of 8 in the Crystal Structure of Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution


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 Predicted Acetamidase/Formamidase (YP_546212.1) From Methylobacillus Flagellatus Kt at 1.58 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg485

b:28.1
occ:1.00
 O1 D:EDO488 1.8 18.3 1.0
OD1 D:ASN314 1.9 13.9 1.0
OD1 D:ASP316 2.0 11.4 1.0
OD2 D:ASP341 2.0 18.7 1.0
OD2 D:ASP316 2.6 13.6 1.0
CG D:ASP316 2.6 12.5 1.0
C1 D:EDO488 2.8 28.0 1.0
CG D:ASN314 2.9 14.7 1.0
CG D:ASP341 3.2 14.1 1.0
ND2 D:ASN314 3.3 12.4 1.0
MG D:MG484 3.5 20.0 1.0
NE2 D:HIS160 3.8 17.4 1.0
C2 D:EDO488 3.8 28.4 1.0
NE2 D:HIS343 3.9 13.1 1.0
CE1 D:HIS343 3.9 12.8 1.0
OG1 D:THR292 4.0 17.0 1.0
O2 D:EDO488 4.0 19.8 1.0
OD1 D:ASP341 4.0 16.2 1.0
CB D:ASP316 4.1 13.7 1.0
CA D:GLY291 4.1 11.1 1.0
CB D:ASP341 4.1 13.0 1.0
C D:GLY291 4.2 11.8 1.0
O D:GLY291 4.2 12.4 1.0
CB D:ASN314 4.2 12.4 1.0
CD2 D:HIS160 4.3 18.2 1.0
OE2 D:GLU350 4.3 20.0 1.0
OD2 D:ASP464 4.5 13.0 1.0
CA D:ASN314 4.6 11.5 1.0
CE1 D:HIS160 4.6 19.3 1.0
CA D:ASP316 4.7 10.1 1.0
OE1 D:GLU350 4.7 16.2 1.0
OD1 D:ASP464 4.7 12.7 1.0
O D:ASN314 4.7 11.9 1.0
N D:ASP316 4.7 11.6 1.0
O2 D:EDO493 4.7 22.2 1.0
C D:ASN314 4.8 12.6 1.0
N D:THR292 4.8 12.8 1.0
CD D:GLU350 4.9 17.7 1.0
CG D:ASP464 5.0 13.2 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Wed Aug 14 08:54:58 2024

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