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Magnesium in PDB 5mgy: Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form

Enzymatic activity of Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form

All present enzymatic activity of Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form:
2.7.1.180;

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form, PDB code: 5mgy was solved by L.Zhang, C.Trncik, S.L.A.Andrade, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 138.06 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.656, 91.983, 138.061, 90.00, 90.41, 90.00
R / Rfree (%) 23.2 / 27.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form (pdb code 5mgy). 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 Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form, PDB code: 5mgy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5mgy

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Magnesium binding site 1 out of 8 in the Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form


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 Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:51.0
occ:1.00
 O H:SER183 2.4 34.8 1.0
OD2 H:ASP297 2.4 29.9 1.0
OG1 H:THR301 2.5 38.3 1.0
O H:ASP297 2.9 26.1 1.0
O H:HOH501 3.0 30.4 1.0
C H:SER183 3.2 33.8 1.0
CG H:ASP297 3.3 30.0 1.0
CA H:SER183 3.4 35.4 1.0
C H:ASP297 3.8 29.6 1.0
CB H:THR301 3.9 34.4 1.0
OD1 H:ASP297 3.9 31.8 1.0
CB H:SER183 4.1 36.1 1.0
O H:ASN182 4.2 34.1 1.0
CA H:ASP297 4.2 30.4 1.0
CB H:ASP297 4.3 30.3 1.0
N H:ILE184 4.4 31.1 1.0
N H:SER183 4.6 34.8 1.0
OE2 H:GLU212 4.6 44.7 1.0
N H:THR301 4.6 32.3 1.0
CA H:THR301 4.7 33.7 1.0
CG2 H:THR301 4.8 35.5 1.0
C H:ASN182 4.8 31.9 1.0
N H:GLY298 4.9 28.4 1.0
OG H:SER251 4.9 36.3 1.0

Magnesium binding site 2 out of 8 in 5mgy

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Magnesium binding site 2 out of 8 in the Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form


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 Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:45.1
occ:1.00
 OD2 B:ASP297 2.3 30.4 1.0
OG1 B:THR301 2.4 30.5 1.0
O B:HOH501 2.5 26.5 1.0
O B:SER183 2.8 29.4 1.0
O B:ASP297 2.8 27.1 1.0
C B:SER183 3.4 29.5 1.0
CG B:ASP297 3.5 27.7 1.0
CA B:SER183 3.5 30.2 1.0
CB B:THR301 3.8 29.4 1.0
C B:ASP297 3.8 29.5 1.0
CB B:SER183 4.1 30.8 1.0
OD1 B:ASP297 4.2 27.4 1.0
OE2 B:GLU212 4.2 44.6 1.0
O B:ASN182 4.3 34.7 1.0
CA B:ASP297 4.4 28.4 1.0
CB B:ASP297 4.5 28.8 1.0
CG2 B:THR301 4.5 29.1 1.0
OG B:SER300 4.5 29.3 1.0
CA B:THR301 4.6 30.6 1.0
N B:ILE184 4.6 32.0 1.0
N B:THR301 4.6 31.7 1.0
N B:SER183 4.7 31.0 1.0
N B:GLY298 4.9 28.1 1.0
C B:ASN182 4.9 31.1 1.0

Magnesium binding site 3 out of 8 in 5mgy

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Magnesium binding site 3 out of 8 in the Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form


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 Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:61.8
occ:1.00
 OG1 G:THR301 2.1 45.5 1.0
OD2 G:ASP297 2.2 41.1 1.0
O G:HOH502 2.5 29.3 1.0
O G:ASP297 2.6 40.7 1.0
O G:SER183 2.8 39.3 1.0
CG G:ASP297 3.3 39.7 1.0
CB G:THR301 3.5 44.6 1.0
C G:ASP297 3.6 43.0 1.0
C G:SER183 3.7 39.3 1.0
CA G:SER183 3.9 38.9 1.0
OG G:SER300 4.0 55.2 1.0
CA G:ASP297 4.0 40.7 1.0
N G:THR301 4.0 48.9 1.0
CA G:THR301 4.2 47.7 1.0
OD1 G:ASP297 4.2 37.8 1.0
CB G:ASP297 4.2 39.1 1.0
OE2 G:GLU212 4.3 68.5 1.0
CB G:SER183 4.4 38.1 1.0
CG2 G:THR301 4.5 46.4 1.0
OG G:SER251 4.5 64.4 1.0
CB G:SER300 4.7 50.5 1.0
N G:GLY298 4.7 43.0 1.0
OG G:SER253 4.9 86.2 1.0
N G:ILE184 5.0 38.2 1.0
O G:ASN182 5.0 35.8 1.0

Magnesium binding site 4 out of 8 in 5mgy

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Magnesium binding site 4 out of 8 in the Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form


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 Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:40.9
occ:1.00
 OG1 A:THR301 2.1 34.3 1.0
O A:ASP297 2.3 28.8 1.0
OD2 A:ASP297 2.4 26.4 1.0
O A:SER183 2.5 34.4 1.0
O A:HOH503 2.6 33.1 1.0
C A:ASP297 3.4 29.5 1.0
C A:SER183 3.4 33.7 1.0
CB A:THR301 3.4 32.5 1.0
CG A:ASP297 3.4 27.4 1.0
CA A:SER183 3.6 36.9 1.0
CA A:ASP297 4.0 29.1 1.0
N A:THR301 4.1 30.3 1.0
CB A:SER183 4.1 40.1 1.0
CB A:ASP297 4.2 29.6 1.0
CA A:THR301 4.2 30.1 1.0
OD1 A:ASP297 4.3 27.1 1.0
N A:GLY298 4.4 30.1 1.0
CG2 A:THR301 4.5 33.6 1.0
N A:ILE184 4.6 32.4 1.0
O A:ASN182 4.6 37.2 1.0
OG A:SER251 4.7 35.1 1.0
CA A:GLY298 4.7 32.3 1.0
OG A:SER300 4.8 27.1 1.0
OE2 A:GLU212 4.9 54.3 1.0
N A:SER183 4.9 36.9 1.0

Magnesium binding site 5 out of 8 in 5mgy

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Magnesium binding site 5 out of 8 in the Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form


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 Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:38.6
occ:1.00
 O C:HOH503 2.2 31.8 1.0
O C:ASP297 2.2 31.4 1.0
OG1 C:THR301 2.3 35.8 1.0
OD2 C:ASP297 2.5 33.8 1.0
O C:SER183 2.7 36.0 1.0
C C:ASP297 3.3 35.1 1.0
CG C:ASP297 3.4 34.7 1.0
C C:SER183 3.6 39.6 1.0
CB C:THR301 3.6 33.2 1.0
CA C:SER183 3.9 40.1 1.0
CA C:ASP297 3.9 35.1 1.0
N C:THR301 4.1 34.5 1.0
OD1 C:ASP297 4.2 37.6 1.0
CB C:ASP297 4.2 36.8 1.0
CA C:THR301 4.3 34.0 1.0
OG C:SER300 4.3 43.2 1.0
OG C:SER251 4.3 43.5 1.0
OE2 C:GLU212 4.4 52.6 1.0
CB C:SER183 4.4 43.1 1.0
N C:GLY298 4.5 32.2 1.0
CB C:SER300 4.7 36.5 1.0
CG2 C:THR301 4.7 32.5 1.0
O C:ASN182 4.8 36.0 1.0
N C:ILE184 4.8 40.0 1.0
CA C:GLY298 4.9 34.1 1.0
C C:SER300 5.0 35.5 1.0

Magnesium binding site 6 out of 8 in 5mgy

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Magnesium binding site 6 out of 8 in the Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form


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 Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:51.8
occ:1.00
 OD2 D:ASP297 2.2 43.3 1.0
OG1 D:THR301 2.4 34.8 1.0
O D:ASP297 3.0 31.6 1.0
O D:SER183 3.2 41.8 1.0
O D:HOH503 3.4 25.3 1.0
CG D:ASP297 3.4 35.6 1.0
CB D:THR301 3.8 30.2 1.0
C D:SER183 3.9 37.4 1.0
C D:ASP297 4.0 33.7 1.0
CA D:SER183 4.0 36.3 1.0
OE2 D:GLU212 4.0 48.5 1.0
OD1 D:ASP297 4.2 36.4 1.0
N D:THR301 4.3 30.8 1.0
CA D:ASP297 4.4 33.2 1.0
CA D:THR301 4.4 30.4 1.0
OG D:SER251 4.4 34.8 1.0
CB D:ASP297 4.5 34.4 1.0
OG D:SER300 4.5 32.2 1.0
CB D:SER183 4.6 34.6 1.0
O D:ASN182 4.6 30.1 1.0
CG2 D:THR301 4.7 29.2 1.0

Magnesium binding site 7 out of 8 in 5mgy

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Magnesium binding site 7 out of 8 in the Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form


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 Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:51.3
occ:1.00
 OD2 E:ASP297 2.7 39.4 1.0
OG1 E:THR301 2.8 38.8 1.0
O E:ASP297 3.3 35.0 1.0
OG E:SER300 3.4 43.8 1.0
OG E:SER251 3.9 54.6 1.0
OE2 E:GLU212 3.9 48.5 1.0
CG E:ASP297 4.0 35.6 1.0
N E:THR301 4.0 36.7 1.0
CB E:THR301 4.0 36.5 1.0
CB E:SER253 4.1 40.2 1.0
CB E:SER300 4.1 38.6 1.0
O E:SER183 4.2 38.2 1.0
CA E:SER253 4.3 36.8 1.0
C E:ASP297 4.3 37.3 1.0
CA E:THR301 4.3 36.5 1.0
CA E:ASP297 4.5 35.5 1.0
N E:SER253 4.5 34.0 1.0
OG E:SER253 4.6 46.6 1.0
C E:SER300 4.7 35.2 1.0
O E:THR252 4.7 40.8 1.0
C E:THR252 4.8 34.7 1.0
OD1 E:ASP297 4.8 36.3 1.0
CB E:ASP297 4.9 36.0 1.0
CD E:GLU212 4.9 40.9 1.0
CA E:SER300 5.0 35.8 1.0

Magnesium binding site 8 out of 8 in 5mgy

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Magnesium binding site 8 out of 8 in the Crystal Structure of Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form


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 Pseudomonas Stutzeri Flavinyl Transferase Apbe, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:46.6
occ:1.00
 OD2 F:ASP297 2.1 35.1 1.0
OG1 F:THR301 2.5 35.9 1.0
O F:SER183 2.9 38.5 1.0
O F:ASP297 3.1 31.3 1.0
CG F:ASP297 3.3 31.7 1.0
C F:SER183 3.7 36.1 1.0
CB F:THR301 3.8 34.5 1.0
CA F:SER183 3.8 38.2 1.0
OD1 F:ASP297 3.9 33.1 1.0
C F:ASP297 4.0 33.9 1.0
OE2 F:GLU212 4.2 52.1 1.0
CB F:ASP297 4.4 32.1 1.0
CA F:ASP297 4.4 32.3 1.0
CB F:SER183 4.5 39.8 1.0
OD2 G:ASP30 4.6 84.3 1.0
O F:ASN182 4.6 42.3 1.0
CA F:THR301 4.6 35.1 1.0
N F:THR301 4.6 33.4 1.0
CG2 F:THR301 4.7 31.2 1.0
OG F:SER251 4.8 43.0 1.0
N F:ILE184 4.9 32.1 1.0
O G:MET29 4.9 90.4 1.0
N F:SER183 5.0 39.6 1.0

Reference:

L.Zhang, C.Trncik, S.L.Andrade, O.Einsle. The Flavinyl Transferase Apbe of Pseudomonas Stutzeri Matures the Nosr Protein Required For Nitrous Oxide Reduction. Biochim. Biophys. Acta V.1858 95 2016.
ISSN: ISSN 0006-3002
PubMed: 27864152
DOI: 10.1016/J.BBABIO.2016.11.008
Page generated: Sun Sep 29 21:22:09 2024

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