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Magnesium in PDB 4gv8: Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert

Enzymatic activity of Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert

All present enzymatic activity of Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert:
3.6.1.23;

Protein crystallography data

The structure of Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert, PDB code: 4gv8 was solved by I.Leveles, V.Harmat, V.Nemeth, A.Bendes, J.Szabo, V.Kadar, I.Zagyva, G.Rona, J.Toth, B.G.Vertessy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.10 / 2.10
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 109.660, 109.660, 169.270, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert (pdb code 4gv8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert, PDB code: 4gv8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4gv8

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Magnesium binding site 1 out of 8 in the Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:25.8
occ:1.00
 O B:HOH365 2.4 37.7 1.0
OD2 B:ASP95 2.5 37.8 1.0
OD1 C:ASP95 2.5 39.3 1.0
O A:HOH372 2.5 38.1 1.0
OD2 C:ASP95 2.5 40.2 1.0
O C:HOH364 2.6 37.0 1.0
OD1 A:ASP95 2.6 39.4 1.0
OD2 A:ASP95 2.6 39.1 1.0
OD1 B:ASP95 2.7 42.3 1.0
CG C:ASP95 2.9 39.3 1.0
CG B:ASP95 2.9 41.7 1.0
CG A:ASP95 3.0 41.7 1.0
NZ A:LYS93 4.2 34.7 1.0
NZ C:LYS93 4.3 34.6 1.0
NZ B:LYS93 4.3 34.5 1.0
CB C:ASP95 4.4 34.0 1.0
O C:ASP95 4.4 40.7 1.0
CB B:ASP95 4.4 37.3 1.0
NE2 C:GLN40 4.4 39.8 1.0
O B:ASP95 4.5 37.4 1.0
O A:ASP95 4.5 41.6 1.0
CB A:ASP95 4.5 35.4 1.0
O A:HOH329 4.5 40.1 1.0
NE2 A:GLN40 4.5 41.1 1.0
O C:HOH317 4.5 41.5 1.0
O B:HOH332 4.6 42.2 1.0
NE2 B:GLN40 4.7 40.0 1.0
OE1 A:GLN40 4.8 45.2 1.0
OE1 B:GLN40 4.8 41.1 1.0
OE1 C:GLN40 4.9 44.5 1.0

Magnesium binding site 2 out of 8 in 4gv8

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Magnesium binding site 2 out of 8 in the Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:47.4
occ:1.00
 O A:HOH366 2.0 43.3 1.0
O1A B:DUP201 2.0 48.4 1.0
O A:HOH365 2.0 52.5 1.0
O1G B:DUP201 2.1 53.6 1.0
O A:HOH364 2.1 47.7 1.0
O1B B:DUP201 2.1 50.3 1.0
PB B:DUP201 3.3 46.0 1.0
PA B:DUP201 3.3 44.8 1.0
PG B:DUP201 3.4 54.7 1.0
O3B B:DUP201 3.7 54.4 1.0
N3A B:DUP201 3.7 42.6 1.0
O2G B:DUP201 4.1 52.6 1.0
OD1 A:ASP28 4.1 50.8 1.0
OE1 A:GLN136 4.2 49.1 1.0
NE A:ARG64 4.3 48.3 1.0
OD2 A:ASP28 4.3 52.5 1.0
O5' B:DUP201 4.3 44.9 1.0
O B:HOH326 4.4 59.1 1.0
O A:HOH367 4.4 69.2 1.0
O2A B:DUP201 4.4 46.7 1.0
O3G B:DUP201 4.5 61.2 1.0
C5' B:DUP201 4.5 44.3 1.0
O A:HOH338 4.5 68.1 1.0
ND2 A:ASN20 4.5 72.4 1.0
NH2 A:ARG64 4.5 50.8 1.0
O2B B:DUP201 4.7 51.1 1.0
OD2 A:ASP24 4.7 58.9 1.0
CG A:ASP28 4.7 45.2 1.0
CZ A:ARG64 4.9 48.8 1.0
CD A:GLN136 4.9 50.8 1.0

Magnesium binding site 3 out of 8 in 4gv8

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Magnesium binding site 3 out of 8 in the Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:43.0
occ:1.00
 O2G C:DUP201 2.0 44.8 1.0
O B:HOH361 2.0 45.3 1.0
O1B C:DUP201 2.1 42.5 1.0
O2A C:DUP201 2.1 42.9 1.0
O B:HOH363 2.1 51.1 1.0
O B:HOH360 2.2 43.2 1.0
PB C:DUP201 3.2 43.0 1.0
PG C:DUP201 3.2 50.4 1.0
PA C:DUP201 3.3 40.7 1.0
O3B C:DUP201 3.5 45.9 1.0
N3A C:DUP201 3.6 40.3 1.0
O B:HOH368 3.8 61.3 1.0
O1G C:DUP201 3.9 50.2 1.0
O B:HOH356 4.1 55.3 1.0
OD1 B:ASP28 4.1 53.2 1.0
NE B:ARG64 4.1 42.5 1.0
ND2 B:ASN20 4.2 80.4 1.0
O B:HOH372 4.2 56.9 1.0
OD2 B:ASP28 4.3 51.1 1.0
O C:HOH361 4.3 51.2 1.0
O1A C:DUP201 4.3 44.2 1.0
NH2 B:ARG64 4.3 44.2 1.0
NE2 B:GLN136 4.3 42.9 1.0
O3G C:DUP201 4.4 54.5 1.0
O5' C:DUP201 4.5 39.7 1.0
O2B C:DUP201 4.5 42.9 1.0
C5' C:DUP201 4.6 41.2 1.0
CG B:ASP28 4.7 48.6 1.0
O C:HOH341 4.7 45.3 1.0
CZ B:ARG64 4.7 46.2 1.0
CB B:ASN20 4.9 82.2 1.0
OE1 B:GLN136 4.9 44.8 1.0
CD B:GLN136 4.9 43.5 1.0

Magnesium binding site 4 out of 8 in 4gv8

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Magnesium binding site 4 out of 8 in the Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:42.1
occ:1.00
 O C:HOH355 2.1 43.2 1.0
O1A A:DUP201 2.1 42.5 1.0
O3G A:DUP201 2.1 48.3 1.0
O C:HOH356 2.1 50.7 1.0
O C:HOH354 2.2 43.5 1.0
O1B A:DUP201 2.3 44.2 1.0
PG A:DUP201 3.4 48.3 1.0
PA A:DUP201 3.4 41.7 1.0
PB A:DUP201 3.4 43.7 1.0
O3B A:DUP201 3.7 49.2 1.0
N3A A:DUP201 3.8 41.1 1.0
O1G A:DUP201 3.9 50.7 1.0
OD1 C:ASP28 4.1 55.5 1.0
O A:HOH369 4.2 53.2 1.0
ND2 C:ASN20 4.3 78.3 1.0
OD2 C:ASP28 4.3 54.4 1.0
NE C:ARG64 4.3 40.6 1.0
O5' A:DUP201 4.4 43.5 1.0
O2A A:DUP201 4.4 38.9 1.0
NH2 C:ARG64 4.5 45.4 1.0
O C:HOH327 4.5 54.2 1.0
O A:HOH384 4.5 63.4 1.0
OD2 C:ASP24 4.5 63.3 1.0
OE1 C:GLN136 4.5 43.8 1.0
C5' A:DUP201 4.6 40.8 1.0
O2G A:DUP201 4.6 56.7 1.0
O A:HOH316 4.6 49.6 1.0
CG C:ASP28 4.7 51.0 1.0
O2B A:DUP201 4.7 41.8 1.0
CG C:ASN20 4.7 89.2 1.0
CB C:ASN20 4.8 85.7 1.0
CZ C:ARG64 4.9 43.0 1.0
NE2 C:GLN136 4.9 38.9 1.0
CD C:GLN136 5.0 42.0 1.0

Magnesium binding site 5 out of 8 in 4gv8

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Magnesium binding site 5 out of 8 in the Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:32.8
occ:1.00
 OD2 E:ASP95 2.1 46.4 1.0
O D:HOH307 2.2 41.7 1.0
O F:HOH301 2.3 47.7 1.0
O E:HOH306 2.5 46.6 1.0
OD1 D:ASP95 2.5 59.5 1.0
OD2 D:ASP95 2.5 53.0 1.0
OD1 E:ASP95 2.5 48.2 1.0
OD1 F:ASP95 2.6 57.1 1.0
OD2 F:ASP95 2.6 51.3 1.0
CG E:ASP95 2.7 47.1 1.0
CG D:ASP95 2.8 55.1 1.0
CG F:ASP95 3.0 49.4 1.0
NZ E:LYS93 4.2 45.0 1.0
CB E:ASP95 4.2 46.1 1.0
NZ D:LYS93 4.4 48.3 1.0
CB D:ASP95 4.4 51.2 1.0
NZ F:LYS93 4.4 43.0 1.0
O F:HOH309 4.4 51.8 1.0
O D:ASP95 4.4 50.6 1.0
O E:ASP95 4.4 48.7 1.0
NE2 E:GLN40 4.4 50.8 1.0
CB F:ASP95 4.5 52.3 1.0
O F:ASP95 4.5 46.8 1.0
NE2 D:GLN40 4.6 52.8 1.0
O D:HOH302 4.6 47.0 1.0
O E:HOH316 4.7 51.7 1.0
NE2 F:GLN40 4.7 44.8 1.0
OE1 D:GLN40 4.8 51.0 1.0
OE1 E:GLN40 4.9 52.3 1.0
OE1 F:GLN40 4.9 44.8 1.0

Magnesium binding site 6 out of 8 in 4gv8

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Magnesium binding site 6 out of 8 in the Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:73.4
occ:1.00
 O3G E:DUP201 2.3 76.7 1.0
O D:HOH331 2.3 65.1 1.0
O2B E:DUP201 2.4 68.8 1.0
O1A E:DUP201 2.5 81.4 1.0
OD2 D:ASP28 3.4 91.2 1.0
OD1 D:ASP28 3.4 0.2 1.0
PB E:DUP201 3.6 74.0 1.0
PG E:DUP201 3.6 81.3 1.0
PA E:DUP201 3.7 74.0 1.0
NE D:ARG64 3.8 68.5 1.0
CG D:ASP28 3.9 96.3 1.0
O3B E:DUP201 4.0 81.0 1.0
N3A E:DUP201 4.1 74.2 1.0
NH2 D:ARG64 4.3 67.4 1.0
OE1 D:GLN136 4.3 91.3 1.0
O1G E:DUP201 4.3 82.8 1.0
O2A E:DUP201 4.5 67.0 1.0
CZ D:ARG64 4.5 66.2 1.0
CG D:ARG64 4.7 65.5 1.0
CD D:ARG64 4.7 67.0 1.0
O2G E:DUP201 4.7 81.1 1.0
O1B E:DUP201 4.9 77.0 1.0
CD D:GLN136 5.0 90.1 1.0
O5' E:DUP201 5.0 69.1 1.0

Magnesium binding site 7 out of 8 in 4gv8

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Magnesium binding site 7 out of 8 in the Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:65.9
occ:1.00
 O E:HOH329 1.8 60.1 1.0
O E:HOH330 2.1 65.3 1.0
O1G F:DUP201 2.1 60.7 1.0
O1A F:DUP201 2.2 62.4 1.0
O E:HOH331 2.3 62.4 1.0
O1B F:DUP201 2.4 63.0 1.0
PG F:DUP201 3.5 70.2 1.0
PA F:DUP201 3.5 66.5 1.0
PB F:DUP201 3.5 65.1 1.0
ND2 E:ASN20 3.6 93.1 1.0
OD1 E:ASP28 3.8 74.1 1.0
N3A F:DUP201 3.9 60.7 1.0
O3B F:DUP201 3.9 67.5 1.0
O2G F:DUP201 4.1 68.6 1.0
O E:HOH309 4.1 57.4 1.0
NE E:ARG64 4.2 59.8 1.0
OE1 E:GLN136 4.3 67.2 1.0
O F:HOH333 4.3 61.7 1.0
NH2 E:ARG64 4.5 59.6 1.0
O2A F:DUP201 4.5 59.2 1.0
O5' F:DUP201 4.6 60.1 1.0
CG E:ASN20 4.6 98.6 1.0
OD2 E:ASP28 4.6 75.4 1.0
CB E:ASN20 4.7 0.5 1.0
CG E:ASP28 4.7 77.7 1.0
O3G F:DUP201 4.7 65.3 1.0
C5' F:DUP201 4.7 65.2 1.0
O E:HOH333 4.7 69.7 1.0
OD2 E:ASP24 4.8 97.4 1.0
CZ E:ARG64 4.9 63.3 1.0
O2B F:DUP201 4.9 60.2 1.0
CD E:GLN136 4.9 68.7 1.0

Magnesium binding site 8 out of 8 in 4gv8

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Magnesium binding site 8 out of 8 in the Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Dutpase From Phage PHI11 of S.Aureus: Visualization of the Species- Specific Insert within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:80.9
occ:1.00
 O2G D:DUP201 1.8 69.0 1.0
O D:HOH327 1.9 67.8 1.0
O D:HOH328 2.1 60.3 1.0
O2A D:DUP201 2.3 75.7 1.0
O1B D:DUP201 2.6 71.1 1.0
PG D:DUP201 3.2 72.4 1.0
PB D:DUP201 3.6 69.4 1.0
PA D:DUP201 3.7 74.0 1.0
O3B D:DUP201 3.7 83.5 1.0
O1G D:DUP201 3.9 78.3 1.0
OD2 F:ASP28 4.0 72.5 1.0
OD2 F:ASP24 4.0 83.5 1.0
N3A D:DUP201 4.1 72.9 1.0
OD1 F:ASP28 4.1 79.0 1.0
ND2 F:ASN20 4.2 87.0 1.0
O3G D:DUP201 4.3 72.1 1.0
CG F:ASP28 4.5 73.7 1.0
OE1 F:GLN136 4.6 74.4 1.0
O5' D:DUP201 4.6 76.2 1.0
CB F:ASN20 4.7 0.9 1.0
C5' D:DUP201 4.7 76.0 1.0
NE F:ARG64 4.7 62.2 1.0
O1A D:DUP201 4.8 73.3 1.0
OD2 D:ASP81 4.8 83.6 1.0
CG F:ASN20 4.9 0.6 1.0
NH2 F:ARG64 4.9 73.4 1.0
O2B D:DUP201 5.0 74.6 1.0

Reference:

I.Leveles, V.Nemeth, J.E.Szabo, V.Harmat, K.Nyiri, A.A.Bendes, V.Papp-Kadar, I.Zagyva, G.Rona, O.Ozohanics, K.Vekey, J.Toth, B.G.Vertessy. Structure and Enzymatic Mechanism of A Moonlighting Dutpase Acta Crystallogr.,Sect.D V. 69 2298 2013.
ISSN: ISSN 0907-4449
PubMed: 24311572
DOI: 10.1107/S0907444913021136
Page generated: Mon Aug 11 13:37:57 2025

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