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Magnesium in PDB 1w2y: The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp

Enzymatic activity of The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp

All present enzymatic activity of The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp:
3.6.1.23;

Protein crystallography data

The structure of The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp, PDB code: 1w2y was solved by O.V.Moroz, M.Harkiolaki, M.Y.Galperin, A.A.Vagin, D.Gonzalez-Pacanowska, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.90 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.963, 70.629, 92.850, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp (pdb code 1w2y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp, PDB code: 1w2y:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1w2y

Go back to Magnesium Binding Sites List in 1w2y
Magnesium binding site 1 out of 6 in the The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1231

b:17.9
occ:1.00
 O1A A:DUN1230 2.0 17.8 1.0
OE2 A:GLU46 2.0 28.7 1.0
OE1 A:GLU49 2.1 28.5 1.0
O3B A:DUN1230 2.1 15.1 1.0
O A:HOH2054 2.2 17.9 1.0
O A:HOH2195 2.2 15.7 1.0
CD A:GLU46 2.9 27.8 1.0
CD A:GLU49 3.1 29.1 1.0
PA A:DUN1230 3.2 18.8 1.0
OE1 A:GLU46 3.2 27.0 1.0
PB A:DUN1230 3.3 20.8 1.0
N3A A:DUN1230 3.4 18.1 1.0
OE2 A:GLU49 3.4 29.3 1.0
MG A:MG1232 3.4 18.6 1.0
O A:HOH2050 3.9 16.7 1.0
NZ B:LYS57 3.9 29.4 1.0
C5' A:DUN1230 4.1 17.7 1.0
O5' A:DUN1230 4.1 19.3 1.0
O B:HOH2063 4.2 31.1 1.0
O2B A:DUN1230 4.2 30.3 1.0
CG A:GLU46 4.3 26.9 1.0
O2A A:DUN1230 4.4 18.5 1.0
O A:HOH2052 4.4 27.9 1.0
O1B A:DUN1230 4.4 29.6 1.0
CG A:GLU49 4.4 29.0 1.0
CE B:LYS57 4.6 31.7 1.0
OD2 A:ASP77 4.8 28.1 1.0
O A:HOH2193 4.8 16.4 1.0
O A:HOH2194 4.8 30.4 1.0
O B:HOH2078 4.8 27.0 1.0

Magnesium binding site 2 out of 6 in 1w2y

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Magnesium binding site 2 out of 6 in the The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1232

b:18.6
occ:1.00
 OE1 A:GLU46 2.0 27.0 1.0
OE1 A:GLU74 2.1 29.1 1.0
O3B A:DUN1230 2.1 15.1 1.0
OE2 A:GLU49 2.1 29.3 1.0
OD2 A:ASP77 2.1 28.1 1.0
O A:HOH2193 2.2 16.4 1.0
CD A:GLU49 3.0 29.1 1.0
CD A:GLU74 3.1 30.1 1.0
CD A:GLU46 3.1 27.8 1.0
CG A:ASP77 3.2 29.7 1.0
PB A:DUN1230 3.2 20.8 1.0
MG A:MG1233 3.3 17.0 0.5
OE1 A:GLU49 3.3 28.5 1.0
MG A:MG1231 3.4 17.9 1.0
OE2 A:GLU74 3.4 32.0 1.0
OE2 A:GLU46 3.5 28.7 1.0
O2B A:DUN1230 3.7 30.3 1.0
CB A:ASP77 3.7 29.1 1.0
O1B A:DUN1230 3.7 29.6 1.0
O A:HOH2194 4.2 30.4 1.0
OD1 A:ASP77 4.3 29.1 1.0
CG A:GLU49 4.3 29.0 1.0
CB A:GLU49 4.4 29.8 1.0
CG A:GLU46 4.4 26.9 1.0
CG A:GLU74 4.5 28.4 1.0
N3A A:DUN1230 4.6 18.1 1.0
CA A:GLU74 4.7 28.3 1.0
O A:HOH2054 4.7 17.9 1.0
NZ A:LYS175 4.8 29.9 1.0
O1A A:DUN1230 4.8 17.8 1.0
CB A:GLU46 4.8 27.7 1.0
CB A:GLU74 4.8 29.5 1.0
CG2 A:ILE73 4.9 39.3 1.0
O A:HOH2091 4.9 23.7 1.0
O A:HOH2177 4.9 26.8 1.0
C5' A:DUN1230 5.0 17.7 1.0

Magnesium binding site 3 out of 6 in 1w2y

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Magnesium binding site 3 out of 6 in the The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1233

b:17.0
occ:0.50
 O A:HOH2091 1.9 23.7 1.0
O A:HOH2194 2.0 30.4 1.0
OE2 A:GLU74 2.1 32.0 1.0
OE2 A:GLU49 2.2 29.3 1.0
O A:HOH2193 2.2 16.4 1.0
O A:HOH2177 2.2 26.8 1.0
CD A:GLU74 3.1 30.1 1.0
CD A:GLU49 3.2 29.1 1.0
MG A:MG1232 3.3 18.6 1.0
OE1 A:GLU74 3.4 29.1 1.0
O2B A:DUN1230 3.7 30.3 1.0
CG A:GLU49 3.8 29.0 1.0
CB A:GLU49 3.9 29.8 1.0
O A:HOH2016 4.0 40.9 1.0
O3B A:DUN1230 4.0 15.1 1.0
OE1 A:GLU49 4.2 28.5 1.0
ND2 A:ASN70 4.2 34.1 1.0
O A:HOH2053 4.3 23.6 1.0
OE2 A:GLU200 4.3 22.9 0.5
CG A:GLU74 4.4 28.4 1.0
PB A:DUN1230 4.4 20.8 1.0
OD1 A:ASN70 4.4 36.1 1.0
ND2 A:ASN202 4.6 32.4 1.0
CG A:ASN70 4.8 33.0 1.0
OD2 A:ASP77 4.9 28.1 1.0
OE1 A:GLU46 4.9 27.0 1.0
OE1 A:GLU200 4.9 29.0 0.5
O A:HOH2054 5.0 17.9 1.0

Magnesium binding site 4 out of 6 in 1w2y

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Magnesium binding site 4 out of 6 in the The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1231

b:19.8
occ:1.00
 OE2 B:GLU46 2.0 31.6 1.0
OE1 B:GLU49 2.0 30.9 1.0
O1A B:DUN1230 2.0 19.5 1.0
O B:HOH2187 2.1 18.6 1.0
O3B B:DUN1230 2.1 18.2 1.0
O B:HOH2056 2.2 20.6 1.0
CD B:GLU46 2.9 31.9 1.0
CD B:GLU49 3.0 31.7 1.0
PA B:DUN1230 3.2 22.5 1.0
OE1 B:GLU46 3.2 30.2 1.0
PB B:DUN1230 3.3 23.3 1.0
OE2 B:GLU49 3.4 31.6 1.0
N3A B:DUN1230 3.4 22.6 1.0
MG B:MG1232 3.4 19.4 1.0
O B:HOH2053 3.8 17.9 1.0
NZ A:LYS57 4.0 29.8 1.0
O2B B:DUN1230 4.1 32.4 1.0
C5' B:DUN1230 4.1 22.1 1.0
O A:HOH2058 4.2 30.2 1.0
O5' B:DUN1230 4.2 22.3 1.0
CG B:GLU46 4.2 28.5 1.0
O B:HOH2055 4.3 33.0 1.0
CG B:GLU49 4.4 28.9 1.0
O1B B:DUN1230 4.4 29.7 1.0
O2A B:DUN1230 4.4 23.8 1.0
CE A:LYS57 4.6 28.2 1.0
O A:HOH2066 4.7 36.5 1.0
OD2 B:ASP77 4.8 30.1 1.0
O B:HOH2104 4.8 18.0 1.0
O B:HOH2188 4.9 31.5 1.0

Magnesium binding site 5 out of 6 in 1w2y

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Magnesium binding site 5 out of 6 in the The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1232

b:19.4
occ:1.00
 OE1 B:GLU46 2.0 30.2 1.0
OE1 B:GLU74 2.1 30.4 1.0
OD2 B:ASP77 2.1 30.1 1.0
O3B B:DUN1230 2.1 18.2 1.0
OE2 B:GLU49 2.1 31.6 1.0
O B:HOH2104 2.2 18.0 1.0
CD B:GLU49 3.0 31.7 1.0
CD B:GLU46 3.0 31.9 1.0
CD B:GLU74 3.1 29.5 1.0
CG B:ASP77 3.2 31.7 1.0
PB B:DUN1230 3.2 23.3 1.0
MG B:MG1233 3.3 16.9 0.5
OE1 B:GLU49 3.3 30.9 1.0
MG B:MG1231 3.4 19.8 1.0
OE2 B:GLU46 3.4 31.6 1.0
OE2 B:GLU74 3.4 33.2 1.0
O1B B:DUN1230 3.7 29.7 1.0
CB B:ASP77 3.7 30.5 1.0
O2B B:DUN1230 3.8 32.4 1.0
O B:HOH2188 4.2 31.5 1.0
OD1 B:ASP77 4.2 30.0 1.0
CG B:GLU49 4.3 28.9 1.0
CG B:GLU46 4.4 28.5 1.0
CB B:GLU49 4.4 30.6 1.0
CG B:GLU74 4.5 29.7 1.0
NZ B:LYS175 4.6 28.3 1.0
N3A B:DUN1230 4.6 22.6 1.0
CA B:GLU74 4.6 30.9 1.0
O B:HOH2056 4.7 20.6 1.0
CB B:GLU46 4.8 29.0 1.0
O1A B:DUN1230 4.8 19.5 1.0
CB B:GLU74 4.8 32.0 1.0
O B:HOH2105 4.8 23.2 1.0
CG2 B:ILE73 4.8 39.2 1.0
C5' B:DUN1230 4.9 22.1 1.0
O B:HOH2171 4.9 27.0 1.0

Magnesium binding site 6 out of 6 in 1w2y

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Magnesium binding site 6 out of 6 in the The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Dupnhp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1233

b:16.9
occ:0.50
 O B:HOH2105 1.8 23.2 1.0
OE2 B:GLU74 2.0 33.2 1.0
O B:HOH2188 2.1 31.5 1.0
O B:HOH2104 2.2 18.0 1.0
OE2 B:GLU49 2.2 31.6 1.0
O B:HOH2171 2.2 27.0 1.0
CD B:GLU74 3.0 29.5 1.0
CD B:GLU49 3.2 31.7 1.0
MG B:MG1232 3.3 19.4 1.0
OE1 B:GLU74 3.3 30.4 1.0
O2B B:DUN1230 3.7 32.4 1.0
CG B:GLU49 3.8 28.9 1.0
CB B:GLU49 3.8 30.6 1.0
O B:HOH2017 4.0 41.4 1.0
O3B B:DUN1230 4.1 18.2 1.0
ND2 B:ASN70 4.2 35.2 1.0
O B:HOH2054 4.2 23.9 1.0
OE1 B:GLU49 4.2 30.9 1.0
OE1 B:GLU200 4.3 30.0 0.0
CG B:GLU74 4.3 29.7 1.0
OD1 B:ASN70 4.4 37.1 1.0
PB B:DUN1230 4.5 23.3 1.0
ND2 B:ASN202 4.5 30.7 1.0
OE2 B:GLU200 4.5 30.0 0.0
CG B:ASN70 4.8 33.8 1.0
OE1 B:GLU46 4.8 30.2 1.0
OD2 B:ASP77 4.8 30.1 1.0
CD B:GLU200 4.9 30.0 0.0

Reference:

O.V.Moroz, M.Harkiolaki, M.Y.Galperin, A.A.Vagin, D.Gonzalez-Pacanowska, K.S.Wilson. The Crystal Structure of A Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Sheds Light on the Mechanism and Suggests the "Basic Module" For Dimeric D(C/U)Tpases J.Mol.Biol. V. 342 1583 2004.
ISSN: ISSN 0022-2836
PubMed: 15364583
DOI: 10.1016/J.JMB.2004.07.050
Page generated: Mon Dec 14 07:00:43 2020

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