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Magnesium in PDB 4brf: Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp

Enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp

All present enzymatic activity of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp:
3.6.1.5;

Protein crystallography data

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp, PDB code: 4brf was solved by M.Zebisch, P.Schaefer, P.Lauble, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.144, 85.970, 71.888, 90.00, 106.14, 90.00
R / Rfree (%) 12.546 / 18.43

Other elements in 4brf:

The structure of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp also contains other interesting chemical elements:

Molybdenum (Mo) 4 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp (pdb code 4brf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp, PDB code: 4brf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4brf

Go back to Magnesium Binding Sites List in 4brf
Magnesium binding site 1 out of 6 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1396

b:13.7
occ:1.00
 O2 A:MOO1395 2.0 12.7 1.0
O A:HOH2298 2.1 14.3 1.0
O A:HOH2010 2.1 13.2 1.0
O A:HOH2123 2.1 12.3 1.0
O A:HOH2134 2.1 12.3 1.0
O A:HOH2011 2.2 12.9 1.0
MO A:MOO1395 3.6 13.8 1.0
OE2 A:GLU159 3.9 14.3 1.0
O A:HOH2122 4.0 11.8 1.0
O A:HOH2133 4.0 14.9 1.0
NE1 A:TRP384 4.1 12.4 1.0
O3 A:MOO1395 4.1 12.9 1.0
O A:HOH2138 4.2 25.4 1.0
OD2 A:ASP49 4.2 20.4 1.0
OD1 A:ASP49 4.2 13.2 1.0
O A:HOH2021 4.2 34.6 1.0
OD2 A:ASP186 4.3 13.8 1.0
OD1 A:ASP186 4.3 13.7 1.0
OG1 A:THR118 4.4 12.8 1.0
O A:HOH2074 4.5 14.1 1.0
O A:HOH2009 4.5 33.7 1.0
O4 A:MOO1395 4.5 13.9 1.0
CD1 A:TRP384 4.6 11.1 1.0
CG A:ASP49 4.7 14.3 1.0
CG A:ASP186 4.7 11.8 1.0
CA A:GLY188 4.7 12.8 1.0
O1 A:MOO1395 5.0 11.9 1.0

Magnesium binding site 2 out of 6 in 4brf

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Magnesium binding site 2 out of 6 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1399

b:36.6
occ:1.00
 O A:HOH2003 2.0 41.3 1.0
O A:HOH2002 2.3 22.0 1.0
O1 A:GOL1400 2.5 31.1 1.0
O A:CYS39 2.5 31.8 1.0
O A:HOH2005 2.7 35.5 1.0
O2 A:GOL1400 2.8 27.3 1.0
C1 A:GOL1400 3.5 29.2 1.0
C2 A:GOL1400 3.5 30.6 1.0
C A:CYS39 3.6 28.6 1.0
CB A:CYS39 3.8 22.3 1.0
CA A:CYS39 4.3 20.8 1.0
ND2 A:ASN110 4.5 27.7 1.0
OD1 A:ASN110 4.6 27.2 1.0
N A:GLU40 4.7 25.6 1.0
CG2 A:ILE111 4.7 17.8 1.0
O A:ASN110 4.8 19.9 1.0
O A:HIS42 4.8 20.8 1.0
CG A:ASN110 4.9 24.1 1.0
OE2 A:GLU40 5.0 84.8 1.0

Magnesium binding site 3 out of 6 in 4brf

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Magnesium binding site 3 out of 6 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1404

b:43.0
occ:1.00
 O A:HOH2211 2.2 35.4 1.0
O A:HOH2212 2.3 29.6 1.0
O A:HOH2302 2.3 39.9 1.0
OG A:SER270 2.6 16.4 0.7
O B:SER274 2.7 15.9 1.0
OG A:SER270 3.0 13.0 0.3
O A:HOH2214 3.0 45.0 1.0
CB A:SER270 3.2 14.2 0.3
CB A:SER270 3.3 16.2 0.7
NZ B:LYS277 3.9 38.9 1.0
C B:SER274 3.9 13.7 1.0
O B:VAL275 4.1 16.6 1.0
CA A:GLU267 4.1 13.6 1.0
CA B:VAL275 4.3 13.1 1.0
O A:GLU266 4.3 14.7 1.0
O A:GLU267 4.3 13.8 1.0
CE B:LYS277 4.3 41.5 1.0
O A:HOH2215 4.5 32.8 1.0
N B:VAL275 4.6 15.9 1.0
O B:HOH2242 4.7 54.1 1.0
O A:HOH2213 4.7 19.5 1.0
C B:VAL275 4.7 13.7 1.0
CA A:SER270 4.7 13.2 0.3
CA A:SER270 4.7 14.0 0.7
C A:GLU267 4.7 11.5 1.0
CB A:GLU267 4.8 14.7 1.0
CG A:GLU267 4.9 13.2 1.0
N A:GLU267 4.9 11.8 1.0
C A:GLU266 4.9 11.7 1.0
O A:HOH2210 5.0 27.6 1.0

Magnesium binding site 4 out of 6 in 4brf

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Magnesium binding site 4 out of 6 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1397

b:14.1
occ:1.00
 O2 B:MOO1396 2.1 13.2 1.0
O B:HOH2113 2.1 11.8 1.0
O B:HOH2006 2.1 13.3 1.0
O B:HOH2241 2.1 14.5 1.0
O B:HOH2007 2.2 13.1 1.0
O B:HOH2120 2.2 13.5 1.0
MO B:MOO1396 3.7 13.4 1.0
OE2 B:GLU159 3.9 14.0 1.0
O B:HOH2121 4.0 17.9 1.0
O B:HOH2112 4.0 13.4 1.0
NE1 B:TRP384 4.0 12.2 1.0
O B:HOH2244 4.1 25.5 1.0
O1 B:GOL1400 4.1 19.5 1.0
O3 B:MOO1396 4.1 16.4 1.0
OD2 B:ASP49 4.2 17.8 1.0
OD1 B:ASP49 4.2 12.2 1.0
O B:HOH2124 4.2 22.9 1.0
OD2 B:ASP186 4.3 14.3 1.0
O B:HOH2016 4.3 27.2 1.0
OG1 B:THR118 4.3 11.9 1.0
OD1 B:ASP186 4.4 13.3 1.0
O B:HOH2069 4.5 11.8 1.0
CD1 B:TRP384 4.5 12.7 1.0
O4 B:MOO1396 4.6 14.2 1.0
CG B:ASP49 4.6 13.9 1.0
CG B:ASP186 4.8 12.3 1.0
CA B:GLY188 4.9 12.5 1.0
CA B:GLY51 5.0 12.4 1.0

Magnesium binding site 5 out of 6 in 4brf

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Magnesium binding site 5 out of 6 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1401

b:36.8
occ:1.00
 O B:HOH2167 2.3 41.7 1.0
O A:HOH2219 2.3 25.8 1.0
O A:HOH2217 2.4 38.9 1.0
O A:HOH2218 2.5 41.8 1.0
OG B:SER270 2.5 9.8 0.5
O A:SER274 2.6 18.6 1.0
OG B:SER270 3.2 17.5 0.5
CB B:SER270 3.4 18.5 0.5
CB B:SER270 3.4 11.2 0.5
C A:SER274 3.8 14.7 1.0
NZ A:LYS277 3.8 21.5 0.5
O A:VAL275 4.2 20.6 1.0
CA B:GLU267 4.3 13.6 1.0
CA A:VAL275 4.3 14.6 1.0
O B:GLU267 4.3 13.8 1.0
O B:GLU266 4.5 16.7 1.0
N A:VAL275 4.5 14.3 1.0
O A:HOH2220 4.6 22.7 1.0
O B:HOH2169 4.6 33.4 1.0
C A:VAL275 4.7 16.2 1.0
CA B:SER270 4.8 12.5 0.5
CA B:SER270 4.8 13.5 0.5
C B:GLU267 4.8 13.0 1.0
CE A:LYS277 4.8 35.5 0.5
CA A:SER274 4.9 15.0 1.0
CG B:GLU267 4.9 15.6 1.0
CB B:GLU267 5.0 12.4 1.0
CE A:LYS277 5.0 20.9 0.5

Magnesium binding site 6 out of 6 in 4brf

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Magnesium binding site 6 out of 6 in the Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Legionella Pneumophila NTPDASE1 Crystal Form II (Closed) in Complex with A Distorted Orthomolybdate Ion and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1402

b:33.5
occ:1.00
 O A:HOH2165 1.9 32.5 1.0
O A:HOH2168 2.0 41.5 1.0
O B:HOH2138 2.1 33.5 1.0
O B:HOH2139 2.1 40.1 1.0
O B:HOH2245 2.1 33.8 1.0
O A:HOH2167 2.2 32.5 1.0
OE2 B:GLU233 4.0 21.6 1.0
OE2 A:GLU233 4.0 24.2 1.0
O A:HOH2023 4.3 40.8 1.0
O B:HOH2142 4.3 29.9 1.0
O A:HOH2172 4.3 26.4 1.0
CE1 B:HIS236 4.4 15.6 1.0
CE1 A:HIS236 4.5 13.4 1.0
O A:HOH2022 4.8 24.4 1.0
O B:HOH2017 4.8 23.1 1.0
CD B:GLU233 4.9 16.6 1.0
O B:HOH2140 4.9 20.4 1.0
ND1 B:HIS236 4.9 14.9 1.0
OE1 B:GLU233 4.9 23.1 1.0
ND1 A:HIS236 4.9 13.2 1.0
CD A:GLU233 5.0 19.2 1.0
O A:HOH2166 5.0 23.7 1.0

Reference:

M.Zebisch, M.Krauss, P.Schaefer, P.Lauble, N.Straeter. Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases Structure V. 21 1460 2013.
ISSN: ISSN 0969-2126
PubMed: 23830739
DOI: 10.1016/J.STR.2013.05.016
Page generated: Thu Aug 15 16:31:59 2024

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