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Magnesium in PDB 5dou: Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form

Enzymatic activity of Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form

All present enzymatic activity of Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form:
6.3.4.16;

Protein crystallography data

The structure of Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form, PDB code: 5dou was solved by S.De Cima, L.M.Polo, I.Fita, V.Rubio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.919, 98.558, 214.890, 90.66, 98.65, 90.08
R / Rfree (%) 19.5 / 22.9

Other elements in 5dou:

The structure of Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form also contains other interesting chemical elements:

Nickel (Ni) 4 atoms
Potassium (K) 18 atoms
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form (pdb code 5dou). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form, PDB code: 5dou:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 5dou

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Magnesium binding site 1 out of 12 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:13.3
occ:1.00
 O1 A:PO42007 1.8 11.3 1.0
OE2 A:GLU714 2.0 15.1 1.0
OD1 A:ASN716 2.1 14.7 1.0
O A:HOH2114 2.1 13.5 1.0
O1B A:ADP2008 2.1 11.4 1.0
OE1 A:GLU714 2.3 15.8 1.0
CD A:GLU714 2.5 15.6 1.0
CG A:ASN716 2.9 15.4 1.0
P A:PO42007 3.1 12.8 1.0
ND2 A:ASN716 3.1 16.4 1.0
MG A:MG2003 3.2 9.2 1.0
PB A:ADP2008 3.4 12.4 1.0
O3 A:PO42007 3.4 12.8 1.0
O2 A:PO42007 3.7 13.6 1.0
O3B A:ADP2008 3.8 11.3 1.0
K A:K2005 3.9 31.4 1.0
NH1 A:ARG718 3.9 17.1 1.0
CG A:GLU714 4.0 15.6 1.0
O A:ALA591 4.2 14.7 1.0
O3A A:ADP2008 4.2 10.5 1.0
O A:HOH2121 4.2 16.5 1.0
CB A:ASN716 4.3 15.3 1.0
CA A:LEU592 4.3 13.7 1.0
O4 A:PO42007 4.4 12.2 1.0
O2B A:ADP2008 4.4 12.6 1.0
CB A:LEU592 4.5 13.3 1.0
O2A A:ADP2008 4.5 10.9 1.0
OE1 A:GLN700 4.6 15.3 1.0
NH2 A:ARG547 4.7 26.8 1.0
PA A:ADP2008 4.8 10.3 1.0
CB A:GLU714 4.9 15.8 1.0
O A:HOH2279 4.9 21.1 1.0

Magnesium binding site 2 out of 12 in 5dou

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Magnesium binding site 2 out of 12 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound 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 Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:9.2
occ:1.00
 OE2 A:GLU714 1.7 15.1 1.0
O3 A:PO42007 1.9 12.8 1.0
O2A A:ADP2008 2.0 10.9 1.0
O3B A:ADP2008 2.2 11.3 1.0
OE1 A:GLN700 2.2 15.3 1.0
O A:HOH2206 2.4 20.3 1.0
CD A:GLU714 2.8 15.6 1.0
PB A:ADP2008 3.0 12.4 1.0
P A:PO42007 3.0 12.8 1.0
O1 A:PO42007 3.1 11.3 1.0
MG A:MG2002 3.2 13.3 1.0
CD A:GLN700 3.2 14.7 1.0
PA A:ADP2008 3.2 10.3 1.0
O1B A:ADP2008 3.2 11.4 1.0
O3A A:ADP2008 3.4 10.5 1.0
NE2 A:GLN700 3.5 14.8 1.0
CG A:GLU714 3.6 15.6 1.0
OE1 A:GLU714 3.8 15.8 1.0
K A:K2006 3.8 46.5 1.0
ND2 A:ASN716 4.0 16.4 1.0
NE2 A:HIS659 4.0 12.9 1.0
O4 A:PO42007 4.0 12.2 1.0
O2 A:PO42007 4.1 13.6 1.0
O5' A:ADP2008 4.3 9.5 1.0
O1A A:ADP2008 4.4 9.9 1.0
CE1 A:HIS659 4.4 13.0 1.0
O2B A:ADP2008 4.4 12.6 1.0
C5' A:ADP2008 4.5 8.8 1.0
CG A:GLN700 4.6 14.7 1.0
OD1 A:ASN716 4.7 14.7 1.0
O3' A:ADP2008 4.7 7.9 1.0
OG1 A:THR660 4.7 14.9 1.0
CG A:ASN716 4.8 15.4 1.0
CD2 A:HIS659 4.9 12.9 1.0
CB A:GLU714 5.0 15.8 1.0

Magnesium binding site 3 out of 12 in 5dou

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Magnesium binding site 3 out of 12 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound 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 Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2011

b:41.6
occ:1.00
 O3B A:ADP2009 2.1 47.9 1.0
OE2 A:GLU1255 2.3 52.9 1.0
OE1 A:GLN1243 2.5 44.3 1.0
O A:HOH2320 2.7 39.6 1.0
O2A A:ADP2009 2.8 38.7 1.0
O A:HOH2319 3.2 38.1 1.0
CD A:GLU1255 3.5 56.4 1.0
CD A:GLN1243 3.6 38.0 1.0
PB A:ADP2009 3.6 44.8 1.0
PA A:ADP2009 3.9 42.1 1.0
NE2 A:GLN1243 4.1 39.7 1.0
ND2 A:ASN1257 4.1 42.7 1.0
OE1 A:GLU1255 4.1 64.7 1.0
O3A A:ADP2009 4.2 42.8 1.0
OD1 A:ASN1257 4.3 42.5 1.0
O2B A:ADP2009 4.4 47.9 1.0
CG A:ASN1257 4.6 39.5 1.0
O1B A:ADP2009 4.6 46.5 1.0
CG A:GLU1255 4.6 51.0 1.0
O1A A:ADP2009 4.8 40.4 1.0
CB A:GLU1255 4.8 44.6 1.0
O A:HOH2327 4.9 29.1 1.0
CG A:GLN1243 4.9 33.8 1.0

Magnesium binding site 4 out of 12 in 5dou

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Magnesium binding site 4 out of 12 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound 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 Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:21.8
occ:1.00
 O1 B:PO42007 2.0 26.8 1.0
O1B B:ADP2008 2.1 25.1 1.0
OD1 B:ASN716 2.3 49.8 1.0
OE1 B:GLU714 2.5 46.3 1.0
OE2 B:GLU714 2.8 42.1 1.0
CD B:GLU714 3.1 45.1 1.0
O B:ALA591 3.3 38.8 1.0
K B:K2005 3.3 42.4 1.0
CG B:ASN716 3.3 49.5 1.0
PB B:ADP2008 3.4 26.1 1.0
P B:PO42007 3.5 27.5 1.0
ND2 B:ASN716 3.8 49.8 1.0
CA B:LEU592 3.8 34.5 1.0
NH1 B:ARG718 3.8 40.3 1.0
O3B B:ADP2008 3.9 26.1 1.0
CB B:LEU592 4.0 34.9 1.0
O2B B:ADP2008 4.1 25.4 1.0
O3 B:PO42007 4.2 29.8 1.0
NH2 B:ARG547 4.2 63.9 1.0
C B:ALA591 4.3 36.5 1.0
O2 B:PO42007 4.3 26.7 1.0
O4 B:PO42007 4.4 29.9 1.0
N B:LEU592 4.5 35.0 1.0
O3A B:ADP2008 4.6 28.5 1.0
CG B:GLU714 4.6 44.3 1.0
CB B:ASN716 4.6 48.4 1.0
OE2 B:GLU545 4.7 49.7 1.0
MG B:MG2003 4.9 35.0 1.0
C B:LEU592 4.9 33.5 1.0
NH1 B:ARG547 5.0 57.9 1.0
CZ B:ARG718 5.0 39.9 1.0

Magnesium binding site 5 out of 12 in 5dou

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Magnesium binding site 5 out of 12 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound 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 Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2003

b:35.0
occ:1.00
 O2A B:ADP2008 1.9 28.7 1.0
OE1 B:GLN700 2.1 49.9 1.0
O3 B:PO42007 2.2 29.8 1.0
O3B B:ADP2008 2.4 26.1 1.0
OE2 B:GLU714 2.6 42.1 1.0
CD B:GLN700 2.9 50.4 1.0
NE2 B:GLN700 3.0 49.3 1.0
PA B:ADP2008 3.3 29.6 1.0
K B:K2006 3.5 65.9 1.0
P B:PO42007 3.5 27.5 1.0
NE2 B:HIS659 3.5 38.2 1.0
PB B:ADP2008 3.5 26.1 1.0
CD B:GLU714 3.6 45.1 1.0
O3A B:ADP2008 3.7 28.5 1.0
O1 B:PO42007 3.8 26.8 1.0
C5' B:ADP2008 3.9 29.1 1.0
O4 B:PO42007 3.9 29.9 1.0
OG1 B:THR660 3.9 39.9 1.0
CE1 B:HIS659 3.9 37.6 1.0
O1B B:ADP2008 4.0 25.1 1.0
O5' B:ADP2008 4.1 28.6 1.0
CG B:GLU714 4.1 44.3 1.0
O3' B:ADP2008 4.2 32.4 1.0
CG B:GLN700 4.3 51.3 1.0
CD2 B:HIS659 4.3 38.6 1.0
C3' B:ADP2008 4.4 29.8 1.0
O1A B:ADP2008 4.5 29.0 1.0
ND2 B:ASN716 4.6 49.8 1.0
C4' B:ADP2008 4.6 29.4 1.0
OE1 B:GLU714 4.7 46.3 1.0
O2 B:PO42007 4.7 26.7 1.0
CG2 B:THR660 4.7 38.8 1.0
ND1 B:HIS659 4.8 37.1 1.0
O2B B:ADP2008 4.9 25.4 1.0
MG B:MG2002 4.9 21.8 1.0
CB B:THR660 5.0 38.9 1.0
CG B:HIS659 5.0 38.7 1.0

Magnesium binding site 6 out of 12 in 5dou

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Magnesium binding site 6 out of 12 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound 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 Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2011

b:15.6
occ:1.00
 O3B B:ADP2009 2.1 36.0 1.0
O2A B:ADP2009 2.2 28.7 1.0
OE1 B:GLN1243 2.3 37.5 1.0
OE2 B:GLU1255 2.4 48.6 1.0
O B:HOH2178 2.5 35.9 1.0
CD B:GLN1243 3.3 35.3 1.0
PA B:ADP2009 3.5 29.2 1.0
PB B:ADP2009 3.5 34.0 1.0
O B:HOH2171 3.6 37.2 1.0
NE2 B:GLN1243 3.6 37.6 1.0
CD B:GLU1255 3.6 49.8 1.0
O3A B:ADP2009 3.8 35.7 1.0
OE1 B:GLU1255 4.3 52.7 1.0
ND2 B:ASN1257 4.4 42.2 1.0
O1B B:ADP2009 4.5 37.5 1.0
O5' B:ADP2009 4.5 29.2 1.0
O2B B:ADP2009 4.5 34.8 1.0
O1A B:ADP2009 4.6 31.8 1.0
CG B:GLN1243 4.7 33.5 1.0
OD1 B:ASN1257 4.7 42.0 1.0
CG B:GLU1255 4.7 46.4 1.0
CB B:GLU1255 4.7 44.2 1.0
C5' B:ADP2009 4.8 29.1 1.0
NE2 B:HIS1202 4.8 40.8 1.0
OG B:SER1203 4.9 34.3 1.0
CE1 B:HIS1202 4.9 42.2 1.0

Magnesium binding site 7 out of 12 in 5dou

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Magnesium binding site 7 out of 12 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound 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 Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:20.0
occ:1.00
 O1 C:PO42007 1.9 34.1 1.0
OD1 C:ASN716 2.0 49.4 1.0
O1B C:ADP2008 2.2 29.3 1.0
OE1 C:GLU714 2.5 44.5 1.0
OE2 C:GLU714 2.7 44.4 1.0
CD C:GLU714 3.0 46.7 1.0
CG C:ASN716 3.0 49.8 1.0
P C:PO42007 3.2 35.1 1.0
ND2 C:ASN716 3.5 50.3 1.0
O3 C:PO42007 3.5 34.7 1.0
K C:K2005 3.5 45.1 1.0
PB C:ADP2008 3.5 29.4 1.0
O C:ALA591 3.6 54.4 1.0
NH1 C:ARG718 3.7 45.0 1.0
O3B C:ADP2008 4.0 28.6 1.0
CA C:LEU592 4.0 48.0 1.0
CB C:LEU592 4.1 46.5 1.0
O2 C:PO42007 4.2 32.5 1.0
O4 C:PO42007 4.2 34.3 1.0
CB C:ASN716 4.3 48.9 1.0
O2B C:ADP2008 4.5 27.9 1.0
NH2 C:ARG547 4.5 82.1 1.0
CG C:GLU714 4.5 48.9 1.0
C C:ALA591 4.5 50.0 1.0
O3A C:ADP2008 4.6 29.1 1.0
MG C:MG2003 4.7 20.6 1.0
N C:LEU592 4.7 49.3 1.0
OE2 C:GLU545 4.8 60.9 1.0
CZ C:ARG718 4.8 44.9 1.0
O C:HOH2129 5.0 48.6 1.0
O2A C:ADP2008 5.0 26.9 1.0

Magnesium binding site 8 out of 12 in 5dou

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Magnesium binding site 8 out of 12 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound 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 Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:20.6
occ:1.00
 O2A C:ADP2008 1.9 26.9 1.0
O3 C:PO42007 2.0 34.7 1.0
OE1 C:GLN700 2.2 60.0 1.0
O3B C:ADP2008 2.3 28.6 1.0
OE2 C:GLU714 2.6 44.4 1.0
CD C:GLN700 3.0 62.4 1.0
NE2 C:GLN700 3.2 60.4 1.0
P C:PO42007 3.3 35.1 1.0
K C:K2006 3.3 78.7 1.0
PA C:ADP2008 3.4 26.6 1.0
PB C:ADP2008 3.4 29.4 1.0
O4 C:PO42007 3.5 34.3 1.0
NE2 C:HIS659 3.5 46.9 1.0
CD C:GLU714 3.6 46.7 1.0
O3A C:ADP2008 3.8 29.1 1.0
O3' C:ADP2008 3.8 29.3 1.0
CE1 C:HIS659 3.9 47.1 1.0
OG1 C:THR660 3.9 45.0 1.0
O1B C:ADP2008 3.9 29.3 1.0
O1 C:PO42007 4.0 34.1 1.0
CG C:GLU714 4.1 48.9 1.0
O5' C:ADP2008 4.3 27.9 1.0
CD2 C:HIS659 4.3 47.2 1.0
O2 C:PO42007 4.3 32.5 1.0
C5' C:ADP2008 4.4 28.5 1.0
CG C:GLN700 4.4 63.4 1.0
C3' C:ADP2008 4.4 28.4 1.0
O1A C:ADP2008 4.5 28.4 1.0
ND2 C:ASN716 4.5 50.3 1.0
OE1 C:GLU714 4.6 44.5 1.0
MG C:MG2002 4.7 20.0 1.0
ND1 C:HIS659 4.7 45.7 1.0
O2B C:ADP2008 4.8 27.9 1.0
C4' C:ADP2008 4.8 28.2 1.0
CG2 C:THR660 4.8 46.3 1.0
CG C:HIS659 5.0 46.9 1.0

Magnesium binding site 9 out of 12 in 5dou

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Magnesium binding site 9 out of 12 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2011

b:41.7
occ:1.00
 O3B C:ADP2009 2.0 35.8 1.0
OE2 C:GLU1255 2.1 41.6 1.0
OE1 C:GLN1243 2.4 38.5 1.0
O2A C:ADP2009 2.7 34.2 1.0
PB C:ADP2009 3.2 35.4 1.0
CD C:GLU1255 3.4 40.8 1.0
O3A C:ADP2009 3.4 37.9 1.0
CD C:GLN1243 3.4 39.4 1.0
PA C:ADP2009 3.6 36.7 1.0
O2B C:ADP2009 3.8 38.9 1.0
NE2 C:GLN1243 3.8 42.2 1.0
OE1 C:GLU1255 4.0 43.8 1.0
ND2 C:ASN1257 4.3 40.2 1.0
OD1 C:ASN1257 4.4 44.6 1.0
CG C:GLU1255 4.5 37.7 1.0
O1B C:ADP2009 4.5 33.3 1.0
CB C:GLU1255 4.6 35.4 1.0
O5' C:ADP2009 4.6 34.9 1.0
CG C:GLN1243 4.8 36.8 1.0
O1A C:ADP2009 4.8 37.6 1.0
CG C:ASN1257 4.8 39.9 1.0
NE2 C:HIS1202 5.0 42.9 1.0

Magnesium binding site 10 out of 12 in 5dou

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Magnesium binding site 10 out of 12 in the Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Human Carbamoyl Phosphate Synthetase I (CPS1), Ligand-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2002

b:13.3
occ:1.00
 OD1 D:ASN716 2.0 17.0 1.0
OE1 D:GLU714 2.1 15.6 1.0
O1B D:ADP2008 2.1 10.5 1.0
O1 D:PO42007 2.2 11.7 1.0
OE2 D:GLU714 2.4 14.1 1.0
CD D:GLU714 2.6 15.5 1.0
CG D:ASN716 3.0 16.4 1.0
K D:K2005 3.3 30.9 1.0
ND2 D:ASN716 3.4 17.1 1.0
PB D:ADP2008 3.5 10.6 1.0
P D:PO42007 3.6 13.6 1.0
O D:ALA591 3.8 14.1 1.0
MG D:MG2003 3.9 13.3 1.0
O3 D:PO42007 4.0 13.2 1.0
NH1 D:ARG718 4.0 21.6 1.0
O3B D:ADP2008 4.0 9.8 1.0
CG D:GLU714 4.1 15.6 1.0
NH2 D:ARG547 4.2 24.9 1.0
O3A D:ADP2008 4.3 9.7 1.0
O2 D:PO42007 4.3 14.2 1.0
CA D:LEU592 4.3 13.7 1.0
CB D:ASN716 4.4 15.8 1.0
O D:HOH2280 4.4 14.2 1.0
CB D:LEU592 4.5 13.7 1.0
O2B D:ADP2008 4.6 10.8 1.0
O4 D:PO42007 4.7 11.9 1.0
C D:ALA591 4.8 15.1 1.0
NH1 D:ARG547 4.8 24.9 1.0
CB D:GLU714 4.8 16.0 1.0
O2A D:ADP2008 4.8 9.0 1.0
OE2 D:GLU545 4.9 20.8 1.0
CA D:ASN716 5.0 16.4 1.0
CZ D:ARG547 5.0 24.2 1.0

Reference:

S.De Cima, L.M.Polo, C.Diez-Fernandez, A.I.Martinez, J.Cervera, I.Fita, V.Rubio. Structure of Human Carbamoyl Phosphate Synthetase: Deciphering the on/Off Switch of Human Ureagenesis. Sci Rep V. 5 16950 2015.
ISSN: ESSN 2045-2322
PubMed: 26592762
DOI: 10.1038/SREP16950
Page generated: Sun Sep 29 02:56:11 2024

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