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Calcium in PDB 2e1q: Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL

Enzymatic activity of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL

All present enzymatic activity of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL, PDB code: 2e1q was solved by Y.Yamaguchi, T.Matsumura, K.Ichida, K.Okamoto, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.571, 140.944, 176.484, 90.00, 91.49, 90.00
R / Rfree (%) 19.2 / 24.6

Other elements in 2e1q:

The structure of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL also contains other interesting chemical elements:

Molybdenum (Mo) 4 atoms
Iron (Fe) 16 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL (pdb code 2e1q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL, PDB code: 2e1q:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2e1q

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Calcium binding site 1 out of 8 in the Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7001

b:20.4
occ:1.00
 O A:GLY838 2.4 30.3 1.0
OE2 A:GLU741 2.6 37.1 1.0
ND1 A:HIS742 2.7 22.0 1.0
OG1 A:THR837 2.8 19.5 1.0
OH A:TYR744 2.9 10.1 1.0
CE1 A:HIS742 3.1 22.1 1.0
CB A:THR837 3.5 19.1 1.0
C A:GLY838 3.6 30.0 1.0
CD A:GLU741 3.7 36.4 1.0
CZ A:TYR744 3.8 10.6 1.0
CG A:HIS742 3.9 22.1 1.0
C A:THR837 3.9 21.3 1.0
O A:THR837 3.9 21.3 1.0
OE1 A:GLU741 4.1 36.4 1.0
N A:GLY838 4.2 29.6 1.0
CE2 A:TYR744 4.3 10.6 1.0
OD1 A:ASP833 4.3 24.9 1.0
CA A:THR837 4.3 21.3 1.0
NE2 A:HIS742 4.4 22.1 1.0
N A:HIS742 4.5 22.4 1.0
CA A:GLY839 4.5 18.3 1.0
CB A:HIS742 4.5 22.1 1.0
N A:GLY839 4.5 18.5 1.0
CA A:GLY838 4.6 29.8 1.0
CG2 A:THR837 4.7 19.1 1.0
CA A:GLY801 4.7 28.8 1.0
CD2 A:HIS742 4.7 21.9 1.0
O A:ASP833 4.8 21.3 1.0
CE1 A:TYR744 4.8 10.7 1.0
O A:GLY801 4.8 28.9 1.0
CG A:GLU741 4.9 36.1 1.0

Calcium binding site 2 out of 8 in 2e1q

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Calcium binding site 2 out of 8 in the Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7002

b:18.5
occ:1.00
 OG A:SER806 2.7 16.2 1.0
OG1 A:THR773 2.7 14.0 1.0
OG A:SER810 3.0 18.2 1.0
C A:SER806 3.0 19.9 1.0
N A:THR807 3.1 31.1 1.0
O A:SER806 3.2 19.9 1.0
CA A:THR807 3.3 29.6 1.0
CG2 A:THR773 3.3 13.8 1.0
CB A:SER806 3.3 16.3 1.0
CB A:THR773 3.5 14.0 1.0
CG2 A:THR807 3.6 9.4 1.0
CA A:SER806 3.8 20.2 1.0
OG1 A:THR767 3.8 14.3 1.0
CG1 A:VAL765 3.8 19.6 1.0
CB A:SER810 3.8 17.9 1.0
CB A:THR767 4.0 14.5 1.0
CB A:THR807 4.0 9.0 1.0
CA A:THR773 4.3 21.2 1.0
CG2 A:THR767 4.4 14.3 1.0
C A:THR807 4.6 29.2 1.0
O A:HOH7034 4.6 16.9 1.0
N A:SER806 4.7 20.5 1.0
CB A:VAL765 4.9 19.5 1.0
O A:ASN769 5.0 22.6 1.0

Calcium binding site 3 out of 8 in 2e1q

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Calcium binding site 3 out of 8 in the Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca7003

b:20.4
occ:1.00
 O B:GLY838 2.4 20.7 1.0
OG1 B:THR837 2.6 8.4 1.0
OH B:TYR744 2.9 18.5 1.0
ND1 B:HIS742 3.0 11.0 1.0
OE2 B:GLU741 3.4 48.8 1.0
CB B:THR837 3.4 8.2 1.0
O B:THR837 3.5 16.6 1.0
CE1 B:HIS742 3.5 10.8 1.0
C B:GLY838 3.6 20.6 1.0
C B:THR837 3.7 16.8 1.0
OE1 B:GLU741 3.9 49.2 1.0
CZ B:TYR744 4.0 18.7 1.0
CD B:GLU741 4.0 48.5 1.0
CG B:HIS742 4.1 11.0 1.0
N B:GLY838 4.2 20.1 1.0
CA B:THR837 4.2 16.8 1.0
OD1 B:ASP833 4.2 28.3 1.0
CE2 B:TYR744 4.3 18.4 1.0
CA B:GLY838 4.5 20.4 1.0
CB B:HIS742 4.6 11.5 1.0
N B:GLY839 4.6 26.3 1.0
CA B:GLY839 4.6 26.4 1.0
CG2 B:THR837 4.6 8.1 1.0
N B:HIS742 4.7 17.5 1.0
NE2 B:HIS742 4.7 10.8 1.0
NE2 B:HIS748 4.7 16.7 1.0
O B:ASP833 4.8 31.6 1.0
CA B:GLY801 4.8 19.8 1.0
O B:GLY801 4.9 20.4 1.0

Calcium binding site 4 out of 8 in 2e1q

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Calcium binding site 4 out of 8 in the Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca7004

b:18.5
occ:1.00
 OG B:SER810 2.8 21.9 1.0
OG B:SER806 2.8 11.2 1.0
OG1 B:THR773 2.9 18.1 1.0
N B:THR807 3.0 26.3 1.0
CA B:THR807 3.2 25.0 1.0
C B:SER806 3.2 20.0 1.0
CG2 B:THR773 3.4 17.7 1.0
CG1 B:VAL765 3.5 10.9 1.0
CB B:SER806 3.5 11.3 1.0
O B:SER806 3.5 20.2 1.0
CB B:SER810 3.6 22.0 1.0
CG2 B:THR807 3.6 22.3 1.0
CB B:THR773 3.7 18.0 1.0
CB B:THR807 3.9 21.8 1.0
CA B:SER806 4.0 20.2 1.0
CB B:THR767 4.0 22.9 1.0
OG1 B:THR767 4.1 22.8 1.0
CA B:THR773 4.3 17.2 1.0
O B:HOH7017 4.3 26.2 1.0
CG2 B:THR767 4.4 22.7 1.0
C B:THR807 4.5 24.4 1.0
CB B:VAL765 4.5 11.0 1.0
CG2 B:VAL765 4.8 11.1 1.0
CA B:SER810 4.9 24.3 1.0
N B:SER806 4.9 20.4 1.0
N B:SER810 4.9 24.6 1.0
OG1 B:THR750 5.0 26.9 1.0
O B:THR807 5.0 24.2 1.0

Calcium binding site 5 out of 8 in 2e1q

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Calcium binding site 5 out of 8 in the Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca7005

b:20.4
occ:1.00
 O C:GLY838 2.4 24.9 1.0
OG1 C:THR837 2.5 29.0 1.0
OE2 C:GLU741 2.6 32.2 1.0
ND1 C:HIS742 2.8 12.6 1.0
OH C:TYR744 2.9 16.3 1.0
CE1 C:HIS742 3.3 12.4 1.0
CB C:THR837 3.3 28.6 1.0
C C:GLY838 3.6 24.8 1.0
CD C:GLU741 3.8 31.5 1.0
C C:THR837 3.8 31.3 1.0
CZ C:TYR744 3.9 16.2 1.0
O C:THR837 3.9 31.3 1.0
N C:GLY838 4.0 24.8 1.0
CG C:HIS742 4.0 12.7 1.0
CA C:THR837 4.2 31.3 1.0
OD1 C:ASP833 4.2 24.7 1.0
CE2 C:TYR744 4.3 16.3 1.0
O C:ASP833 4.4 21.4 1.0
CG C:GLU741 4.4 30.9 1.0
CA C:GLY838 4.4 24.8 1.0
NE2 C:HIS742 4.5 12.4 1.0
CG2 C:THR837 4.6 28.9 1.0
N C:GLY839 4.6 25.6 1.0
CA C:GLY839 4.6 25.5 1.0
CB C:HIS742 4.6 12.8 1.0
N C:HIS742 4.7 16.0 1.0
OE1 C:GLU741 4.8 31.4 1.0
CE1 C:TYR744 4.9 16.0 1.0
CD2 C:HIS742 4.9 12.5 1.0
NE2 C:HIS748 4.9 20.0 1.0
N C:THR837 5.0 31.1 1.0

Calcium binding site 6 out of 8 in 2e1q

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Calcium binding site 6 out of 8 in the Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca7006

b:18.5
occ:1.00
 OG C:SER806 2.5 23.1 1.0
OG1 C:THR773 2.9 9.6 1.0
OG C:SER810 3.0 25.2 1.0
C C:SER806 3.1 16.4 1.0
CB C:SER806 3.1 23.0 1.0
N C:THR807 3.2 22.6 1.0
O C:SER806 3.2 16.4 1.0
CA C:THR807 3.5 21.2 1.0
CG1 C:VAL765 3.6 7.8 1.0
CG2 C:THR773 3.6 9.2 1.0
CA C:SER806 3.7 16.8 1.0
CB C:THR767 3.7 16.5 1.0
CG2 C:THR807 3.7 22.7 1.0
OG1 C:THR767 3.8 16.5 1.0
CB C:THR773 3.8 9.7 1.0
CB C:SER810 3.9 25.1 1.0
CG2 C:THR767 4.2 16.0 1.0
CB C:THR807 4.2 22.2 1.0
CA C:THR773 4.5 17.7 1.0
O C:HOH7023 4.5 17.6 1.0
N C:SER806 4.6 16.9 1.0
CB C:VAL765 4.7 7.8 1.0
C C:THR807 4.8 20.8 1.0
O C:ASN769 5.0 15.1 1.0

Calcium binding site 7 out of 8 in 2e1q

Go back to Calcium Binding Sites List in 2e1q
Calcium binding site 7 out of 8 in the Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca7007

b:20.4
occ:1.00
 O D:GLY838 2.4 18.6 1.0
OG1 D:THR837 2.7 20.1 1.0
OE2 D:GLU741 2.7 51.8 1.0
ND1 D:HIS742 2.9 11.9 1.0
OH D:TYR744 3.1 18.1 1.0
O D:THR837 3.4 15.9 1.0
CE1 D:HIS742 3.5 11.7 1.0
C D:GLY838 3.6 18.5 1.0
CB D:THR837 3.6 20.1 1.0
C D:THR837 3.7 15.8 1.0
CD D:GLU741 3.9 51.2 1.0
CG D:HIS742 4.0 12.0 1.0
CZ D:TYR744 4.1 18.4 1.0
O D:HOH7119 4.2 29.4 1.0
N D:GLY838 4.2 18.2 1.0
CE2 D:TYR744 4.3 18.2 1.0
CA D:THR837 4.3 16.0 1.0
CB D:HIS742 4.5 12.2 1.0
OE1 D:GLU741 4.5 51.5 1.0
CA D:GLY838 4.5 18.3 1.0
OD1 D:ASP833 4.5 24.8 1.0
CA D:GLY839 4.5 22.1 1.0
N D:GLY839 4.5 22.0 1.0
N D:HIS742 4.6 25.6 1.0
NE2 D:HIS742 4.7 11.7 1.0
CA D:GLY801 4.7 14.1 1.0
O D:ASP833 4.8 38.7 1.0
O D:GLY801 4.9 14.4 1.0
NE2 D:HIS748 4.9 17.8 1.0
CG2 D:THR837 4.9 20.1 1.0
CD2 D:HIS742 4.9 11.8 1.0

Calcium binding site 8 out of 8 in 2e1q

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Calcium binding site 8 out of 8 in the Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human Xanthine Oxidoreductase Mutant, GLU803VAL within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca7008

b:23.3
occ:1.00
 OG1 D:THR750 2.7 19.0 1.0
O D:SER806 2.7 13.7 1.0
O D:HOH7147 2.7 13.5 1.0
OG D:SER810 3.2 20.8 1.0
CB D:VAL809 3.3 17.5 1.0
C D:SER806 3.5 13.6 1.0
N D:SER810 3.6 25.0 1.0
CB D:SER806 3.7 22.1 1.0
CG1 D:VAL809 3.8 17.2 1.0
CA D:SER806 3.8 13.8 1.0
CG1 D:VAL765 3.8 16.6 1.0
CB D:THR750 3.9 18.8 1.0
O D:CYS749 4.0 26.3 1.0
C D:CYS749 4.1 26.3 1.0
N D:CYS749 4.1 25.8 1.0
C D:VAL809 4.1 17.3 1.0
CA D:VAL809 4.2 17.5 1.0
CG2 D:VAL809 4.2 17.3 1.0
O D:HOH7131 4.2 16.7 1.0
CB D:SER810 4.3 20.3 1.0
CA D:SER810 4.3 24.8 1.0
N D:THR750 4.4 30.0 1.0
N D:VAL809 4.4 18.0 1.0
ND1 D:HIS748 4.4 18.0 1.0
OG D:SER806 4.4 22.1 1.0
CB D:HIS748 4.6 18.1 1.0
CA D:CYS749 4.6 26.3 1.0
CA D:THR750 4.6 30.1 1.0
N D:THR807 4.7 26.6 1.0
C D:HIS748 4.9 20.0 1.0
O D:SER766 4.9 16.2 1.0
CG D:HIS748 4.9 18.1 1.0
CG2 D:THR750 5.0 18.6 1.0

Reference:

Y.Yamaguchi, T.Matsumura, K.Ichida, K.Okamoto, T.Nishino. Human Xanthine Oxidase Changes Its Substrate Specificity to Aldehyde Oxidase Type Upon Mutation of Amino Acid Residues in the Active Site: Roles of Active Site Residues in Binding and Activation of Purine Substrate J.Biochem.(Tokyo) V. 141 513 2007.
ISSN: ISSN 0021-924X
PubMed: 17301077
DOI: 10.1093/JB/MVM053
Page generated: Fri Jul 12 10:00:15 2024

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