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Calcium in PDB 3an1: Crystal Structure of Rat D428A Mutant, Urate Bound Form

Enzymatic activity of Crystal Structure of Rat D428A Mutant, Urate Bound Form

All present enzymatic activity of Crystal Structure of Rat D428A Mutant, Urate Bound Form:
1.17.1.4; 1.17.3.2;

Protein crystallography data

The structure of Crystal Structure of Rat D428A Mutant, Urate Bound Form, PDB code: 3an1 was solved by K.Okamoto, Y.Kawaguchi, B.T.Eger, E.F.Pai, T.Nishino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.35 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.536, 138.242, 222.473, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19.8

Other elements in 3an1:

The structure of Crystal Structure of Rat D428A Mutant, Urate Bound Form also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat D428A Mutant, Urate Bound Form (pdb code 3an1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Rat D428A Mutant, Urate Bound Form, PDB code: 3an1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3an1

Go back to Calcium Binding Sites List in 3an1
Calcium binding site 1 out of 4 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1332

b:13.6
occ:1.00
 O A:GLY837 2.7 14.6 1.0
OG1 A:THR836 2.7 12.6 1.0
OE2 A:GLU740 2.8 14.9 1.0
O A:HOH1482 2.9 14.1 1.0
OH A:TYR743 3.0 12.3 1.0
ND1 A:HIS741 3.0 11.3 1.0
OE1 A:GLU740 3.2 14.5 1.0
CD A:GLU740 3.4 13.1 1.0
CE1 A:HIS741 3.7 8.3 1.0
CB A:THR836 3.8 11.9 1.0
CZ A:TYR743 3.8 12.7 1.0
C A:GLY837 3.9 13.8 1.0
OD2 A:ASP832 4.0 13.2 1.0
O A:THR836 4.1 12.3 1.0
C A:THR836 4.1 12.1 1.0
CG A:HIS741 4.1 9.5 1.0
CE1 A:TYR743 4.1 8.7 1.0
N A:HIS741 4.3 8.6 1.0
N A:GLY837 4.3 13.2 1.0
CB A:HIS741 4.5 11.0 1.0
CA A:THR836 4.6 11.2 1.0
O A:ASP832 4.6 11.3 1.0
O A:HOH1627 4.7 16.7 1.0
O A:HOH1557 4.7 11.5 1.0
CA A:GLY837 4.8 11.2 1.0
CE2 A:TYR743 4.8 11.0 1.0
N A:GLY838 4.9 11.9 1.0
CG A:GLU740 4.9 12.6 1.0
NE2 A:HIS741 4.9 11.2 1.0
CA A:GLY800 4.9 9.3 1.0
CA A:GLY838 5.0 11.3 1.0
CG2 A:THR836 5.0 12.5 1.0

Calcium binding site 2 out of 4 in 3an1

Go back to Calcium Binding Sites List in 3an1
Calcium binding site 2 out of 4 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4009

b:15.2
occ:1.00
 O A:THR870 2.7 15.2 1.0
O A:ASN908 2.7 12.3 1.0
OG A:SER874 2.7 14.5 1.0
O A:GLY867 2.7 15.8 1.0
OG A:SER907 2.7 12.8 1.0
O A:GLU871 2.9 13.4 1.0
C A:GLU871 3.5 16.1 1.0
N A:ASN908 3.5 12.8 1.0
CB A:ASP872 3.7 14.8 1.0
C A:GLY867 3.7 14.8 1.0
C A:ASN908 3.7 11.8 1.0
C A:THR870 3.8 13.6 1.0
CB A:SER907 3.9 12.0 1.0
CB A:SER874 3.9 13.4 1.0
C A:SER907 4.0 11.5 1.0
CA A:SER907 4.1 13.5 1.0
CA A:GLY867 4.1 14.8 1.0
CA A:ASN908 4.1 11.8 1.0
NE2 A:HIS840 4.2 15.8 1.0
N A:ASP872 4.2 15.2 1.0
CA A:GLU871 4.2 15.5 1.0
OG1 A:THR870 4.4 15.2 1.0
CA A:ASP872 4.5 14.9 1.0
N A:GLU871 4.5 15.1 1.0
N A:SER874 4.6 12.7 1.0
CE1 A:HIS840 4.7 15.5 1.0
N A:THR870 4.8 13.6 1.0
CA A:SER874 4.8 13.8 1.0
CB A:ASN908 4.8 13.0 1.0
CG A:ASP872 4.8 19.2 1.0
N A:LEU873 4.9 12.8 1.0
CA A:THR870 4.9 15.4 1.0
N A:GLY868 4.9 12.5 1.0
C A:ASP872 4.9 15.4 1.0
OD1 A:ASP872 4.9 14.8 1.0
N A:THR909 5.0 12.7 1.0
CE1 A:TYR708 5.0 14.8 1.0
O A:SER907 5.0 13.4 1.0

Calcium binding site 3 out of 4 in 3an1

Go back to Calcium Binding Sites List in 3an1
Calcium binding site 3 out of 4 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4019

b:11.6
occ:1.00
 O B:THR870 2.6 11.7 1.0
O B:ASN908 2.7 11.5 1.0
O B:GLY867 2.7 10.9 1.0
OG B:SER874 2.7 11.3 1.0
OG B:SER907 2.8 9.5 1.0
O B:GLU871 2.9 10.6 1.0
C B:GLU871 3.5 11.8 1.0
N B:ASN908 3.5 10.3 1.0
CB B:ASP872 3.7 11.0 1.0
C B:GLY867 3.7 9.7 1.0
C B:ASN908 3.8 9.9 1.0
C B:THR870 3.8 11.5 1.0
CB B:SER874 3.9 10.6 1.0
CB B:SER907 4.0 10.6 1.0
CA B:GLY867 4.1 10.6 1.0
C B:SER907 4.1 11.2 1.0
CA B:ASN908 4.1 9.6 1.0
NE2 B:HIS840 4.1 10.3 1.0
CA B:SER907 4.2 10.6 1.0
CA B:GLU871 4.2 10.4 1.0
N B:ASP872 4.2 10.0 1.0
CA B:ASP872 4.4 9.4 1.0
OG1 B:THR870 4.4 13.6 1.0
N B:GLU871 4.5 10.2 1.0
N B:SER874 4.6 11.3 1.0
CE1 B:HIS840 4.7 10.1 1.0
N B:THR870 4.8 10.8 1.0
CA B:SER874 4.8 10.8 1.0
CB B:ASN908 4.8 9.4 1.0
CG B:ASP872 4.8 13.8 1.0
CA B:THR870 4.8 11.1 1.0
N B:GLY868 4.8 10.8 1.0
N B:LEU873 4.9 9.5 1.0
C B:ASP872 4.9 11.3 1.0
OD1 B:ASP872 4.9 13.1 1.0
N B:THR909 4.9 8.7 1.0

Calcium binding site 4 out of 4 in 3an1

Go back to Calcium Binding Sites List in 3an1
Calcium binding site 4 out of 4 in the Crystal Structure of Rat D428A Mutant, Urate Bound Form


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 Rat D428A Mutant, Urate Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1335

b:11.1
occ:1.00
 O B:GLY837 2.7 11.7 1.0
OG1 B:THR836 2.7 10.6 1.0
O B:HOH1392 2.8 11.2 1.0
OE2 B:GLU740 2.8 14.4 1.0
ND1 B:HIS741 2.9 8.9 1.0
OH B:TYR743 3.0 9.9 1.0
OE1 B:GLU740 3.3 12.8 1.0
CD B:GLU740 3.4 12.8 1.0
CE1 B:HIS741 3.6 9.8 1.0
CZ B:TYR743 3.8 7.6 1.0
CB B:THR836 3.8 11.2 1.0
C B:GLY837 3.9 10.7 1.0
CE1 B:TYR743 4.0 6.7 1.0
CG B:HIS741 4.0 9.4 1.0
OD2 B:ASP832 4.1 10.7 1.0
O B:THR836 4.1 12.0 1.0
C B:THR836 4.1 9.1 1.0
N B:HIS741 4.3 7.5 1.0
N B:GLY837 4.4 9.0 1.0
CB B:HIS741 4.4 8.4 1.0
CA B:THR836 4.6 8.9 1.0
O B:ASP832 4.6 10.7 1.0
O B:HOH1514 4.7 13.6 1.0
O B:HOH1358 4.7 11.0 1.0
CA B:GLY837 4.8 9.9 1.0
NE2 B:HIS741 4.8 8.7 1.0
CE2 B:TYR743 4.9 7.5 1.0
N B:GLY838 4.9 9.9 1.0
CG B:GLU740 4.9 9.6 1.0
CA B:GLY838 4.9 9.3 1.0
CA B:GLY800 5.0 8.6 1.0
CG2 B:THR836 5.0 9.9 1.0

Reference:

K.Okamoto, Y.Kawaguchi, B.T.Eger, E.F.Pai, T.Nishino. Crystal Structures of Urate Bound Form of Xanthine Oxidoreductase: Substrate Orientation and Structure of the Key Reaction Intermediate J.Am.Chem.Soc. V. 132 17080 2010.
ISSN: ISSN 0002-7863
PubMed: 21077683
DOI: 10.1021/JA1077574
Page generated: Sat Jul 13 07:55:45 2024

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