Manganese in PDB 3bg9: Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant
Enzymatic activity of Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant
All present enzymatic activity of Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant:
6.4.1.1;
Protein crystallography data
The structure of Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant, PDB code: 3bg9
was solved by
S.Xiang,
L.Tong,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
3.00
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
107.540,
107.540,
524.470,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.9 /
23.6
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant
(pdb code 3bg9). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant, PDB code: 3bg9:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 3bg9
Go back to
Manganese Binding Sites List in 3bg9
Manganese binding site 1 out
of 4 in the Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn2001
b:87.3
occ:1.00
|
NE2
|
A:HIS771
|
2.3
|
47.5
|
1.0
|
OD1
|
A:ASP572
|
2.5
|
47.5
|
1.0
|
NZ
|
A:LYS741
|
2.7
|
78.2
|
1.0
|
NE2
|
A:HIS773
|
2.9
|
47.5
|
1.0
|
CE1
|
A:HIS773
|
3.1
|
47.5
|
1.0
|
CE1
|
A:HIS771
|
3.2
|
47.5
|
1.0
|
CD2
|
A:HIS771
|
3.3
|
47.5
|
1.0
|
CG
|
A:ASP572
|
3.5
|
47.5
|
1.0
|
OD2
|
A:ASP572
|
3.9
|
47.5
|
1.0
|
CE
|
A:LYS741
|
4.1
|
77.7
|
1.0
|
CD2
|
A:HIS773
|
4.1
|
47.5
|
1.0
|
CB
|
A:MET743
|
4.2
|
47.5
|
1.0
|
ND1
|
A:HIS773
|
4.3
|
47.5
|
1.0
|
ND1
|
A:HIS771
|
4.3
|
47.5
|
1.0
|
CG
|
A:HIS771
|
4.4
|
47.5
|
1.0
|
NH2
|
A:ARG571
|
4.4
|
47.5
|
1.0
|
CA
|
A:MET743
|
4.4
|
47.5
|
1.0
|
OE1
|
A:GLN807
|
4.7
|
47.5
|
1.0
|
CG
|
A:LYS741
|
4.8
|
78.4
|
1.0
|
CB
|
A:ASP572
|
4.8
|
47.5
|
1.0
|
CG
|
A:HIS773
|
4.8
|
47.5
|
1.0
|
CD
|
A:LYS741
|
4.9
|
78.0
|
1.0
|
|
Manganese binding site 2 out
of 4 in 3bg9
Go back to
Manganese Binding Sites List in 3bg9
Manganese binding site 2 out
of 4 in the Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn2001
b:87.3
occ:1.00
|
NE2
|
B:HIS771
|
2.3
|
47.5
|
1.0
|
OD1
|
B:ASP572
|
2.4
|
47.5
|
1.0
|
NZ
|
B:LYS741
|
2.8
|
78.2
|
1.0
|
NE2
|
B:HIS773
|
3.0
|
47.5
|
1.0
|
CE1
|
B:HIS771
|
3.1
|
47.5
|
1.0
|
CE1
|
B:HIS773
|
3.2
|
47.5
|
1.0
|
CD2
|
B:HIS771
|
3.3
|
47.5
|
1.0
|
CG
|
B:ASP572
|
3.5
|
47.5
|
1.0
|
OD2
|
B:ASP572
|
4.0
|
47.5
|
1.0
|
CD2
|
B:HIS773
|
4.2
|
47.5
|
1.0
|
CE
|
B:LYS741
|
4.2
|
77.7
|
1.0
|
ND1
|
B:HIS771
|
4.2
|
47.5
|
1.0
|
NH2
|
B:ARG571
|
4.4
|
47.5
|
1.0
|
CG
|
B:HIS771
|
4.4
|
47.5
|
1.0
|
CB
|
B:MET743
|
4.4
|
47.5
|
1.0
|
ND1
|
B:HIS773
|
4.4
|
47.5
|
1.0
|
CA
|
B:MET743
|
4.5
|
47.5
|
1.0
|
OE1
|
B:GLN807
|
4.7
|
47.5
|
1.0
|
CB
|
B:ASP572
|
4.7
|
47.5
|
1.0
|
CG
|
B:LYS741
|
4.9
|
78.4
|
1.0
|
CG
|
B:HIS773
|
4.9
|
47.5
|
1.0
|
|
Manganese binding site 3 out
of 4 in 3bg9
Go back to
Manganese Binding Sites List in 3bg9
Manganese binding site 3 out
of 4 in the Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn2001
b:87.3
occ:1.00
|
NE2
|
C:HIS771
|
2.3
|
47.5
|
1.0
|
OD1
|
C:ASP572
|
2.4
|
47.5
|
1.0
|
NZ
|
C:LYS741
|
2.5
|
78.2
|
1.0
|
NE2
|
C:HIS773
|
3.1
|
47.5
|
1.0
|
CE1
|
C:HIS771
|
3.1
|
47.5
|
1.0
|
CD2
|
C:HIS771
|
3.2
|
47.5
|
1.0
|
CE1
|
C:HIS773
|
3.3
|
47.5
|
1.0
|
CG
|
C:ASP572
|
3.6
|
47.5
|
1.0
|
CE
|
C:LYS741
|
4.0
|
77.7
|
1.0
|
OD2
|
C:ASP572
|
4.0
|
47.5
|
1.0
|
ND1
|
C:HIS771
|
4.2
|
47.5
|
1.0
|
CB
|
C:MET743
|
4.2
|
47.5
|
1.0
|
CD2
|
C:HIS773
|
4.2
|
47.5
|
1.0
|
CG
|
C:HIS771
|
4.2
|
47.5
|
1.0
|
NH2
|
C:ARG571
|
4.3
|
47.5
|
1.0
|
CA
|
C:MET743
|
4.4
|
47.5
|
1.0
|
ND1
|
C:HIS773
|
4.5
|
47.5
|
1.0
|
CG
|
C:LYS741
|
4.6
|
78.4
|
1.0
|
OE1
|
C:GLN807
|
4.7
|
47.5
|
1.0
|
CB
|
C:ASP572
|
4.8
|
47.5
|
1.0
|
CD
|
C:LYS741
|
4.8
|
78.0
|
1.0
|
CG
|
C:HIS773
|
5.0
|
47.5
|
1.0
|
|
Manganese binding site 4 out
of 4 in 3bg9
Go back to
Manganese Binding Sites List in 3bg9
Manganese binding site 4 out
of 4 in the Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus) F1077A Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn2001
b:87.3
occ:1.00
|
NE2
|
D:HIS771
|
2.5
|
47.5
|
1.0
|
OD1
|
D:ASP572
|
2.5
|
47.5
|
1.0
|
NZ
|
D:LYS741
|
2.6
|
78.2
|
1.0
|
NE2
|
D:HIS773
|
3.0
|
47.5
|
1.0
|
CE1
|
D:HIS773
|
3.2
|
47.5
|
1.0
|
CE1
|
D:HIS771
|
3.3
|
47.5
|
1.0
|
CD2
|
D:HIS771
|
3.4
|
47.5
|
1.0
|
CG
|
D:ASP572
|
3.5
|
47.5
|
1.0
|
OD2
|
D:ASP572
|
3.8
|
47.5
|
1.0
|
CE
|
D:LYS741
|
4.1
|
77.7
|
1.0
|
CD2
|
D:HIS773
|
4.2
|
47.5
|
1.0
|
NH2
|
D:ARG571
|
4.3
|
47.5
|
1.0
|
CB
|
D:MET743
|
4.3
|
47.5
|
1.0
|
ND1
|
D:HIS771
|
4.3
|
47.5
|
1.0
|
CG
|
D:HIS771
|
4.4
|
47.5
|
1.0
|
ND1
|
D:HIS773
|
4.4
|
47.5
|
1.0
|
CA
|
D:MET743
|
4.5
|
47.5
|
1.0
|
OE1
|
D:GLN807
|
4.7
|
47.5
|
1.0
|
CB
|
D:ASP572
|
4.8
|
47.5
|
1.0
|
CG
|
D:LYS741
|
4.8
|
78.4
|
1.0
|
CG
|
D:HIS773
|
5.0
|
47.5
|
1.0
|
CD
|
D:LYS741
|
5.0
|
78.0
|
1.0
|
|
Reference:
S.Xiang,
L.Tong.
Crystal Structures of Human and Staphylococcus Aureus Pyruvate Carboxylase and Molecular Insights Into the Carboxyltransfer Reaction. Nat.Struct.Mol.Biol. V. 15 295 2008.
ISSN: ISSN 1545-9993
PubMed: 18297087
DOI: 10.1038/NSMB.1393
Page generated: Sat Oct 5 15:56:59 2024
|