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Manganese in PDB 4hnv: Crystal Structure of R54E Mutant of S. Aureus Pyruvate Carboxylase

Enzymatic activity of Crystal Structure of R54E Mutant of S. Aureus Pyruvate Carboxylase

All present enzymatic activity of Crystal Structure of R54E Mutant of S. Aureus Pyruvate Carboxylase:
6.4.1.1;

Protein crystallography data

The structure of Crystal Structure of R54E Mutant of S. Aureus Pyruvate Carboxylase, PDB code: 4hnv was solved by L.P.C.Yu, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.434, 256.742, 127.045, 90.00, 109.33, 90.00
R / Rfree (%) 19.4 / 26.2

Other elements in 4hnv:

The structure of Crystal Structure of R54E Mutant of S. Aureus Pyruvate Carboxylase also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of R54E Mutant of S. Aureus Pyruvate Carboxylase (pdb code 4hnv). 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 R54E Mutant of S. Aureus Pyruvate Carboxylase, PDB code: 4hnv:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4hnv

Go back to Manganese Binding Sites List in 4hnv
Manganese binding site 1 out of 4 in the Crystal Structure of R54E Mutant of S. Aureus Pyruvate Carboxylase


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 R54E Mutant of S. Aureus Pyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1202

b:94.3
occ:1.00
 NZ A:LYS741 2.7 38.0 1.0
OD1 A:ASP572 2.8 49.8 1.0
NE2 A:HIS771 2.9 39.1 1.0
NE2 A:HIS773 3.0 43.0 1.0
OD2 A:ASP572 3.5 45.5 1.0
CG A:ASP572 3.5 40.4 1.0
CE1 A:HIS771 3.5 40.2 1.0
CE1 A:HIS773 3.7 44.5 1.0
CD2 A:HIS771 3.9 36.5 1.0
CD2 A:HIS773 4.1 37.8 1.0
CE A:LYS741 4.2 38.8 1.0
NH2 A:ARG571 4.4 36.3 1.0
ND1 A:HIS771 4.6 36.5 1.0
CG A:HIS771 4.8 34.8 1.0
OE1 A:GLN807 4.8 38.2 1.0
CB A:ASP572 4.9 32.9 1.0
ND1 A:HIS773 4.9 40.9 1.0
CG A:LYS741 4.9 33.7 1.0

Manganese binding site 2 out of 4 in 4hnv

Go back to Manganese Binding Sites List in 4hnv
Manganese binding site 2 out of 4 in the Crystal Structure of R54E Mutant of S. Aureus Pyruvate Carboxylase


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 R54E Mutant of S. Aureus Pyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1203

b:83.5
occ:1.00
 NE2 B:HIS771 2.2 53.1 1.0
NE2 B:HIS773 2.7 45.7 1.0
OD1 B:ASP572 2.8 48.9 1.0
NZ B:LYS741 2.8 48.3 1.0
CE1 B:HIS771 2.9 54.0 1.0
CD2 B:HIS771 3.1 51.4 1.0
CE1 B:HIS773 3.5 47.8 1.0
CD2 B:HIS773 3.8 45.8 1.0
CG B:ASP572 3.9 42.3 1.0
ND1 B:HIS771 3.9 52.7 1.0
CE B:LYS741 4.0 49.0 1.0
CG B:HIS771 4.0 50.2 1.0
OD2 B:ASP572 4.3 43.7 1.0
CG B:LYS741 4.6 43.7 1.0
NH2 B:ARG571 4.6 37.7 1.0
ND1 B:HIS773 4.7 47.4 1.0
CB B:MET743 4.8 44.8 1.0
NE2 B:GLN807 4.8 46.7 1.0
CA B:MET743 4.9 45.0 1.0
CG B:HIS773 4.9 45.3 1.0
CD B:LYS741 4.9 47.9 1.0

Manganese binding site 3 out of 4 in 4hnv

Go back to Manganese Binding Sites List in 4hnv
Manganese binding site 3 out of 4 in the Crystal Structure of R54E Mutant of S. Aureus Pyruvate Carboxylase


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 R54E Mutant of S. Aureus Pyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1201

b:55.2
occ:1.00
 NZ C:LYS741 2.1 29.6 1.0
NE2 C:HIS773 2.4 41.8 1.0
NE2 C:HIS771 2.4 48.5 1.0
OD1 C:ASP572 2.5 46.8 1.0
CE1 C:HIS773 3.1 41.5 1.0
CE1 C:HIS771 3.1 45.2 1.0
CG C:ASP572 3.2 44.4 1.0
OD2 C:ASP572 3.4 46.1 1.0
CD2 C:HIS771 3.4 46.0 1.0
CE C:LYS741 3.5 35.8 1.0
CD2 C:HIS773 3.6 43.6 1.0
NH2 C:ARG571 4.0 36.7 1.0
ND1 C:HIS771 4.2 42.5 1.0
ND1 C:HIS773 4.3 41.1 1.0
CG C:HIS771 4.4 42.9 1.0
CB C:ASP572 4.6 40.3 1.0
CG C:HIS773 4.6 41.1 1.0
CD C:LYS741 4.6 40.7 1.0
OE1 C:GLN807 4.8 44.0 1.0
CZ C:ARG571 4.9 34.2 1.0

Manganese binding site 4 out of 4 in 4hnv

Go back to Manganese Binding Sites List in 4hnv
Manganese binding site 4 out of 4 in the Crystal Structure of R54E Mutant of S. Aureus Pyruvate Carboxylase


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 R54E Mutant of S. Aureus Pyruvate Carboxylase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1203

b:85.8
occ:1.00
 NE2 D:HIS771 2.8 34.0 1.0
NZ D:LYS741 2.9 31.7 1.0
OD1 D:ASP572 2.9 45.1 1.0
NE2 D:HIS773 2.9 37.4 1.0
CD2 D:HIS771 3.6 33.1 1.0
CE1 D:HIS771 3.7 32.6 1.0
CE1 D:HIS773 3.7 33.3 1.0
CG D:ASP572 3.8 36.1 1.0
OD2 D:ASP572 4.0 41.9 1.0
CD2 D:HIS773 4.0 35.6 1.0
CE D:LYS741 4.2 30.9 1.0
NH2 D:ARG571 4.5 34.4 1.0
CG D:HIS771 4.7 31.6 1.0
ND1 D:HIS771 4.8 32.9 1.0
CG D:LYS741 4.8 28.4 1.0
CA D:MET743 4.9 27.2 1.0
ND1 D:HIS773 4.9 36.1 1.0

Reference:

L.P.Yu, C.Y.Chou, P.H.Choi, L.Tong. Characterizing the Importance of the Biotin Carboxylase Domain Dimer For Staphylococcus Aureus Pyruvate Carboxylase Catalysis. Biochemistry V. 52 488 2013.
ISSN: ISSN 0006-2960
PubMed: 23286247
DOI: 10.1021/BI301294D
Page generated: Tue Dec 15 04:22:01 2020

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