Manganese in PDB 3bg3: Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus)

Enzymatic activity of Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus)

All present enzymatic activity of Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus):
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), PDB code: 3bg3 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 / 2.80
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	81.274, 173.321, 118.194, 90.00, 95.87, 90.00
*R / R_free (%)*	21.6 / 27.1

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) (pdb code 3bg3). 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), PDB code: 3bg3:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3bg3

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Manganese Binding Sites List in 3bg3

Manganese binding site 1 out of 4 in the Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus)

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) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn2001 b:72.0 occ:1.00	OQ1	A:KCX741	2.0	66.8	1.0
	OD1	A:ASP572	2.1	59.4	1.0
	NE2	A:HIS773	2.2	58.9	1.0
	NE2	A:HIS771	2.3	58.3	1.0
	OQ2	A:KCX741	2.4	67.2	1.0
	CX	A:KCX741	2.6	67.1	1.0
	CE1	A:HIS771	3.0	58.9	1.0
	CG	A:ASP572	3.1	58.5	1.0
	CE1	A:HIS773	3.2	57.7	1.0
	CD2	A:HIS773	3.2	58.7	1.0
	OD2	A:ASP572	3.4	58.8	1.0
	CD2	A:HIS771	3.4	60.4	1.0
	NZ	A:KCX741	3.9	67.8	1.0
	O3	A:PYR2000	4.2	75.4	1.0
	ND1	A:HIS771	4.2	58.9	1.0
	ND1	A:HIS773	4.3	57.0	1.0
	OE1	A:GLN807	4.3	54.9	1.0
	CG	A:HIS773	4.3	56.2	1.0
	CB	A:ASP572	4.4	57.5	1.0
	NE2	A:GLN807	4.5	54.5	1.0
	CG	A:HIS771	4.5	59.7	1.0
	NH2	A:ARG571	4.5	55.0	1.0
	CA	A:MET743	4.8	65.0	1.0
	CD	A:GLN807	4.8	53.5	1.0
	CB	A:MET743	5.0	66.0	1.0
	CE	A:KCX741	5.0	69.6	1.0

Manganese binding site 2 out of 4 in 3bg3

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Manganese Binding Sites List in 3bg3

Manganese binding site 2 out of 4 in the Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus)

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) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn2001 b:69.0 occ:1.00	NE2	B:HIS773	2.2	59.9	1.0
	OD1	B:ASP572	2.3	63.5	1.0
	OQ1	B:KCX741	2.3	65.5	1.0
	OQ2	B:KCX741	2.3	65.5	1.0
	NE2	B:HIS771	2.4	59.9	1.0
	CX	B:KCX741	2.7	65.1	1.0
	CE1	B:HIS773	3.1	58.7	1.0
	CE1	B:HIS771	3.1	59.3	1.0
	CG	B:ASP572	3.1	60.0	1.0
	OD2	B:ASP572	3.2	61.5	1.0
	CD2	B:HIS773	3.3	59.9	1.0
	O3	B:PYR2000	3.4	72.9	1.0
	CD2	B:HIS771	3.6	62.0	1.0
	NZ	B:KCX741	4.0	64.9	1.0
	OE1	B:GLN807	4.0	58.8	1.0
	NH2	B:ARG571	4.2	58.0	1.0
	ND1	B:HIS773	4.3	58.5	1.0
	ND1	B:HIS771	4.3	60.2	1.0
	CG	B:HIS773	4.4	59.6	1.0
	C2	B:PYR2000	4.5	73.9	1.0
	CB	B:ASP572	4.5	57.8	1.0
	CG	B:HIS771	4.6	61.5	1.0
	CA	B:MET743	4.7	63.8	1.0
	C3	B:PYR2000	4.7	74.3	1.0
	CE	B:KCX741	4.9	66.2	1.0

Manganese binding site 3 out of 4 in 3bg3

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Manganese Binding Sites List in 3bg3

Manganese binding site 3 out of 4 in the Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus)

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) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mn2001 b:77.0 occ:1.00	OQ2	C:KCX741	2.1	72.2	1.0
	OD1	C:ASP572	2.1	67.2	1.0
	NE2	C:HIS773	2.2	63.5	1.0
	NE2	C:HIS771	2.3	63.5	1.0
	OQ1	C:KCX741	2.8	75.2	1.0
	CX	C:KCX741	2.8	74.1	1.0
	CE1	C:HIS773	2.9	62.0	1.0
	CE1	C:HIS771	3.0	63.8	1.0
	CG	C:ASP572	3.1	66.7	1.0
	OD2	C:ASP572	3.2	67.5	1.0
	CD2	C:HIS773	3.3	62.5	1.0
	CD2	C:HIS771	3.4	64.8	1.0
	O3	C:PYR2000	3.9	89.2	1.0
	NE2	C:GLN807	4.1	61.2	1.0
	NZ	C:KCX741	4.1	74.8	1.0
	ND1	C:HIS773	4.1	61.6	1.0
	ND1	C:HIS771	4.2	64.0	1.0
	CG	C:HIS773	4.4	61.8	1.0
	CG	C:HIS771	4.4	65.1	1.0
	CB	C:ASP572	4.4	65.6	1.0
	CA	C:MET743	4.5	67.0	1.0
	NH1	C:ARG571	4.6	66.2	1.0
	CB	C:MET743	4.8	68.4	1.0
	NH2	C:ARG571	4.8	70.1	1.0
	CE	C:KCX741	4.9	74.4	1.0
	CD	C:GLN807	4.9	62.4	1.0

Manganese binding site 4 out of 4 in 3bg3

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Manganese Binding Sites List in 3bg3

Manganese binding site 4 out of 4 in the Crystal Structure of Human Pyruvate Carboxylase (Missing the Biotin Carboxylase Domain at the N-Terminus)

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) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mn2001 b:68.0 occ:1.00	OD1	D:ASP572	2.0	57.4	1.0
	OQ2	D:KCX741	2.1	54.1	1.0
	NE2	D:HIS771	2.2	55.9	1.0
	NE2	D:HIS773	2.4	56.2	1.0
	OQ1	D:KCX741	2.6	59.0	1.0
	CX	D:KCX741	2.7	57.4	1.0
	CE1	D:HIS771	3.0	55.6	1.0
	CG	D:ASP572	3.1	57.5	1.0
	CE1	D:HIS773	3.1	55.4	1.0
	CD2	D:HIS771	3.4	57.7	1.0
	CD2	D:HIS773	3.5	54.8	1.0
	OD2	D:ASP572	3.5	58.1	1.0
	O3	D:PYR2000	3.8	76.6	1.0
	OE1	D:GLN807	4.0	54.5	1.0
	NZ	D:KCX741	4.1	59.8	1.0
	NH2	D:ARG571	4.1	60.2	1.0
	ND1	D:HIS771	4.2	56.5	1.0
	ND1	D:HIS773	4.3	53.8	1.0
	CG	D:HIS771	4.4	57.5	1.0
	CB	D:ASP572	4.4	57.0	1.0
	CG	D:HIS773	4.5	53.5	1.0
	CD	D:GLN807	4.8	53.6	1.0
	CA	D:MET743	4.8	56.3	1.0
	CE	D:KCX741	5.0	59.5	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 15:56:40 2024

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