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

Go back to

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

Go back to

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

Go back to

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

Go back to

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy