Manganese in PDB 3pmn: Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

Enzymatic activity of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

All present enzymatic activity of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site, PDB code: 3pmn was solved by K.Bebenek, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	25.27 / 2.20
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	56.390, 62.417, 139.881, 90.00, 90.00, 90.00
*R / R_free (%)*	21.3 / 24.3

Other elements in 3pmn:

The structure of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site (pdb code 3pmn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site, PDB code: 3pmn:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 3pmn

Go back to

Manganese Binding Sites List in 3pmn

Manganese binding site 1 out of 3 in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn2 b:23.2 occ:1.00	OD2	A:ASP490	2.1	27.0	1.0
	OD1	A:ASP427	2.1	21.6	1.0
	OD2	A:ASP429	2.1	24.4	1.0
	O2A	A:1GC1	2.3	20.7	1.0
	O	A:HOH577	2.4	19.0	1.0
	O3'	C:DG6	2.5	21.3	1.0
	CG	A:ASP427	3.1	24.8	1.0
	CG	A:ASP490	3.2	28.0	1.0
	CG	A:ASP429	3.2	24.3	1.0
	PA	A:1GC1	3.3	23.8	1.0
	OD2	A:ASP427	3.5	23.0	1.0
	C3'	C:DG6	3.5	19.6	1.0
	MG	A:MG576	3.5	17.9	1.0
	O1A	A:1GC1	3.5	23.6	1.0
	OD1	A:ASP429	3.6	22.7	1.0
	O5'	A:1GC1	3.8	24.4	1.0
	CB	A:ASP490	3.8	24.7	1.0
	O	A:HOH3	4.0	25.8	1.0
	C5'	A:1GC1	4.1	23.7	1.0
	OD1	A:ASP490	4.2	26.8	1.0
	C4'	C:DG6	4.2	21.2	1.0
	C5'	C:DG6	4.2	17.2	1.0
	CB	A:ASP427	4.4	23.5	1.0
	CB	A:ASP429	4.5	24.2	1.0
	NH2	A:ARG488	4.5	18.0	1.0
	O5'	C:DG6	4.6	22.2	1.0
	C2'	C:DG6	4.7	20.2	1.0
	O	C:HOH7	4.8	33.5	1.0
	O1G	A:1GC1	4.8	22.0	1.0
	OP1	C:DG6	4.8	19.7	1.0
	O2B	A:1GC1	4.9	20.5	1.0
	C3A	A:1GC1	4.9	24.3	1.0

Manganese binding site 2 out of 3 in 3pmn

Go back to

Manganese Binding Sites List in 3pmn

Manganese binding site 2 out of 3 in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn6 b:45.3 occ:1.00	OD1	A:ASP382	2.1	28.8	1.0
	O	A:HOH590	2.5	38.3	1.0
	ND1	A:HIS486	2.6	28.3	1.0
	O	A:HOH588	2.6	21.1	1.0
	O	A:HOH589	2.7	33.7	1.0
	CL	A:CL8	3.0	55.1	1.0
	CG	A:ASP382	3.2	28.8	1.0
	CE1	A:HIS486	3.3	30.6	1.0
	N	A:HIS486	3.6	28.1	1.0
	OD2	A:ASP382	3.6	25.2	1.0
	CG	A:HIS486	3.7	28.2	1.0
	CB	A:HIS486	4.0	24.6	1.0
	CA	A:ARG485	4.4	30.3	1.0
	NH1	A:ARG478	4.4	39.1	1.0
	C	A:ARG485	4.4	30.8	1.0
	CA	A:HIS486	4.4	26.4	1.0
	ND1	A:HIS379	4.4	26.3	1.0
	CB	A:ASP382	4.5	26.1	1.0
	NE2	A:HIS486	4.6	31.4	1.0
	O	A:HOH37	4.6	27.9	1.0
	O	A:ARG484	4.7	29.0	1.0
	CD2	A:HIS486	4.7	29.5	1.0
	O	A:HOH638	4.7	53.4	1.0
	CE1	A:HIS379	4.9	27.9	1.0

Manganese binding site 3 out of 3 in 3pmn

Go back to

Manganese Binding Sites List in 3pmn

Manganese binding site 3 out of 3 in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn7 b:85.8 occ:1.00	NE2	A:HIS530	2.2	36.0	1.0
	OP1	B:DA8	2.4	31.2	1.0
	O	A:HOH30	2.5	30.6	1.0
	O	A:HOH602	2.7	52.9	1.0
	CE1	A:HIS530	2.8	34.0	1.0
	CD2	A:HIS530	3.4	32.4	1.0
	O	A:HOH596	3.6	35.6	1.0
	P	B:DA8	3.7	31.0	1.0
	O3'	B:DT7	3.9	28.1	1.0
	C5'	B:DA8	4.0	30.9	1.0
	ND1	A:HIS530	4.1	34.9	1.0
	O	A:HOH598	4.1	53.2	1.0
	O	B:HOH327	4.2	58.3	1.0
	O5'	B:DA8	4.2	30.5	1.0
	OG1	A:THR471	4.3	45.4	1.0
	CG	A:HIS530	4.3	33.5	1.0
	OE2	A:GLU529	4.8	32.6	1.0
	OP2	B:DA8	5.0	31.8	1.0

Reference:

K.Bebenek, L.C.Pedersen, T.A.Kunkel. Replication Infidelity Via A Mismatch with Watson-Crick Geometry. Proc.Natl.Acad.Sci.Usa V. 108 1862 2011.
ISSN: ISSN 0027-8424
PubMed: 21233421
DOI: 10.1073/PNAS.1012825108

Page generated: Sat Oct 5 17:32:08 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