mm:parameters:iron:cc_fe_ss_fe_cc

Table of Contents

Iron(III)/Iron(III) - CC[FE]SS[FE]CC

Iron(III)/Iron(III) - CC[FE]SS[FE]CC

Ferredoxin is a binuclear iron center with four cysteine residues and two sulfurs, having a redox potential of 400 mV.

COORDINATION SPHERE
	Oxidation State: Fe(III)/Fe(III) Spin Multiplicity: 1

Structure chosen to parameterize

TEST PROTEIN
Protein	[2Fe-2S] Ferredoxin
PDB Code	4FXC
Crystallographic Resolution	2.50 Å
Organism	Spirulina platensis
[Fukuyama, 1995]

Parameters Determined

Atom Types

ATOM TYPE	NEW ATOM TYPE	MASS	STRUCTURE
FE	FE	55.845
SG	SX	32.065
S	S	32.065

Bond Parameters

BOND	K_l / kcal mol^-1 Å^-2	l / Å	REFERENCE
FE-S	93.4	2.17	[Carvalho, 2013]
FE-SX	82.6	2.23	[Carvalho, 2013]
CT-SX	237.00	1.8100
SX-CT	227.00	1.8100

Angle Parameters

ANGLE	K_θ / kcal mol^-1 rad^-2	θ / deg	REFERENCE
S-FE-S	17.3	102.84	[Carvalho, 2013]
SX-FE-S	17.3	102.84
FE-S-FE	18.0	77.200
SX-FE-SX	65.5	108.44
FE-SX-CT	65.5	108.44
HS-SX-FE	65.5	108.44
SX-CT-H1	50.00	109.5000
SX-FE-SX	33.15	109.8650
CT-CT-SX	50.00	108.6000
CT-SX-CT	62.00	98.9000
CT-CT-SX	50.00	114.7000

Van der Waals Parameters

ATOM TYPE	R_i / Å	ε_i / kcal mol^-1	REFERENCE
FE	2.6500	0.0450	[Giammona, 1984]
S	2.0000	0.2500	[Cornell, 1995]
SX	2.0000	0.2500	[Cornell, 1995]

Downloads

Parameter File	.frcmod
Coordination Sphere Charges	.off
Ferredoxin’s PDB File (4FXC.pdb)\ LEAPRC file	.pdb, leaprc

References

A.T.P. Carvalho, A.F.S. Teixeira, MJ.Ramos. Parameters for Molecular Dynamics Simulations of Iron-Sulfur Proteins. J. Comput. Chem., 2013, 34, 1540-1548

D. A. Giammona, Ph.D. Thesis; University of California: Davis, 1984

mm/parameters/iron/cc_fe_ss_fe_cc.txt · Last modified: 2013/10/03 19:00 by ruineves