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Iron in PDB 4amf: Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp

Enzymatic activity of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp

All present enzymatic activity of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp:
3.1.3.1;

Protein crystallography data

The structure of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp, PDB code: 4amf was solved by S.C.Yong, P.Roversi, J.E.D.Lillington, O.B.Zeldin, E.F.Garman, S.M.Lea, B.C.Berks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.25 / 1.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.490, 70.380, 227.870, 90.00, 90.00, 90.00
R / Rfree (%) 15.47 / 18.31

Other elements in 4amf:

The structure of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp also contains other interesting chemical elements:

Calcium (Ca) 6 atoms
Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp (pdb code 4amf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp, PDB code: 4amf:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4amf

Go back to Iron Binding Sites List in 4amf
Iron binding site 1 out of 4 in the Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1595

b:12.3
occ:0.87
 FE1 A:FEO1595 0.0 12.3 0.9
O A:FEO1595 1.9 13.2 1.0
OE2 A:GLU90 2.0 11.3 1.0
OE1 A:GLU194 2.1 14.3 1.0
O2G A:ACP1589 2.1 12.7 0.8
O A:HOH2132 2.3 14.9 1.0
SG A:CYS179 2.6 15.6 1.0
CD A:GLU194 3.0 16.4 1.0
CD A:GLU90 3.1 13.8 1.0
HB2 A:CYS179 3.1 14.1 1.0
PG A:ACP1589 3.2 13.1 0.8
OE2 A:GLU194 3.3 11.8 1.0
FE2 A:FEO1595 3.4 12.8 1.0
CB A:CYS179 3.5 11.9 1.0
OE1 A:GLU90 3.5 16.8 1.0
CA A:CA1592 3.6 12.1 0.8
O1G A:ACP1589 3.7 12.2 0.8
O3G A:ACP1589 3.7 13.0 0.8
HA A:CYS179 3.8 14.4 1.0
OD2 A:ASP69 4.0 16.3 1.0
O A:HOH2161 4.0 25.4 1.0
O A:HOH2160 4.0 17.6 1.0
HB3 A:GLU194 4.1 12.8 1.0
O A:HOH2131 4.1 14.1 1.0
OE2 A:GLU273 4.2 13.6 1.0
O A:HOH2162 4.2 15.2 1.0
HD21 A:ASN195 4.2 14.6 1.0
CA A:CYS179 4.3 12.2 1.0
OE1 A:GLU273 4.3 13.3 1.0
HG3 A:GLU90 4.3 6.4 1.0
HB3 A:CYS179 4.3 12.8 1.0
CG A:GLU90 4.3 8.4 1.0
CG A:GLU194 4.4 10.5 1.0
CD A:GLU273 4.5 10.5 1.0
HB2 A:GLU194 4.6 10.3 1.0
CB A:GLU194 4.6 11.5 1.0
OE2 A:GLU387 4.6 13.8 1.0
C3B A:ACP1589 4.8 11.4 0.8
HD22 A:ASN195 4.8 13.7 1.0
ND2 A:ASN195 4.9 15.1 1.0
HG2 A:GLU90 4.9 8.5 1.0
HG2 A:GLU194 5.0 12.9 1.0
HG3 A:GLU194 5.0 7.3 1.0
H3B2 A:ACP1589 5.0 12.3 0.8

Iron binding site 2 out of 4 in 4amf

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Iron binding site 2 out of 4 in the Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1595

b:12.8
occ:0.99
 FE2 A:FEO1595 0.0 12.8 1.0
O A:FEO1595 2.0 13.2 1.0
OE2 A:GLU194 2.0 11.8 1.0
O3G A:ACP1589 2.0 13.0 0.8
OE1 A:GLU273 2.1 13.3 1.0
OD2 A:ASP292 2.1 14.7 1.0
OE2 A:GLU387 2.1 13.8 1.0
HG2 A:GLU387 3.0 13.0 1.0
CD A:GLU273 3.0 10.5 1.0
CD A:GLU194 3.1 16.4 1.0
CD A:GLU387 3.1 18.4 1.0
CG A:ASP292 3.1 15.0 1.0
PG A:ACP1589 3.2 13.1 0.8
OE2 A:GLU273 3.2 13.6 1.0
HB3 A:ASP292 3.3 9.6 1.0
FE1 A:FEO1595 3.4 12.3 0.9
HH21 A:ARG385 3.4 15.2 1.0
OE1 A:GLU194 3.5 14.3 1.0
HB2 A:ASP292 3.5 8.7 1.0
CB A:ASP292 3.5 10.6 1.0
CG A:GLU387 3.6 11.5 1.0
CA A:CA1592 3.6 12.1 0.8
O2G A:ACP1589 3.7 12.7 0.8
O1G A:ACP1589 3.7 12.2 0.8
O A:HOH2322 3.7 14.8 1.0
CA A:CA1593 4.0 13.3 1.0
NH2 A:ARG385 4.2 14.2 1.0
SG A:CYS179 4.2 15.6 1.0
OE1 A:GLU387 4.2 15.8 1.0
HB2 A:GLU273 4.2 11.2 1.0
OD1 A:ASP292 4.2 15.4 1.0
HH22 A:ARG385 4.2 15.2 1.0
HB3 A:GLU387 4.3 12.2 1.0
CG A:GLU273 4.4 10.8 1.0
HG3 A:GLU387 4.4 11.8 1.0
CG A:GLU194 4.4 10.5 1.0
HG3 A:GLU194 4.4 7.3 1.0
HA A:GLU387 4.5 12.2 1.0
HD22 A:ASN195 4.5 13.7 1.0
CB A:GLU387 4.5 12.1 1.0
OD2 A:ASP479 4.6 13.0 1.0
C3B A:ACP1589 4.6 11.4 0.8
O A:HOH2132 4.6 14.9 1.0
H3B1 A:ACP1589 4.7 11.0 0.8
CB A:GLU273 4.8 11.4 1.0
HA A:GLU273 4.8 9.7 1.0
HG2 A:GLU194 4.8 12.9 1.0
O1B A:ACP1589 4.9 14.2 0.8
HG3 A:GLU273 4.9 11.0 1.0
OD1 A:ASP479 4.9 16.4 1.0
HG2 A:GLU273 5.0 10.2 1.0

Iron binding site 3 out of 4 in 4amf

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Iron binding site 3 out of 4 in the Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1593

b:11.7
occ:0.84
 FE1 B:FEO1593 0.0 11.7 0.8
O B:FEO1593 1.9 14.9 1.0
OE2 B:GLU90 2.0 13.9 1.0
OE1 B:GLU194 2.0 14.1 1.0
O2G B:ACP1589 2.2 14.4 0.8
O B:HOH2117 2.4 15.8 1.0
SG B:CYS179 2.6 14.7 1.0
CD B:GLU194 3.0 15.4 1.0
CD B:GLU90 3.0 13.5 1.0
HB2 B:CYS179 3.1 12.0 1.0
PG B:ACP1589 3.2 13.8 0.8
OE2 B:GLU194 3.3 12.5 1.0
FE2 B:FEO1593 3.4 12.1 1.0
CB B:CYS179 3.4 10.4 1.0
OE1 B:GLU90 3.5 13.9 1.0
O3G B:ACP1589 3.6 13.6 0.8
CA B:CA1590 3.6 14.2 1.0
O1G B:ACP1589 3.7 12.7 0.8
HA B:CYS179 3.8 7.0 1.0
O B:HOH2141 3.9 27.2 1.0
OD2 B:ASP69 4.0 18.9 1.0
HB3 B:GLU194 4.0 5.2 1.0
O B:HOH2139 4.0 15.3 1.0
O B:HOH2116 4.1 15.4 1.0
OE2 B:GLU273 4.2 13.2 1.0
CA B:CYS179 4.2 10.2 1.0
O B:HOH2140 4.2 14.3 1.0
OE1 B:GLU273 4.2 10.6 1.0
HB3 B:CYS179 4.3 9.7 1.0
CG B:GLU194 4.3 11.5 1.0
CG B:GLU90 4.4 10.1 1.0
HG3 B:GLU90 4.4 11.4 1.0
HD21 B:ASN195 4.4 17.5 1.0
CD B:GLU273 4.4 10.3 1.0
HB2 B:GLU194 4.5 10.4 1.0
CB B:GLU194 4.6 8.4 1.0
OE2 B:GLU387 4.7 11.9 1.0
C3B B:ACP1589 4.8 13.3 0.8
HG2 B:GLU90 4.9 9.0 1.0
HG3 B:GLU194 4.9 11.2 1.0
HD22 B:ASN195 4.9 15.5 1.0
ND2 B:ASN195 4.9 16.0 1.0
HG2 B:GLU194 4.9 9.8 1.0

Iron binding site 4 out of 4 in 4amf

Go back to Iron Binding Sites List in 4amf
Iron binding site 4 out of 4 in the Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Pseudomonas Fluorescens Phox in Complex with the Substrate Analogue Appcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1593

b:12.1
occ:0.97
 FE2 B:FEO1593 0.0 12.1 1.0
O B:FEO1593 1.9 14.9 1.0
OE1 B:GLU273 2.0 10.6 1.0
OD2 B:ASP292 2.0 14.5 1.0
OE2 B:GLU194 2.0 12.5 1.0
O3G B:ACP1589 2.1 13.6 0.8
OE2 B:GLU387 2.1 11.9 1.0
CD B:GLU273 2.9 10.3 1.0
HG2 B:GLU387 3.0 16.4 1.0
CD B:GLU194 3.1 15.4 1.0
CG B:ASP292 3.1 12.6 1.0
CD B:GLU387 3.1 17.3 1.0
PG B:ACP1589 3.2 13.8 0.8
OE2 B:GLU273 3.2 13.2 1.0
HB3 B:ASP292 3.3 13.5 1.0
HH21 B:ARG385 3.4 16.4 1.0
FE1 B:FEO1593 3.4 11.7 0.8
OE1 B:GLU194 3.4 14.1 1.0
CB B:ASP292 3.5 14.0 1.0
HB2 B:ASP292 3.5 13.5 1.0
CG B:GLU387 3.6 15.7 1.0
O2G B:ACP1589 3.6 14.4 0.8
CA B:CA1590 3.7 14.2 1.0
O1G B:ACP1589 3.7 12.7 0.8
O B:HOH2271 3.9 17.5 1.0
CA B:CA1591 4.0 13.8 1.0
NH2 B:ARG385 4.1 16.3 1.0
SG B:CYS179 4.1 14.7 1.0
HB2 B:GLU273 4.2 8.1 1.0
HH22 B:ARG385 4.2 18.9 1.0
OD1 B:ASP292 4.2 15.1 1.0
OE1 B:GLU387 4.2 14.6 1.0
HB3 B:GLU387 4.3 12.1 1.0
CG B:GLU273 4.3 11.7 1.0
HG3 B:GLU194 4.3 11.2 1.0
CG B:GLU194 4.4 11.5 1.0
HG3 B:GLU387 4.4 16.6 1.0
HA B:GLU387 4.5 10.6 1.0
CB B:GLU387 4.5 11.8 1.0
C3B B:ACP1589 4.6 13.3 0.8
HD22 B:ASN195 4.6 15.5 1.0
O B:HOH2117 4.6 15.8 1.0
H3B1 B:ACP1589 4.7 11.2 0.8
OD2 B:ASP479 4.7 12.1 1.0
CB B:GLU273 4.7 9.9 1.0
HA B:GLU273 4.8 10.5 1.0
HG2 B:GLU194 4.8 9.8 1.0
HG2 B:GLU273 4.8 13.2 1.0
HG3 B:GLU273 4.9 10.9 1.0
O1B B:ACP1589 4.9 13.5 0.8
OD1 B:ASP479 4.9 15.1 1.0

Reference:

S.C.Yong, P.Roversi, J.Lillington, F.Rodriguez, M.Krehenbrink, O.B.Zeldin, E.F.Garman, S.M.Lea, B.C.Berks. A Complex Iron-Calcium Cofactor Catalyzing Phosphotransfer Chemistry Science V. 345 1170 2014.
ISSN: ISSN 0036-8075
PubMed: 25190793
DOI: 10.1126/SCIENCE.1254237
Page generated: Sun Aug 4 23:40:02 2024

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