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Iron in PDB 4fe1: Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution

Enzymatic activity of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution

All present enzymatic activity of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution:
1.97.1.12;

Protein crystallography data

The structure of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution, PDB code: 4fe1 was solved by R.Fromme, P.D.Adams, P.Fromme, M.Levitt, G.F.Schroeder, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.97 / 4.92
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 281.000, 281.000, 165.200, 90.00, 90.00, 120.00
R / Rfree (%) 27.4 / 31.5

Other elements in 4fe1:

The structure of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 96 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution (pdb code 4fe1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution, PDB code: 4fe1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 4fe1

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Iron binding site 1 out of 12 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe856

b:0.2
occ:1.00
 FE1 A:SF4856 0.0 0.2 1.0
S2 A:SF4856 2.2 0.2 1.0
S4 A:SF4856 2.2 50.1 1.0
S3 A:SF4856 2.2 49.7 1.0
SG B:CYS574 2.3 0.8 1.0
CB B:CYS574 3.0 1.0 1.0
FE4 A:SF4856 3.1 49.9 1.0
FE2 A:SF4856 3.1 0.7 1.0
FE3 A:SF4856 3.1 50.4 1.0
CA B:CYS574 3.7 0.8 1.0
CZ3 B:TRP673 3.8 80.8 1.0
S1 A:SF4856 3.8 49.1 1.0
N B:CYS574 3.9 0.0 1.0
CD1 A:ILE724 3.9 53.5 1.0
CG2 A:ILE724 4.3 52.7 1.0
CE3 B:TRP673 4.6 85.7 1.0
CH2 B:TRP673 4.6 76.2 1.0
CG1 A:ILE724 4.7 54.2 1.0
NH2 A:ARG728 4.9 50.2 1.0

Iron binding site 2 out of 12 in 4fe1

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Iron binding site 2 out of 12 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe856

b:0.7
occ:1.00
 FE2 A:SF4856 0.0 0.7 1.0
S3 A:SF4856 2.2 49.7 1.0
S4 A:SF4856 2.2 50.1 1.0
S1 A:SF4856 2.2 49.1 1.0
SG A:CYS587 2.3 0.4 1.0
CB A:CYS587 3.0 66.8 1.0
FE4 A:SF4856 3.1 49.9 1.0
FE1 A:SF4856 3.1 0.2 1.0
FE3 A:SF4856 3.1 50.4 1.0
CE3 B:TRP673 3.8 85.7 1.0
CA A:CYS587 3.8 69.0 1.0
S2 A:SF4856 3.8 0.2 1.0
CD1 B:ILE708 3.9 62.1 1.0
CZ3 B:TRP673 4.0 80.8 1.0
N A:CYS587 4.2 69.2 1.0
CG1 B:ILE708 4.7 59.9 1.0
NH2 A:ARG728 4.8 50.2 1.0
CD2 B:TRP673 4.9 63.6 1.0
CB A:CYS578 4.9 59.7 1.0
CG2 B:ILE708 4.9 60.2 1.0
SG A:CYS578 5.0 0.2 1.0

Iron binding site 3 out of 12 in 4fe1

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Iron binding site 3 out of 12 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe856

b:50.4
occ:1.00
 FE3 A:SF4856 0.0 50.4 1.0
S2 A:SF4856 2.2 0.2 1.0
S1 A:SF4856 2.2 49.1 1.0
S4 A:SF4856 2.2 50.1 1.0
SG A:CYS578 2.3 0.2 1.0
FE4 A:SF4856 3.1 49.9 1.0
FE1 A:SF4856 3.1 0.2 1.0
FE2 A:SF4856 3.1 0.7 1.0
CB A:CYS578 3.2 59.7 1.0
S3 A:SF4856 3.8 49.7 1.0
O A:PRO577 4.3 50.1 1.0
CA A:CYS578 4.5 62.4 1.0
CD1 A:ILE724 4.5 53.5 1.0
C A:PRO577 4.5 72.0 1.0
N B:PRO568 4.7 0.4 1.0
CB B:PRO568 4.7 0.5 1.0
CD B:PRO568 4.7 71.5 1.0
N A:CYS578 4.7 65.5 1.0
N A:GLY580 4.7 66.0 1.0
CA A:GLY580 4.8 49.7 1.0
CB A:PRO577 4.8 74.6 1.0
CA A:CYS587 4.8 69.0 1.0
SG A:CYS587 4.9 0.4 1.0
CB A:CYS587 4.9 66.8 1.0
CA B:PRO568 4.9 0.4 1.0
C B:GLY567 5.0 71.0 1.0
C A:GLY580 5.0 48.8 1.0

Iron binding site 4 out of 12 in 4fe1

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Iron binding site 4 out of 12 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe856

b:49.9
occ:1.00
 FE4 A:SF4856 0.0 49.9 1.0
S3 A:SF4856 2.2 49.7 1.0
S1 A:SF4856 2.2 49.1 1.0
S2 A:SF4856 2.2 0.2 1.0
SG B:CYS565 2.2 96.8 1.0
FE2 A:SF4856 3.1 0.7 1.0
FE1 A:SF4856 3.1 0.2 1.0
FE3 A:SF4856 3.1 50.4 1.0
CB B:CYS565 3.1 78.8 1.0
S4 A:SF4856 3.8 50.1 1.0
CD1 B:ILE708 4.4 62.1 1.0
N B:GLY567 4.5 68.8 1.0
CA B:CYS565 4.6 78.2 1.0
CD A:PRO581 4.6 50.4 1.0
CB A:PRO581 4.6 73.1 1.0
CA B:GLY567 4.6 69.7 1.0
N A:PRO581 4.6 49.7 1.0
O B:PRO564 4.7 79.6 1.0
C B:GLY567 4.8 71.0 1.0
CA A:PRO581 4.9 49.0 1.0
CA B:CYS574 4.9 0.8 1.0
C B:PRO564 4.9 91.5 1.0
N B:CYS565 4.9 91.5 1.0
SG A:CYS587 5.0 0.4 1.0

Iron binding site 5 out of 12 in 4fe1

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Iron binding site 5 out of 12 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:49.2
occ:1.00
 FE1 C:SF4101 0.0 49.2 1.0
S2 C:SF4101 2.2 49.1 1.0
S4 C:SF4101 2.2 48.9 1.0
S3 C:SF4101 2.2 49.0 1.0
SG C:CYS50 2.2 49.5 1.0
FE3 C:SF4101 3.1 48.8 1.0
FE4 C:SF4101 3.1 48.9 1.0
FE2 C:SF4101 3.1 48.7 1.0
N C:LYS51 3.3 49.6 1.0
N C:CYS50 3.5 58.8 1.0
CB C:CYS50 3.6 49.8 1.0
S1 C:SF4101 3.8 62.5 1.0
N C:ARG52 3.8 0.4 1.0
CA C:CYS50 3.9 49.8 1.0
C C:CYS50 3.9 49.8 1.0
CD C:PRO21 4.0 83.2 1.0
CA C:LYS51 4.0 96.1 1.0
C C:GLY49 4.4 94.7 1.0
C C:LYS51 4.4 0.4 1.0
N C:GLY49 4.6 0.4 1.0
CB C:ARG52 4.6 49.5 1.0
CG C:PRO21 4.6 49.4 1.0
CG2 C:VAL48 4.7 80.8 1.0
N C:CYS53 4.7 76.5 1.0
CA C:ARG52 4.8 49.5 1.0
CA C:GLY49 4.8 0.7 1.0
SG C:CYS53 4.9 0.5 1.0
O C:CYS50 4.9 49.9 1.0
SG C:CYS20 5.0 0.5 1.0

Iron binding site 6 out of 12 in 4fe1

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Iron binding site 6 out of 12 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:48.7
occ:1.00
 FE2 C:SF4101 0.0 48.7 1.0
S4 C:SF4101 2.2 48.9 1.0
S3 C:SF4101 2.2 49.0 1.0
S1 C:SF4101 2.2 62.5 1.0
SG C:CYS20 2.3 0.5 1.0
CB C:CYS20 3.0 98.1 1.0
FE3 C:SF4101 3.1 48.8 1.0
FE4 C:SF4101 3.1 48.9 1.0
FE1 C:SF4101 3.1 49.2 1.0
CA C:CYS20 3.6 98.9 1.0
CG2 C:VAL24 3.8 48.4 1.0
CB C:VAL24 3.8 48.2 1.0
S2 C:SF4101 3.8 49.1 1.0
CD C:PRO21 4.0 83.2 1.0
OG1 C:THR22 4.2 0.5 1.0
C C:CYS20 4.5 92.4 1.0
N C:VAL24 4.6 75.3 1.0
N C:PRO21 4.6 85.7 1.0
CG1 C:VAL24 4.7 48.1 1.0
N C:CYS20 4.7 0.7 1.0
CD1 C:LEU25 4.8 48.1 1.0
CA C:VAL24 4.8 48.0 1.0
CG C:LEU25 4.9 48.0 1.0
SG C:CYS50 4.9 49.5 1.0
N C:THR22 5.0 67.5 1.0

Iron binding site 7 out of 12 in 4fe1

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Iron binding site 7 out of 12 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:48.8
occ:1.00
 FE3 C:SF4101 0.0 48.8 1.0
S4 C:SF4101 2.2 48.9 1.0
S2 C:SF4101 2.2 49.1 1.0
S1 C:SF4101 2.2 62.5 1.0
SG C:CYS53 2.3 0.5 1.0
CB C:CYS53 3.0 76.9 1.0
FE1 C:SF4101 3.1 49.2 1.0
FE2 C:SF4101 3.1 48.7 1.0
FE4 C:SF4101 3.1 48.9 1.0
S3 C:SF4101 3.8 49.0 1.0
N C:CYS53 3.8 76.5 1.0
CG2 C:VAL66 3.9 0.5 1.0
CA C:CYS53 4.0 80.6 1.0
CA C:LYS51 4.6 96.1 1.0
N C:ARG52 4.6 0.4 1.0
CD1 C:LEU25 4.6 48.1 1.0
N C:LYS51 4.7 49.6 1.0
C C:LYS51 4.8 0.4 1.0
C C:ARG52 5.0 51.6 1.0
CG1 C:VAL4 5.0 49.7 1.0

Iron binding site 8 out of 12 in 4fe1

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Iron binding site 8 out of 12 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:48.9
occ:1.00
 FE4 C:SF4101 0.0 48.9 1.0
S2 C:SF4101 2.2 49.1 1.0
S3 C:SF4101 2.2 49.0 1.0
S1 C:SF4101 2.2 62.5 1.0
SG C:CYS47 2.3 0.7 1.0
FE1 C:SF4101 3.1 49.2 1.0
FE2 C:SF4101 3.1 48.7 1.0
FE3 C:SF4101 3.1 48.8 1.0
CB C:CYS47 3.5 96.7 1.0
N C:GLY49 3.8 0.4 1.0
S4 C:SF4101 3.8 48.9 1.0
CA C:CYS47 3.9 0.6 1.0
N C:VAL48 4.1 0.1 1.0
CA C:GLY49 4.2 0.7 1.0
CG2 C:VAL24 4.3 48.4 1.0
CG2 C:VAL4 4.3 49.9 1.0
C C:CYS47 4.3 0.8 1.0
CG1 C:VAL66 4.6 0.1 1.0
N C:CYS50 4.7 58.8 1.0
CB C:VAL24 4.7 48.2 1.0
CG2 C:VAL66 4.8 0.5 1.0
CG1 C:VAL24 4.8 48.1 1.0
C C:GLY49 4.8 94.7 1.0
C C:VAL48 4.9 0.8 1.0

Iron binding site 9 out of 12 in 4fe1

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Iron binding site 9 out of 12 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe102

b:48.0
occ:1.00
 FE1 C:SF4102 0.0 48.0 1.0
S4 C:SF4102 2.2 48.1 1.0
S2 C:SF4102 2.2 0.1 1.0
S3 C:SF4102 2.2 47.8 1.0
SG C:CYS57 2.3 0.1 1.0
CB C:CYS57 3.1 0.5 1.0
FE2 C:SF4102 3.1 0.9 1.0
FE3 C:SF4102 3.1 81.8 1.0
FE4 C:SF4102 3.1 47.5 1.0
CA C:CYS57 3.7 0.4 1.0
S1 C:SF4102 3.8 47.6 1.0
CB C:SER63 4.0 0.7 1.0
CG2 C:ILE64 4.0 60.5 1.0
CD C:PRO58 4.1 0.5 1.0
N C:ILE64 4.4 0.6 1.0
N C:SER63 4.5 0.1 1.0
CB C:ILE64 4.6 60.2 1.0
OG C:SER63 4.6 51.9 1.0
C C:CYS57 4.7 0.7 1.0
CA C:SER63 4.7 0.0 1.0
N C:CYS57 4.8 0.2 1.0
N C:PRO58 4.8 0.3 1.0
C C:SER63 4.9 0.1 1.0
CG2 C:THR59 4.9 69.7 1.0

Iron binding site 10 out of 12 in 4fe1

Go back to Iron Binding Sites List in 4fe1
Iron binding site 10 out of 12 in the Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe102

b:0.9
occ:1.00
 FE2 C:SF4102 0.0 0.9 1.0
S3 C:SF4102 2.2 47.8 1.0
S1 C:SF4102 2.2 47.6 1.0
S4 C:SF4102 2.2 48.1 1.0
SG C:CYS16 2.2 70.5 1.0
FE4 C:SF4102 3.1 47.5 1.0
FE3 C:SF4102 3.1 81.8 1.0
FE1 C:SF4102 3.1 48.0 1.0
CB C:CYS16 3.1 49.7 1.0
N C:CYS16 3.7 71.2 1.0
S2 C:SF4102 3.8 0.1 1.0
CB C:ALA39 3.9 54.1 1.0
CA C:CYS16 4.0 57.8 1.0
CG2 C:ILE64 4.6 60.5 1.0
N C:GLN15 4.7 60.8 1.0
N C:VAL17 4.8 56.5 1.0
CB C:ILE64 4.8 60.2 1.0
C C:GLN15 4.9 0.1 1.0
N C:THR14 4.9 0.9 1.0
C C:THR14 4.9 48.7 1.0
C C:CYS16 5.0 59.1 1.0
CA C:THR14 5.0 0.9 1.0
SG C:CYS13 5.0 94.4 1.0

Reference:

A.T.Brunger, P.D.Adams, P.Fromme, R.Fromme, M.Levitt, G.F.Schroder. Improving the Accuracy of Macromolecular Structure Refinement at 7 A Resolution. Structure V. 20 957 2012.
ISSN: ISSN 0969-2126
PubMed: 22681901
DOI: 10.1016/J.STR.2012.04.020
Page generated: Mon Aug 5 02:14:08 2024

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